diff --git a/404.html b/404.html
index 80671ba..fddf9e4 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://james-thorson-noaa.github.io/phylosem/index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -53,7 +53,14 @@
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
 </form>
 
-      <ul class="navbar-nav"></ul>
+      <ul class="navbar-nav">
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
 </div>
 
     
diff --git a/articles/comparison.html b/articles/comparison.html
index c7cf947..de71fe1 100644
--- a/articles/comparison.html
+++ b/articles/comparison.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -55,7 +55,14 @@
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
 </form>
 
-      <ul class="navbar-nav"></ul>
+      <ul class="navbar-nav">
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
 </div>
 
     
@@ -72,7 +79,7 @@ <h4 data-toc-skip class="author">James T.
 Thorson and Wouter van der Bijl</h4>
             
       
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/vignettes/comparison.Rmd" class="external-link"><code>vignettes/comparison.Rmd</code></a></small>
       <div class="d-none name"><code>comparison.Rmd</code></div>
     </div>
 
@@ -159,7 +166,7 @@ <h2 id="comparison-with-phylolm">Comparison with phylolm<a class="anchor" aria-l
 <span><span class="va">start_time</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">plm_bm</span> <span class="op">=</span> <span class="fu">phylolm</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/phylolm/man/phylolm.html" class="external-link">phylolm</a></span><span class="op">(</span><span class="va">y</span> <span class="op">~</span> <span class="fl">1</span> <span class="op">+</span> <span class="va">x</span>, data<span class="op">=</span><span class="va">Data</span>, phy<span class="op">=</span><span class="va">tree</span>, model<span class="op">=</span><span class="st">"BM"</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.00622654 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.00464797 secs</span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">plm_bm</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
@@ -192,9 +199,9 @@ <h2 id="comparison-with-phylolm">Comparison with phylolm<a class="anchor" aria-l
 <span><span class="va">psem_bm</span> <span class="op">=</span> <span class="fu"><a href="../reference/phylosem.html">phylosem</a></span><span class="op">(</span> sem <span class="op">=</span> <span class="st">"x -&gt; y, p"</span>,</span>
 <span>          data <span class="op">=</span> <span class="va">Data</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">tree</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.1971586 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.09037399 secs</span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">psem_bm</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
@@ -254,16 +261,16 @@ <h2 id="comparison-with-phylolm">Comparison with phylolm<a class="anchor" aria-l
 <span><span class="va">start_time</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">plm_ou</span> <span class="op">=</span> <span class="fu">phylolm</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/phylolm/man/phylolm.html" class="external-link">phylolm</a></span><span class="op">(</span><span class="va">y</span> <span class="op">~</span> <span class="fl">1</span> <span class="op">+</span> <span class="va">x</span>, data<span class="op">=</span><span class="va">Data</span>, phy<span class="op">=</span><span class="va">tree</span>, model<span class="op">=</span><span class="st">"OUrandomRoot"</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.0199275 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.008813143 secs</span></span>
 <span></span>
 <span><span class="va">start_time</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">psem_ou</span> <span class="op">=</span> <span class="fu"><a href="../reference/phylosem.html">phylosem</a></span><span class="op">(</span> sem <span class="op">=</span> <span class="st">"x -&gt; y, p"</span>,</span>
 <span>          data <span class="op">=</span> <span class="va">Data</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">tree</span>,</span>
 <span>          estimate_ou <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.2294426 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.1400571 secs</span></span>
 <span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">psem_ou</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@@ -370,16 +377,16 @@ <h2 id="comparison-with-phylolm">Comparison with phylolm<a class="anchor" aria-l
 <span><span class="va">start_time</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">plm_lambda</span> <span class="op">=</span> <span class="fu">phylolm</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/phylolm/man/phylolm.html" class="external-link">phylolm</a></span><span class="op">(</span><span class="va">y</span> <span class="op">~</span> <span class="fl">1</span> <span class="op">+</span> <span class="va">x</span>, data<span class="op">=</span><span class="va">Data</span>, phy<span class="op">=</span><span class="va">tree</span>, model<span class="op">=</span><span class="st">"lambda"</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.04079676 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.01395488 secs</span></span>
 <span></span>
 <span><span class="va">start_time</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">psem_lambda</span> <span class="op">=</span> <span class="fu"><a href="../reference/phylosem.html">phylosem</a></span><span class="op">(</span> sem <span class="op">=</span> <span class="st">"x -&gt; y, p"</span>,</span>
 <span>          data <span class="op">=</span> <span class="va">Data</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">tree</span>,</span>
 <span>          estimate_lambda <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.1857631 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.07518101 secs</span></span>
 <span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">psem_lambda</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@@ -486,16 +493,16 @@ <h2 id="comparison-with-phylolm">Comparison with phylolm<a class="anchor" aria-l
 <span><span class="va">start_time</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">plm_kappa</span> <span class="op">=</span> <span class="fu">phylolm</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/phylolm/man/phylolm.html" class="external-link">phylolm</a></span><span class="op">(</span><span class="va">y</span> <span class="op">~</span> <span class="fl">1</span> <span class="op">+</span> <span class="va">x</span>, data<span class="op">=</span><span class="va">Data</span>, phy<span class="op">=</span><span class="va">tree</span>, model<span class="op">=</span><span class="st">"kappa"</span>, lower.bound <span class="op">=</span> <span class="fl">0</span>, upper.bound <span class="op">=</span> <span class="fl">3</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.01002622 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.1530089 secs</span></span>
 <span></span>
 <span><span class="va">start_time</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">psem_kappa</span> <span class="op">=</span> <span class="fu"><a href="../reference/phylosem.html">phylosem</a></span><span class="op">(</span> sem <span class="op">=</span> <span class="st">"x -&gt; y, p"</span>,</span>
 <span>          data <span class="op">=</span> <span class="va">Data</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">tree</span>,</span>
 <span>          estimate_kappa <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.1860392 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.07159591 secs</span></span>
 <span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">psem_kappa</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@@ -692,7 +699,7 @@ <h3 id="poisson-distributed-response">Poisson-distributed response<a class="anch
 <span>          data <span class="op">=</span> <span class="va">Data</span>,</span>
 <span>          family <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"fixed"</span>,<span class="st">"poisson"</span><span class="op">)</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">tree</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pgsem</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
@@ -755,20 +762,20 @@ <h3 id="poisson-distributed-response">Poisson-distributed response<a class="anch
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/paul-buerkner/brms" class="external-link">brms</a></span><span class="op">)</span></span>
 <span><span class="va">Amat</span> <span class="op">&lt;-</span> <span class="fu">ape</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/ape/man/vcv.phylo.html" class="external-link">vcv.phylo</a></span><span class="op">(</span><span class="va">tree</span><span class="op">)</span></span>
 <span><span class="va">Data</span><span class="op">$</span><span class="va">tips</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">Data</span><span class="op">)</span></span>
-<span><span class="va">mcmc</span> <span class="op">&lt;-</span> <span class="fu">brm</span><span class="op">(</span></span>
-<span>  <span class="va">y</span> <span class="op">~</span> <span class="fl">1</span> <span class="op">+</span> <span class="va">x</span> <span class="op">+</span> <span class="op">(</span><span class="fl">1</span> <span class="op">|</span> <span class="fu">gr</span><span class="op">(</span><span class="va">tips</span>, cov <span class="op">=</span> <span class="va">A</span><span class="op">)</span><span class="op">)</span>,</span>
+<span><span class="va">mcmc</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://paul-buerkner.github.io/brms/reference/brm.html" class="external-link">brm</a></span><span class="op">(</span></span>
+<span>  <span class="va">y</span> <span class="op">~</span> <span class="fl">1</span> <span class="op">+</span> <span class="va">x</span> <span class="op">+</span> <span class="op">(</span><span class="fl">1</span> <span class="op">|</span> <span class="fu"><a href="https://paul-buerkner.github.io/brms/reference/gr.html" class="external-link">gr</a></span><span class="op">(</span><span class="va">tips</span>, cov <span class="op">=</span> <span class="va">A</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  data <span class="op">=</span> <span class="va">Data</span>, data2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>A <span class="op">=</span> <span class="va">Amat</span><span class="op">)</span>,</span>
 <span>  family <span class="op">=</span> <span class="st">'poisson'</span>,</span>
 <span>  cores <span class="op">=</span> <span class="fl">4</span></span>
 <span><span class="op">)</span></span>
-<span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu">fixef</span><span class="op">(</span><span class="va">mcmc</span><span class="op">)</span>, digits <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span>
+<span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/fixed.effects.html" class="external-link">fixef</a></span><span class="op">(</span><span class="va">mcmc</span><span class="op">)</span>, digits <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Plot them together</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
 <span><span class="va">pdat</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind.data.frame</a></span><span class="op">(</span></span>
 <span>  <span class="fu"><a href="https://rdrr.io/r/stats/coef.html" class="external-link">coef</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pglm</span><span class="op">)</span><span class="op">)</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>,</span>
 <span>  <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>Estimate <span class="op">=</span> <span class="va">pglmm</span><span class="op">$</span><span class="va">B</span>, StdErr <span class="op">=</span> <span class="va">pglmm</span><span class="op">$</span><span class="va">B.se</span><span class="op">)</span>,</span>
-<span>  <span class="fu"><a href="https://rdrr.io/r/stats/setNames.html" class="external-link">setNames</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/as.data.frame.html" class="external-link">as.data.frame</a></span><span class="op">(</span><span class="fu">fixef</span><span class="op">(</span><span class="va">mcmc</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'Estimate'</span>, <span class="st">'StdErr'</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/stats/setNames.html" class="external-link">setNames</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/as.data.frame.html" class="external-link">as.data.frame</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/fixed.effects.html" class="external-link">fixef</a></span><span class="op">(</span><span class="va">mcmc</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'Estimate'</span>, <span class="st">'StdErr'</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  <span class="fu"><a href="https://rdrr.io/r/stats/setNames.html" class="external-link">setNames</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pgsem</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span><span class="op">[</span><span class="fl">2</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'Estimate'</span>, <span class="st">'StdErr'</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="op">)</span></span>
 <span><span class="va">pdat</span><span class="op">$</span><span class="va">Param</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'Intercept'</span>, <span class="st">'Slope'</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span>
@@ -846,7 +853,7 @@ <h3 id="binomial-regression">Binomial regression<a class="anchor" aria-label="an
 <span>          data <span class="op">=</span> <span class="va">Data</span>,</span>
 <span>          family <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"fixed"</span>,<span class="st">"binomial"</span><span class="op">)</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">tree</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pgsem</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
@@ -940,7 +947,7 @@ <h2 id="compare-with-phylopath">Compare with phylopath<a class="anchor" aria-lab
 <span>                    model <span class="op">=</span> <span class="st">"BM"</span>,</span>
 <span>                    measurement_error <span class="op">=</span> <span class="cn">FALSE</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.01152086 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.00779891 secs</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">result</span><span class="op">)</span></span></code></pre></div>
 <p><img src="comparison_files/figure-html/unnamed-chunk-8-1.png" width="576"></p>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
@@ -956,9 +963,9 @@ <h2 id="compare-with-phylopath">Compare with phylopath<a class="anchor" aria-lab
 <span><span class="va">psem</span> <span class="op">=</span> <span class="fu"><a href="../reference/phylosem.html">phylosem</a></span><span class="op">(</span> sem <span class="op">=</span> <span class="va">model</span>,</span>
 <span>          data <span class="op">=</span> <span class="va">rhino_scaled</span><span class="op">[</span>,<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"BM"</span>,<span class="st">"NL"</span>,<span class="st">"DD"</span>,<span class="st">"RS"</span>,<span class="st">"LS"</span><span class="op">)</span><span class="op">]</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">rhino_tree</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.4174633 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.1682889 secs</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span> <span class="fu"><a href="../reference/as_fitted_DAG.html">as_fitted_DAG</a></span><span class="op">(</span><span class="va">psem</span><span class="op">)</span> <span class="op">)</span></span></code></pre></div>
 <p><img src="comparison_files/figure-html/unnamed-chunk-8-2.png" width="576"></p>
 </div>
@@ -1012,7 +1019,7 @@ <h2 id="comparison-with-sem">Comparison with sem<a class="anchor" aria-label="an
 <span><span class="va">start_time</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">Sem</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/sem/man/sem.html" class="external-link">sem</a></span><span class="op">(</span><span class="va">model</span>, data<span class="op">=</span><span class="va">Data</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.01753688 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.01031017 secs</span></span>
 <span></span>
 <span><span class="co"># Specify star phylogeny</span></span>
 <span><span class="va">tree_null</span> <span class="op">=</span> <span class="fu">TreeTools</span><span class="fu">::</span><span class="fu"><a href="https://ms609.github.io/TreeTools/reference/GenerateTree.html" class="external-link">StarTree</a></span><span class="op">(</span><span class="va">n_obs</span><span class="op">)</span></span>
@@ -1024,9 +1031,9 @@ <h2 id="comparison-with-sem">Comparison with sem<a class="anchor" aria-label="an
 <span><span class="va">psem</span> <span class="op">=</span> <span class="fu"><a href="../reference/phylosem.html">phylosem</a></span><span class="op">(</span> data <span class="op">=</span> <span class="va">Data</span>,</span>
 <span>          sem <span class="op">=</span> <span class="va">equations</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">tree_null</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.07997537 secs</span></span></code></pre></div>
+<span><span class="co">#&gt; Time difference of 0.02785897 secs</span></span></code></pre></div>
 <p>We then compare estimated values for standardized coefficients</p>
 <table class="table">
 <thead><tr class="header">
@@ -1162,7 +1169,7 @@ <h2 id="comparison-with-rphylopars">Comparison with Rphylopars<a class="anchor"
 <span>                  phylo_correlated <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>                  pheno_correlated <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.1094489 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.0825429 secs</span></span>
 <span></span>
 <span><span class="co"># Display estimates for missing values</span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">cbind</a></span><span class="op">(</span> <span class="st">"Estimate"</span><span class="op">=</span><span class="va">pars</span><span class="op">$</span><span class="va">anc_recon</span><span class="op">[</span><span class="st">"t1"</span>,<span class="op">]</span>, <span class="st">"Var"</span><span class="op">=</span><span class="va">pars</span><span class="op">$</span><span class="va">anc_var</span><span class="op">[</span><span class="st">"t1"</span>,<span class="op">]</span> <span class="op">)</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
@@ -1208,14 +1215,14 @@ <h2 id="comparison-with-rphylopars">Comparison with Rphylopars<a class="anchor"
 <span>                 tree <span class="op">=</span> <span class="va">tree</span>,</span>
 <span>                 sem <span class="op">=</span> <span class="st">""</span>,</span>
 <span>                 covs <span class="op">=</span> <span class="st">"BM, NL, DD, RS, LS"</span>,</span>
-<span>                 quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>                 control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
-<span><span class="co">#&gt; Time difference of 0.6932356 secs</span></span>
+<span><span class="co">#&gt; Time difference of 0.2777879 secs</span></span>
 <span></span>
 <span><span class="co"># Display estimates for missing values</span></span>
 <span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">cbind</a></span><span class="op">(</span></span>
-<span>  <span class="st">"Estimate"</span><span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="va">psem</span><span class="op">$</span><span class="va">opt</span><span class="op">$</span><span class="va">SD</span>,<span class="st">"Estimate"</span><span class="op">)</span><span class="op">$</span><span class="va">x_vj</span><span class="op">[</span> <span class="fu"><a href="https://ms609.github.io/TreeTools/reference/match.Splits.html" class="external-link">match</a></span><span class="op">(</span><span class="st">"t1"</span>,<span class="va">tree</span><span class="op">$</span><span class="va">tip.label</span><span class="op">)</span>, <span class="op">]</span>,</span>
-<span>  <span class="st">"Var"</span><span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="va">psem</span><span class="op">$</span><span class="va">opt</span><span class="op">$</span><span class="va">SD</span>,<span class="st">"Std. Error"</span><span class="op">)</span><span class="op">$</span><span class="va">x_vj</span><span class="op">[</span> <span class="fu"><a href="https://ms609.github.io/TreeTools/reference/match.Splits.html" class="external-link">match</a></span><span class="op">(</span><span class="st">"t1"</span>,<span class="va">tree</span><span class="op">$</span><span class="va">tip.label</span><span class="op">)</span>, <span class="op">]</span><span class="op">^</span><span class="fl">2</span></span>
+<span>  <span class="st">"Estimate"</span><span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="va">psem</span><span class="op">$</span><span class="va">sdrep</span>,<span class="st">"Estimate"</span><span class="op">)</span><span class="op">$</span><span class="va">x_vj</span><span class="op">[</span> <span class="fu"><a href="https://ms609.github.io/TreeTools/reference/match.Splits.html" class="external-link">match</a></span><span class="op">(</span><span class="st">"t1"</span>,<span class="va">tree</span><span class="op">$</span><span class="va">tip.label</span><span class="op">)</span>, <span class="op">]</span>,</span>
+<span>  <span class="st">"Var"</span><span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="va">psem</span><span class="op">$</span><span class="va">sdrep</span>,<span class="st">"Std. Error"</span><span class="op">)</span><span class="op">$</span><span class="va">x_vj</span><span class="op">[</span> <span class="fu"><a href="https://ms609.github.io/TreeTools/reference/match.Splits.html" class="external-link">match</a></span><span class="op">(</span><span class="st">"t1"</span>,<span class="va">tree</span><span class="op">$</span><span class="va">tip.label</span><span class="op">)</span>, <span class="op">]</span><span class="op">^</span><span class="fl">2</span></span>
 <span><span class="op">)</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
diff --git a/articles/comparison_files/figure-html/unnamed-chunk-5-1.png b/articles/comparison_files/figure-html/unnamed-chunk-5-1.png
deleted file mode 100644
index f1a77fd..0000000
Binary files a/articles/comparison_files/figure-html/unnamed-chunk-5-1.png and /dev/null differ
diff --git a/articles/comparison_files/figure-html/unnamed-chunk-6-1.png b/articles/comparison_files/figure-html/unnamed-chunk-6-1.png
index a1fe9bb..2e2e97b 100644
Binary files a/articles/comparison_files/figure-html/unnamed-chunk-6-1.png and b/articles/comparison_files/figure-html/unnamed-chunk-6-1.png differ
diff --git a/articles/comparison_files/figure-html/unnamed-chunk-7-1.png b/articles/comparison_files/figure-html/unnamed-chunk-7-1.png
deleted file mode 100644
index 11cd16a..0000000
Binary files a/articles/comparison_files/figure-html/unnamed-chunk-7-1.png and /dev/null differ
diff --git a/articles/comparison_files/figure-html/unnamed-chunk-7-2.png b/articles/comparison_files/figure-html/unnamed-chunk-7-2.png
deleted file mode 100644
index 11cd16a..0000000
Binary files a/articles/comparison_files/figure-html/unnamed-chunk-7-2.png and /dev/null differ
diff --git a/articles/comparison_files/figure-html/unnamed-chunk-8-1.png b/articles/comparison_files/figure-html/unnamed-chunk-8-1.png
index 11cd16a..73076aa 100644
Binary files a/articles/comparison_files/figure-html/unnamed-chunk-8-1.png and b/articles/comparison_files/figure-html/unnamed-chunk-8-1.png differ
diff --git a/articles/comparison_files/figure-html/unnamed-chunk-8-2.png b/articles/comparison_files/figure-html/unnamed-chunk-8-2.png
index 11cd16a..73076aa 100644
Binary files a/articles/comparison_files/figure-html/unnamed-chunk-8-2.png and b/articles/comparison_files/figure-html/unnamed-chunk-8-2.png differ
diff --git a/articles/demonstration.html b/articles/demonstration.html
index ce2bb82..c6bc20b 100644
--- a/articles/demonstration.html
+++ b/articles/demonstration.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -55,7 +55,14 @@
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
 </form>
 
-      <ul class="navbar-nav"></ul>
+      <ul class="navbar-nav">
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
 </div>
 
     
@@ -72,7 +79,7 @@ <h4 data-toc-skip class="author">James T.
 Thorson</h4>
             
       
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/vignettes/demonstration.Rmd" class="external-link"><code>vignettes/demonstration.Rmd</code></a></small>
       <div class="d-none name"><code>demonstration.Rmd</code></div>
     </div>
 
@@ -117,15 +124,16 @@ <h2 id="estimability-for-multiple-covariance-transformations">Estimability for m
 <span>          estimate_lambda <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>          estimate_kappa <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>          tree <span class="op">=</span> <span class="va">rhino_tree</span>,</span>
-<span>          getJointPrecision <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>          quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>          control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span></span>
+<span>            getJointPrecision <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>            quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span></span>
 <span><span class="co">#</span></span>
-<span><span class="va">V</span> <span class="op">=</span> <span class="va">psem</span><span class="op">$</span><span class="va">opt</span><span class="op">$</span><span class="va">SD</span><span class="op">$</span><span class="va">cov.fixed</span></span>
+<span><span class="va">V</span> <span class="op">=</span> <span class="va">psem</span><span class="op">$</span><span class="va">sdrep</span><span class="op">$</span><span class="va">cov.fixed</span></span>
 <span><span class="va">Rsub</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cov2cor</a></span><span class="op">(</span><span class="va">V</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'lnalpha'</span>,<span class="st">'logitlambda'</span>,<span class="st">'lnkappa'</span><span class="op">)</span>,<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'lnalpha'</span>,<span class="st">'logitlambda'</span>,<span class="st">'lnkappa'</span><span class="op">)</span><span class="op">]</span></span>
 <span></span>
-<span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"minimum_eigenvalue"</span><span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/eigen.html" class="external-link">eigen</a></span><span class="op">(</span><span class="va">psem</span><span class="op">$</span><span class="va">opt</span><span class="op">$</span><span class="va">SD</span><span class="op">$</span><span class="va">jointPrecision</span><span class="op">)</span><span class="op">$</span><span class="va">values</span><span class="op">)</span>,</span>
-<span>             <span class="st">"maximum_eigenvalue"</span><span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/eigen.html" class="external-link">eigen</a></span><span class="op">(</span><span class="va">psem</span><span class="op">$</span><span class="va">opt</span><span class="op">$</span><span class="va">SD</span><span class="op">$</span><span class="va">jointPrecision</span><span class="op">)</span><span class="op">$</span><span class="va">values</span><span class="op">)</span><span class="op">)</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"minimum_eigenvalue"</span><span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">min</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/eigen.html" class="external-link">eigen</a></span><span class="op">(</span><span class="va">psem</span><span class="op">$</span><span class="va">sdrep</span><span class="op">$</span><span class="va">jointPrecision</span><span class="op">)</span><span class="op">$</span><span class="va">values</span><span class="op">)</span>,</span>
+<span>             <span class="st">"maximum_eigenvalue"</span><span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/eigen.html" class="external-link">eigen</a></span><span class="op">(</span><span class="va">psem</span><span class="op">$</span><span class="va">sdrep</span><span class="op">$</span><span class="va">jointPrecision</span><span class="op">)</span><span class="op">$</span><span class="va">values</span><span class="op">)</span><span class="op">)</span>, digits<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>
@@ -194,7 +202,7 @@ <h2 id="estimability-for-multiple-covariance-transformations">Estimability for m
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
 <span><span class="co"># Compile estimates and SEs</span></span>
-<span><span class="va">pdat</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> <span class="st">"Estimate"</span> <span class="op">=</span> <span class="va">psem</span><span class="op">$</span><span class="va">opt</span><span class="op">$</span><span class="va">SD</span><span class="op">$</span><span class="va">par.fixed</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'lnalpha'</span>,<span class="st">'logitlambda'</span>,<span class="st">'lnkappa'</span><span class="op">)</span><span class="op">]</span>,</span>
+<span><span class="va">pdat</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> <span class="st">"Estimate"</span> <span class="op">=</span> <span class="va">psem</span><span class="op">$</span><span class="va">sdrep</span><span class="op">$</span><span class="va">par.fixed</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'lnalpha'</span>,<span class="st">'logitlambda'</span>,<span class="st">'lnkappa'</span><span class="op">)</span><span class="op">]</span>,</span>
 <span>              <span class="st">"StdErr"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="va">V</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'lnalpha'</span>,<span class="st">'logitlambda'</span>,<span class="st">'lnkappa'</span><span class="op">)</span><span class="op">]</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="va">pdat</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">cbind</a></span><span class="op">(</span> <span class="va">pdat</span>, <span class="st">"Param"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">pdat</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
@@ -263,9 +271,10 @@ <h2 id="scaling-of-runtime-with-increased-tree-size">Scaling of runtime with inc
 <span>  <span class="va">psem_bm</span> <span class="op">=</span> <span class="fu"><a href="../reference/phylosem.html">phylosem</a></span><span class="op">(</span> sem <span class="op">=</span> <span class="st">"x -&gt; y, p"</span>,</span>
 <span>            data <span class="op">=</span> <span class="va">Data</span>,</span>
 <span>            tree <span class="op">=</span> <span class="va">tree</span>,</span>
-<span>            quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>            newtonsteps <span class="op">=</span> <span class="fl">0</span>,</span>
-<span>            getsd <span class="op">=</span> <span class="cn">FALSE</span> <span class="op">)</span></span>
+<span>            control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span></span>
+<span>              quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>              newton_loops <span class="op">=</span> <span class="fl">0</span>,</span>
+<span>              getsd <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">)</span></span>
 <span>  <span class="va">Time_rcz</span><span class="op">[</span><span class="va">rI</span>,<span class="va">cI</span>,<span class="st">"phylosem"</span><span class="op">]</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="va">start_time</span></span>
 <span><span class="op">}</span><span class="op">}</span></span>
 <span></span>
diff --git a/articles/demonstration_files/figure-html/unnamed-chunk-3-1.png b/articles/demonstration_files/figure-html/unnamed-chunk-3-1.png
index 4e82929..6de4306 100644
Binary files a/articles/demonstration_files/figure-html/unnamed-chunk-3-1.png and b/articles/demonstration_files/figure-html/unnamed-chunk-3-1.png differ
diff --git a/articles/demonstration_files/figure-html/unnamed-chunk-4-1.png b/articles/demonstration_files/figure-html/unnamed-chunk-4-1.png
index c55e1bd..e296735 100644
Binary files a/articles/demonstration_files/figure-html/unnamed-chunk-4-1.png and b/articles/demonstration_files/figure-html/unnamed-chunk-4-1.png differ
diff --git a/articles/fisheries.html b/articles/fisheries.html
index 71b310f..7e8ae79 100644
--- a/articles/fisheries.html
+++ b/articles/fisheries.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -55,7 +55,14 @@
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
 </form>
 
-      <ul class="navbar-nav"></ul>
+      <ul class="navbar-nav">
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
 </div>
 
     
@@ -72,7 +79,7 @@ <h4 data-toc-skip class="author">James T.
 Thorson</h4>
             
       
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/vignettes/fisheries.Rmd" class="external-link"><code>vignettes/fisheries.Rmd</code></a></small>
       <div class="d-none name"><code>fisheries.Rmd</code></div>
     </div>
 
@@ -90,7 +97,7 @@ <h4 data-toc-skip class="author">James T.
 <h2 id="preparing-the-then-et-al--mortality-database">Preparing the Then et al. mortality database<a class="anchor" aria-label="anchor" href="#preparing-the-then-et-al--mortality-database"></a>
 </h2>
 <p>To demonstrate the potential role for PCM in fisheries science, we
-re-analyze a foundational dataset compiled by <a href="https://www.vims.edu/research/departments/fisheries/programs/mort_db/index.php" class="external-link">Then
+re-analyze a foundational dataset compiled by <a href="https://www.vims.edu/research/departments/fisheries/programs/mort_db/" class="external-link">Then
 et al.</a>. We specifically download the file “Mlifehist_ver1.0.csv” and
 then include a copy as a data object in package <em>phylosem</em> to
 simplify the following demonstration. This demonstration then provides
@@ -179,11 +186,11 @@ <h2 id="fitting-and-selecting-among-phylogenetic-structural-equation-models">Fit
 <span>                   estimate_ou <span class="op">=</span> <span class="va">Grid</span><span class="op">[</span><span class="va">i</span>,<span class="st">'OU'</span><span class="op">]</span>,</span>
 <span>                   estimate_lambda <span class="op">=</span> <span class="va">Grid</span><span class="op">[</span><span class="va">i</span>,<span class="st">'lambda'</span><span class="op">]</span>,</span>
 <span>                   estimate_kappa <span class="op">=</span> <span class="va">Grid</span><span class="op">[</span><span class="va">i</span>,<span class="st">'kappa'</span><span class="op">]</span>,</span>
-<span>                   quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>                   control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="op">}</span></span>
 <span></span>
 <span><span class="co"># Extract AIC for each model and rank-order by parsimony</span></span>
-<span><span class="va">Grid</span><span class="op">$</span><span class="va">AIC</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span> <span class="va">psem_grid</span>, \<span class="op">(</span><span class="va">m</span><span class="op">)</span> <span class="va">m</span><span class="op">$</span><span class="va">opt</span><span class="op">$</span><span class="va">AIC</span> <span class="op">)</span></span>
+<span><span class="va">Grid</span><span class="op">$</span><span class="va">AIC</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span> <span class="va">psem_grid</span>, \<span class="op">(</span><span class="va">m</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span> <span class="op">)</span></span>
 <span><span class="va">Grid</span> <span class="op">=</span> <span class="va">Grid</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">Grid</span><span class="op">$</span><span class="va">AIC</span>,decreasing<span class="op">=</span><span class="cn">FALSE</span><span class="op">)</span>,<span class="op">]</span></span>
 <span></span>
 <span><span class="co"># Select model with lowest AIC</span></span>
@@ -440,7 +447,7 @@ <h2 id="sensitivity-to-using-taxonomic-tree">Sensitivity to using taxonomic tree
 <span>                 tree <span class="op">=</span> <span class="va">tree</span>,</span>
 <span>                 sem <span class="op">=</span> <span class="va">sem_structure</span>,</span>
 <span>                 estimate_ou <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>                 quiet <span class="op">=</span> <span class="cn">TRUE</span> <span class="op">)</span></span>
+<span>                 control <span class="op">=</span> <span class="fu"><a href="../reference/phylosem_control.html">phylosem_control</a></span><span class="op">(</span>quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Plot path diagram</span></span>
 <span><span class="va">my_fitted_DAG</span> <span class="op">=</span> <span class="fu"><a href="../reference/as_fitted_DAG.html">as_fitted_DAG</a></span><span class="op">(</span><span class="va">psem_taxon</span><span class="op">)</span></span>
diff --git a/articles/fisheries_files/figure-html/unnamed-chunk-5-1.png b/articles/fisheries_files/figure-html/unnamed-chunk-5-1.png
index e9936bb..c14530f 100644
Binary files a/articles/fisheries_files/figure-html/unnamed-chunk-5-1.png and b/articles/fisheries_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/articles/fisheries_files/figure-html/unnamed-chunk-6-1.png b/articles/fisheries_files/figure-html/unnamed-chunk-6-1.png
index ff4e186..f578bf1 100644
Binary files a/articles/fisheries_files/figure-html/unnamed-chunk-6-1.png and b/articles/fisheries_files/figure-html/unnamed-chunk-6-1.png differ
diff --git a/articles/fisheries_files/figure-html/unnamed-chunk-7-1.png b/articles/fisheries_files/figure-html/unnamed-chunk-7-1.png
index ccb77a6..6f2b214 100644
Binary files a/articles/fisheries_files/figure-html/unnamed-chunk-7-1.png and b/articles/fisheries_files/figure-html/unnamed-chunk-7-1.png differ
diff --git a/articles/index.html b/articles/index.html
index 36b7c6c..f9ec811 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
diff --git a/articles/phylopath.html b/articles/phylopath.html
index a5d9fb3..5027dcf 100644
--- a/articles/phylopath.html
+++ b/articles/phylopath.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -55,7 +55,14 @@
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
 </form>
 
-      <ul class="navbar-nav"></ul>
+      <ul class="navbar-nav">
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
 </div>
 
     
@@ -72,7 +79,7 @@ <h4 data-toc-skip class="author">Wouter van der
 Bijl</h4>
             
       
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/vignettes/phylopath.Rmd" class="external-link"><code>vignettes/phylopath.Rmd</code></a></small>
       <div class="d-none name"><code>phylopath.Rmd</code></div>
     </div>
 
diff --git a/articles/phylopath_files/figure-html/unnamed-chunk-10-1.png b/articles/phylopath_files/figure-html/unnamed-chunk-10-1.png
index 8d40e96..c57ba9d 100644
Binary files a/articles/phylopath_files/figure-html/unnamed-chunk-10-1.png and b/articles/phylopath_files/figure-html/unnamed-chunk-10-1.png differ
diff --git a/articles/phylopath_files/figure-html/unnamed-chunk-10-2.png b/articles/phylopath_files/figure-html/unnamed-chunk-10-2.png
index 299e78a..c823481 100644
Binary files a/articles/phylopath_files/figure-html/unnamed-chunk-10-2.png and b/articles/phylopath_files/figure-html/unnamed-chunk-10-2.png differ
diff --git a/articles/phylopath_files/figure-html/unnamed-chunk-9-1.png b/articles/phylopath_files/figure-html/unnamed-chunk-9-1.png
index 0e5acd0..9c22c69 100644
Binary files a/articles/phylopath_files/figure-html/unnamed-chunk-9-1.png and b/articles/phylopath_files/figure-html/unnamed-chunk-9-1.png differ
diff --git a/articles/phylopath_files/figure-html/unnamed-chunk-9-2.png b/articles/phylopath_files/figure-html/unnamed-chunk-9-2.png
index 0e5acd0..9c22c69 100644
Binary files a/articles/phylopath_files/figure-html/unnamed-chunk-9-2.png and b/articles/phylopath_files/figure-html/unnamed-chunk-9-2.png differ
diff --git a/authors.html b/authors.html
index 1994c9b..85fa80d 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -61,7 +67,7 @@ <h2>Authors</h2>
 
     <div class="section level2 citation">
       <h2 id="citation">Citation</h2>
-      <p></p>
+      <p><small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
 
       <p>Thorson, J. T., Maureaud, A. A., Frelat, R., Mérigot, B., Bigman, J. S., Friedman, S. T., Palomares, M. L. D., Pinsky, M. L., Price, S. A., &amp; Wainwright, P. (2023). Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models. Methods in Ecology and Evolution, 14(5), 1259–1275. https://doi.org/10.1111/2041-210X.14076</p>
       <pre>@Article{,
diff --git a/index.html b/index.html
index 7df95e1..932cac1 100644
--- a/index.html
+++ b/index.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -67,7 +67,14 @@
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
 </form>
 
-      <ul class="navbar-nav"></ul>
+      <ul class="navbar-nav">
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
 </div>
 
     
@@ -104,13 +111,14 @@ <h2 id="phylogenetic-structural-equation-models">Phylogenetic structural equatio
 </li>
 </ul>
 <p>Please see package vignettes for more details regarding syntax and features.</p>
-<p><a href="https://cran.r-project.org/package=phylosem" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/phylosem"></a> <a href="https://cran.r-project.org/package=phylosem" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/phylosem"></a></p>
-<p><a href="https://zenodo.org/badge/latestdoi/534386257" class="external-link"><img src="https://zenodo.org/badge/534386257.svg" alt="DOI"></a></p>
+<p><a href="https://cran.r-project.org/package=phylosem" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/phylosem"></a> <a href="https://cran.r-project.org/package=phylosem" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/phylosem"></a> <a href="https://zenodo.org/badge/latestdoi/534386257" class="external-link"><img src="https://zenodo.org/badge/534386257.svg" alt="DOI"></a> <a href="https://app.codecov.io/gh/James-Thorson-NOAA/phylosem/tree/remove-fit_tmb" class="external-link"><img src="https://codecov.io/gh/James-Thorson-NOAA/phylosem/branch/remove-fit_tmb/graph/badge.svg" alt="Codecov test coverage"></a> <a href="https://james-thorson-noaa.github.io/phylosem/"><img src="https://img.shields.io/badge/documentation-phylosem-orange.svg?colorB=E91E63" alt="Documentation"></a></p>
 </div>
   </main><aside class="col-md-3"><div class="links">
 <h2 data-toc-skip>Links</h2>
 <ul class="list-unstyled">
 <li><a href="https://cloud.r-project.org/package=phylosem" class="external-link">View on CRAN</a></li>
+<li><a href="https://github.com/James-Thorson-NOAA/phylosem/" class="external-link">Browse source code</a></li>
+<li><a href="https://github.com/James-Thorson-NOAA/phylosem/issues" class="external-link">Report a bug</a></li>
 </ul>
 </div>
 
diff --git a/news/index.html b/news/index.html
index cd8fd0f..1d28aa5 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,9 +50,15 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Changelog</h1>
-      
+      <small>Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.1.3" id="phylosem-113">phylosem 1.1.3<a class="anchor" aria-label="anchor" href="#phylosem-113"></a></h2><p class="text-muted">CRAN release: 2024-02-01</p>
+<ul><li>Removing fit_tmb to simplify code and remove unnecessary warnings</li>
+<li>Adding codecov and extra tests</li>
+<li>Fixing R-CMD-check to force build Matrix/TMB from source</li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.1.2" id="phylosem-112">phylosem 1.1.2<a class="anchor" aria-label="anchor" href="#phylosem-112"></a></h2><p class="text-muted">CRAN release: 2023-12-20</p>
 <ul><li>Adding new functions to provide warning if Matrix version doesn’t match what’s expected by TMB</li>
diff --git a/pkgdown.yml b/pkgdown.yml
index fb449b9..bfc6e46 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.19.2
+pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
@@ -6,7 +6,7 @@ articles:
   demonstration: demonstration.html
   fisheries: fisheries.html
   phylopath: phylopath.html
-last_built: 2023-12-20T19:54Z
+last_built: 2024-02-01T18:45Z
 urls:
   reference: https://james-thorson-noaa.github.io/phylosem/reference
   article: https://james-thorson-noaa.github.io/phylosem/articles
diff --git a/reference/Mlifehist_ver1_0.html b/reference/Mlifehist_ver1_0.html
index f6b61d2..557a37d 100644
--- a/reference/Mlifehist_ver1_0.html
+++ b/reference/Mlifehist_ver1_0.html
@@ -3,11 +3,11 @@
 Specifically a copy of the Then et al. database doi:10.1093/icesjms/fsu136
  
 using file "Mlifehist_ver1.0.csv" accessed from 
-https://www.vims.edu/research/departments/fisheries/programs/mort_db/index.php'><title>Fisheries natural mortality example — Mlifehist_ver1_0 • phylosem</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fisheries natural mortality example — Mlifehist_ver1_0"><meta property="og:description" content='Data used to demonstrate phylogenetic comparative methods for fisheries science. 
+https://www.vims.edu/research/departments/fisheries/programs/mort_db/'><title>Fisheries natural mortality example — Mlifehist_ver1_0 • phylosem</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fisheries natural mortality example — Mlifehist_ver1_0"><meta property="og:description" content='Data used to demonstrate phylogenetic comparative methods for fisheries science. 
 Specifically a copy of the Then et al. database doi:10.1093/icesjms/fsu136
  
 using file "Mlifehist_ver1.0.csv" accessed from 
-https://www.vims.edu/research/departments/fisheries/programs/mort_db/index.php'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+https://www.vims.edu/research/departments/fisheries/programs/mort_db/'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -44,7 +44,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -52,7 +58,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Fisheries natural mortality example</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
       <div class="d-none name"><code>Mlifehist_ver1_0.Rd</code></div>
     </div>
 
@@ -61,7 +67,7 @@
 Specifically a copy of the Then et al. database <a href="https://doi.org/10.1093/icesjms/fsu136" class="external-link">doi:10.1093/icesjms/fsu136</a>
  
 using file "Mlifehist_ver1.0.csv" accessed from 
-<a href="https://www.vims.edu/research/departments/fisheries/programs/mort_db/index.php" class="external-link">https://www.vims.edu/research/departments/fisheries/programs/mort_db/index.php</a></p>
+<a href="https://www.vims.edu/research/departments/fisheries/programs/mort_db/" class="external-link">https://www.vims.edu/research/departments/fisheries/programs/mort_db/</a></p>
     </div>
 
     <div class="section level2">
diff --git a/reference/Rplot001.png b/reference/Rplot001.png
index edd84e8..4a0b3bb 100644
Binary files a/reference/Rplot001.png and b/reference/Rplot001.png differ
diff --git a/reference/Rplot002.png b/reference/Rplot002.png
index b192df4..049933a 100644
Binary files a/reference/Rplot002.png and b/reference/Rplot002.png differ
diff --git a/reference/Rplot003.png b/reference/Rplot003.png
index da202a8..fb026e5 100644
Binary files a/reference/Rplot003.png and b/reference/Rplot003.png differ
diff --git a/reference/TMBAIC.html b/reference/TMBAIC.html
deleted file mode 100644
index 0cdf17c..0000000
--- a/reference/TMBAIC.html
+++ /dev/null
@@ -1,100 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="TMBAIC calculates AIC for a given model fit"><title>Calculate marginal AIC for a fitted model — TMBAIC • phylosem</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate marginal AIC for a fitted model — TMBAIC"><meta property="og:description" content="TMBAIC calculates AIC for a given model fit"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
-    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
-
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
-    
-    <a class="navbar-brand me-2" href="../index.html">phylosem</a>
-
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
-
-    
-    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
-      <span class="navbar-toggler-icon"></span>
-    </button>
-
-    <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/comparison.html">Comparison with other packages</a>
-    <a class="dropdown-item" href="../articles/demonstration.html">Demonstration of selected features</a>
-    <a class="dropdown-item" href="../articles/fisheries.html">Phylogenetic comparative methods in fisheries science</a>
-    <a class="dropdown-item" href="../articles/phylopath.html">Detailed comparison with `phylopath`</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"></ul></div>
-
-    
-  </div>
-</nav><div class="container template-reference-topic">
-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Calculate marginal AIC for a fitted model</h1>
-      
-      <div class="d-none name"><code>TMBAIC.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p><code>TMBAIC</code> calculates AIC for a given model fit</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">TMBAIC</span><span class="op">(</span><span class="va">opt</span>, k <span class="op">=</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="cn">Inf</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>opt</dt>
-<dd><p>the output from <code>nlminb</code> or <code>optim</code></p></dd>
-
-
-<dt>k</dt>
-<dd><p>the penalty on additional fixed effects (default=2, for AIC)</p></dd>
-
-
-<dt>n</dt>
-<dd><p>the sample size, for use in AICc calculation (default=Inf, for which AICc=AIC)</p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>AIC, where a parsimonious model has a AIC relative to other candidate models</p>
-    </div>
-
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by James Thorson.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
-
-    </footer></div>
-
-  
-
-  
-
-  </body></html>
-
diff --git a/reference/as_fitted_DAG.html b/reference/as_fitted_DAG.html
index 37d7f0a..f10674e 100644
--- a/reference/as_fitted_DAG.html
+++ b/reference/as_fitted_DAG.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Convert phylosem to phylopath output</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/coerce_methods.R" class="external-link"><code>R/coerce_methods.R</code></a></small>
       <div class="d-none name"><code>as_fitted_DAG.Rd</code></div>
     </div>
 
diff --git a/reference/as_phylo4d.html b/reference/as_phylo4d.html
index 755a1d2..11d7563 100644
--- a/reference/as_phylo4d.html
+++ b/reference/as_phylo4d.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Convert phylosem to phylo4d</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/coerce_methods.R" class="external-link"><code>R/coerce_methods.R</code></a></small>
       <div class="d-none name"><code>as_phylo4d.Rd</code></div>
     </div>
 
diff --git a/reference/as_sem.html b/reference/as_sem.html
index 53833a9..a03dfbf 100644
--- a/reference/as_sem.html
+++ b/reference/as_sem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Convert phylosem to sem output</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/coerce_methods.R" class="external-link"><code>R/coerce_methods.R</code></a></small>
       <div class="d-none name"><code>as_sem.Rd</code></div>
     </div>
 
diff --git a/reference/average.compare_phylosem.html b/reference/average.compare_phylosem.html
index f52cdb2..d0db597 100644
--- a/reference/average.compare_phylosem.html
+++ b/reference/average.compare_phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Choose model</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/compare_phylosem.R" class="external-link"><code>R/compare_phylosem.R</code></a></small>
       <div class="d-none name"><code>average.compare_phylosem.Rd</code></div>
     </div>
 
diff --git a/reference/average.html b/reference/average.html
index 0c3ec05..defa480 100644
--- a/reference/average.html
+++ b/reference/average.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Choose model</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/compare_phylosem.R" class="external-link"><code>R/compare_phylosem.R</code></a></small>
       <div class="d-none name"><code>average.Rd</code></div>
     </div>
 
diff --git a/reference/best.compare_phylosem.html b/reference/best.compare_phylosem.html
index ece286c..afe7c0c 100644
--- a/reference/best.compare_phylosem.html
+++ b/reference/best.compare_phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Extract best fitted model</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/compare_phylosem.R" class="external-link"><code>R/compare_phylosem.R</code></a></small>
       <div class="d-none name"><code>best.compare_phylosem.Rd</code></div>
     </div>
 
diff --git a/reference/best.html b/reference/best.html
index 734bb2e..d82784c 100644
--- a/reference/best.html
+++ b/reference/best.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Extract best fitted model</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/compare_phylosem.R" class="external-link"><code>R/compare_phylosem.R</code></a></small>
       <div class="d-none name"><code>best.Rd</code></div>
     </div>
 
diff --git a/reference/checkDepPackageVersion.html b/reference/checkDepPackageVersion.html
index 6ed03b9..6d13aa0 100644
--- a/reference/checkDepPackageVersion.html
+++ b/reference/checkDepPackageVersion.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Check for version mismatch in dependent binary packages</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>checkDepPackageVersion.Rd</code></div>
     </div>
 
diff --git a/reference/choice.compare_phylosem.html b/reference/choice.compare_phylosem.html
index dcdfecd..0fbe8fe 100644
--- a/reference/choice.compare_phylosem.html
+++ b/reference/choice.compare_phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Choose model</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/compare_phylosem.R" class="external-link"><code>R/compare_phylosem.R</code></a></small>
       <div class="d-none name"><code>choice.compare_phylosem.Rd</code></div>
     </div>
 
diff --git a/reference/choice.html b/reference/choice.html
index ef324e3..b95f041 100644
--- a/reference/choice.html
+++ b/reference/choice.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Choose model</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/compare_phylosem.R" class="external-link"><code>R/compare_phylosem.R</code></a></small>
       <div class="d-none name"><code>choice.Rd</code></div>
     </div>
 
diff --git a/reference/coef.phylosem.html b/reference/coef.phylosem.html
index a4a38b7..b27857a 100644
--- a/reference/coef.phylosem.html
+++ b/reference/coef.phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Extract path coefficients</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/phylosem.R" class="external-link"><code>R/phylosem.R</code></a></small>
       <div class="d-none name"><code>coef.phylosem.Rd</code></div>
     </div>
 
diff --git a/reference/compare_phylosem.html b/reference/compare_phylosem.html
index 724ca7e..2a59ffb 100644
--- a/reference/compare_phylosem.html
+++ b/reference/compare_phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compare phylogenetic structural equation models</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/compare_phylosem.R" class="external-link"><code>R/compare_phylosem.R</code></a></small>
       <div class="d-none name"><code>compare_phylosem.Rd</code></div>
     </div>
 
@@ -63,6 +69,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  estimate_ou <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  estimate_lambda <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  estimate_kappa <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  control <span class="op">=</span> <span class="fu"><a href="phylosem_control.html">phylosem_control</a></span><span class="op">(</span><span class="op">)</span>,</span>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -121,6 +128,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 lengths (a.k.a. the Pagel-kappa term) using additional parameter <code>lnkappa</code></p></dd>
 
 
+<dt>control</dt>
+<dd><p>Output from <code><a href="phylosem_control.html">phylosem_control</a></code>, used to define user
+settings, and see documentation for that function for details.</p></dd>
+
+
 <dt>...</dt>
 <dd><p>Additional arguments passed to <code><a href="phylosem.html">phylosem</a></code></p></dd>
 
diff --git a/reference/fit_tmb.html b/reference/fit_tmb.html
deleted file mode 100644
index 6cbe41f..0000000
--- a/reference/fit_tmb.html
+++ /dev/null
@@ -1,210 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="fit_tmb runs a TMB model and generates standard diagnostics"><title>Optimize a TMB model — fit_tmb • phylosem</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Optimize a TMB model — fit_tmb"><meta property="og:description" content="fit_tmb runs a TMB model and generates standard diagnostics"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--></head><body>
-    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
-
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
-    
-    <a class="navbar-brand me-2" href="../index.html">phylosem</a>
-
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
-
-    
-    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
-      <span class="navbar-toggler-icon"></span>
-    </button>
-
-    <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/comparison.html">Comparison with other packages</a>
-    <a class="dropdown-item" href="../articles/demonstration.html">Demonstration of selected features</a>
-    <a class="dropdown-item" href="../articles/fisheries.html">Phylogenetic comparative methods in fisheries science</a>
-    <a class="dropdown-item" href="../articles/phylopath.html">Detailed comparison with `phylopath`</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"></ul></div>
-
-    
-  </div>
-</nav><div class="container template-reference-topic">
-<div class="row">
-  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Optimize a TMB model</h1>
-      
-      <div class="d-none name"><code>fit_tmb.Rd</code></div>
-    </div>
-
-    <div class="ref-description section level2">
-    <p><code>fit_tmb</code> runs a TMB model and generates standard diagnostics</p>
-    </div>
-
-    <div class="section level2">
-    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">fit_tmb</span><span class="op">(</span></span>
-<span>  <span class="va">obj</span>,</span>
-<span>  fn <span class="op">=</span> <span class="va">obj</span><span class="op">$</span><span class="va">fn</span>,</span>
-<span>  gr <span class="op">=</span> <span class="va">obj</span><span class="op">$</span><span class="va">gr</span>,</span>
-<span>  startpar <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  lower <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span>
-<span>  upper <span class="op">=</span> <span class="cn">Inf</span>,</span>
-<span>  getsd <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>eval.max <span class="op">=</span> <span class="fl">10000</span>, iter.max <span class="op">=</span> <span class="fl">10000</span>, trace <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span>
-<span>  bias.correct <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  bias.correct.control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>sd <span class="op">=</span> <span class="cn">FALSE</span>, split <span class="op">=</span> <span class="cn">NULL</span>, nsplit <span class="op">=</span> <span class="cn">NULL</span>, vars_to_correct <span class="op">=</span></span>
-<span>    <span class="cn">NULL</span><span class="op">)</span>,</span>
-<span>  savedir <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  loopnum <span class="op">=</span> <span class="fl">2</span>,</span>
-<span>  newtonsteps <span class="op">=</span> <span class="fl">0</span>,</span>
-<span>  n <span class="op">=</span> <span class="cn">Inf</span>,</span>
-<span>  getReportCovariance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  getJointPrecision <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  getHessian <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  start_time_elapsed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/difftime.html" class="external-link">as.difftime</a></span><span class="op">(</span><span class="st">"0:0:0"</span><span class="op">)</span>,</span>
-<span>  <span class="va">...</span></span>
-<span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div class="section level2">
-    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>obj</dt>
-<dd><p>The compiled TMB object</p></dd>
-
-
-<dt>fn</dt>
-<dd><p>Function to be minimized. Must return a scalar value. .</p></dd>
-
-
-<dt>gr</dt>
-<dd><p>Optional function that takes the same arguments as objective and evaluates the gradient of objective at its first argument. Must return a vector as long as startpar</p></dd>
-
-
-<dt>startpar</dt>
-<dd><p>Starting values for fixed effects (default NULL uses <code>obj$par</code>)</p></dd>
-
-
-<dt>lower, upper</dt>
-<dd><p>vectors of lower and upper bounds, replicated to be as long as
-    <code>start</code>.  If unspecified, all parameters are assumed to be
-    unconstrained.</p></dd>
-
-
-<dt>getsd</dt>
-<dd><p>Boolean indicating whether to run standard error calculation; see <code><a href="https://rdrr.io/pkg/TMB/man/sdreport.html" class="external-link">sdreport</a></code> for details</p></dd>
-
-
-<dt>control</dt>
-<dd><p>A list of control parameters. For details see <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code></p></dd>
-
-
-<dt>bias.correct</dt>
-<dd><p>Boolean indicating whether to do epsilon bias-correction;
-see <code><a href="https://rdrr.io/pkg/TMB/man/sdreport.html" class="external-link">sdreport</a></code> and <code>fit_tmb</code>for details</p></dd>
-
-
-<dt>bias.correct.control</dt>
-<dd><p>tagged list of options for epsilon bias-correction,
-where <code>vars_to_correct</code> is a character-vector of ADREPORT variables that should be bias-corrected</p></dd>
-
-
-<dt>savedir</dt>
-<dd><p>directory to save results (if <code>savedir=NULL</code>, then results aren't saved)</p></dd>
-
-
-<dt>loopnum</dt>
-<dd><p>number of times to re-start optimization (where <code>loopnum=3</code>
-sometimes achieves a lower final gradient than <code>loopnum=1</code>)</p></dd>
-
-
-<dt>newtonsteps</dt>
-<dd><p>Integer specifying the number of extra newton steps to take
-after optimization (alternative to <code>loopnum</code>).
-Each newtonstep requires calculating the Hessian matrix and is therefore slow.
-But for well-behaved models, each Newton step will typically
-decrease the maximum gradient of the loglikelihood with respect to each fixed effect,
-and therefore this option can be used to achieve an arbitrarily low final gradient
-given sufficient time for well-behaved models.  However, this option will also
-perform strangely or have unexpected consequences for poorly-behaved models, e.g.,
-when fixed effects are at upper or lower bounds. There is no need to increase the value
-of newtonsteps if the model appears to be converged (i.e., has low final_gradient and none of
-the standard errors are NA values)</p></dd>
-
-
-<dt>n</dt>
-<dd><p>sample sizes (if <code>n!=Inf</code> then <code>n</code> is used to calculate BIC and AICc)</p></dd>
-
-
-<dt>getReportCovariance</dt>
-<dd><p>Get full covariance matrix of ADREPORTed variables?</p></dd>
-
-
-<dt>getJointPrecision</dt>
-<dd><p>Optional. Return full joint precision matrix of random effects and parameters?</p></dd>
-
-
-<dt>getHessian</dt>
-<dd><p>return Hessian for usage in later code</p></dd>
-
-
-<dt>quiet</dt>
-<dd><p>Boolean whether to print additional messages results to terminal</p></dd>
-
-
-<dt>start_time_elapsed</dt>
-<dd><p>how much time has elapsed prior to calling fit_tmb,
-for use, e.g., when calling <code>fit_tmb</code> multiple times in sequence,
-where <code>start_time_elapsed = opt_previous$time_for_run</code></p></dd>
-
-
-<dt>...</dt>
-<dd><p>list of settings to pass to <code><a href="https://rdrr.io/pkg/TMB/man/sdreport.html" class="external-link">sdreport</a></code></p></dd>
-
-</dl></div>
-    <div class="section level2">
-    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>the standard output from <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code>, except with additional diagnostics and timing info,
-        and a new slot containing the output from <code><a href="https://rdrr.io/pkg/TMB/man/sdreport.html" class="external-link">sdreport</a></code></p>
-
-
-    </div>
-    <div class="section level2">
-    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>For more details see <a href="https://doi.org/10.1016/j.fishres.2015.11.016" class="external-link">doi:10.1016/j.fishres.2015.11.016</a></p>
-    </div>
-
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
-    </nav></aside></div>
-
-
-    <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by James Thorson.</p>
-</div>
-
-<div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
-</div>
-
-    </footer></div>
-
-  
-
-  
-
-  </body></html>
-
diff --git a/reference/index.html b/reference/index.html
index 7480fe3..d6ce392 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -59,16 +65,6 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 
       <dl><dt>
           
-          <code><a href="Mlifehist_ver1_0.html">Mlifehist_ver1_0</a></code> 
-        </dt>
-        <dd>Fisheries natural mortality example</dd>
-      </dl><dl><dt>
-          
-          <code><a href="TMBAIC.html">TMBAIC()</a></code> 
-        </dt>
-        <dd>Calculate marginal AIC for a fitted model</dd>
-      </dl><dl><dt>
-          
           <code><a href="as_fitted_DAG.html">as_fitted_DAG()</a></code> 
         </dt>
         <dd>Convert phylosem to phylopath output</dd>
@@ -84,22 +80,22 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Convert phylosem to sem output</dd>
       </dl><dl><dt>
           
-          <code><a href="average.html">average()</a></code> 
+          <code><a href="average.compare_phylosem.html">average(<i>&lt;compare_phylosem&gt;</i>)</a></code> 
         </dt>
         <dd>Choose model</dd>
       </dl><dl><dt>
           
-          <code><a href="average.compare_phylosem.html">average(<i>&lt;compare_phylosem&gt;</i>)</a></code> 
+          <code><a href="average.html">average()</a></code> 
         </dt>
         <dd>Choose model</dd>
       </dl><dl><dt>
           
-          <code><a href="best.html">best()</a></code> 
+          <code><a href="best.compare_phylosem.html">best(<i>&lt;compare_phylosem&gt;</i>)</a></code> 
         </dt>
         <dd>Extract best fitted model</dd>
       </dl><dl><dt>
           
-          <code><a href="best.compare_phylosem.html">best(<i>&lt;compare_phylosem&gt;</i>)</a></code> 
+          <code><a href="best.html">best()</a></code> 
         </dt>
         <dd>Extract best fitted model</dd>
       </dl><dl><dt>
@@ -109,12 +105,12 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Check for version mismatch in dependent binary packages</dd>
       </dl><dl><dt>
           
-          <code><a href="choice.html">choice()</a></code> 
+          <code><a href="choice.compare_phylosem.html">choice(<i>&lt;compare_phylosem&gt;</i>)</a></code> 
         </dt>
         <dd>Choose model</dd>
       </dl><dl><dt>
           
-          <code><a href="choice.compare_phylosem.html">choice(<i>&lt;compare_phylosem&gt;</i>)</a></code> 
+          <code><a href="choice.html">choice()</a></code> 
         </dt>
         <dd>Choose model</dd>
       </dl><dl><dt>
@@ -129,14 +125,14 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Compare phylogenetic structural equation models</dd>
       </dl><dl><dt>
           
-          <code><a href="fit_tmb.html">fit_tmb()</a></code> 
+          <code><a href="list_parameters.html">list_parameters()</a></code> 
         </dt>
-        <dd>Optimize a TMB model</dd>
+        <dd>List fixed and random effects</dd>
       </dl><dl><dt>
           
-          <code><a href="list_parameters.html">list_parameters()</a></code> 
+          <code><a href="Mlifehist_ver1_0.html">Mlifehist_ver1_0</a></code> 
         </dt>
-        <dd>List fixed and random effects</dd>
+        <dd>Fisheries natural mortality example</dd>
       </dl><dl><dt>
           
           <code><a href="parse_path.html">parse_path()</a></code> 
@@ -149,6 +145,11 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Fit phylogenetic structural equation model</dd>
       </dl><dl><dt>
           
+          <code><a href="phylosem_control.html">phylosem_control()</a></code> 
+        </dt>
+        <dd>Detailed control for phylosem structure</dd>
+      </dl><dl><dt>
+          
           <code><a href="print.phylosem.html">print(<i>&lt;phylosem&gt;</i>)</a></code> 
         </dt>
         <dd>Print parameter estimates and standard errors.</dd>
diff --git a/reference/list_parameters.html b/reference/list_parameters.html
index b38cfc4..4d1b85c 100644
--- a/reference/list_parameters.html
+++ b/reference/list_parameters.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>List fixed and random effects</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/list_parameters.R" class="external-link"><code>R/list_parameters.R</code></a></small>
       <div class="d-none name"><code>list_parameters.Rd</code></div>
     </div>
 
diff --git a/reference/parse_path.html b/reference/parse_path.html
index 7076c00..e12d538 100644
--- a/reference/parse_path.html
+++ b/reference/parse_path.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Parse path</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/parse_path.R" class="external-link"><code>R/parse_path.R</code></a></small>
       <div class="d-none name"><code>parse_path.Rd</code></div>
     </div>
 
diff --git a/reference/phylosem-1.png b/reference/phylosem-1.png
index 65d292d..ab34146 100644
Binary files a/reference/phylosem-1.png and b/reference/phylosem-1.png differ
diff --git a/reference/phylosem-2.png b/reference/phylosem-2.png
index 468f9b6..7f33cd6 100644
Binary files a/reference/phylosem-2.png and b/reference/phylosem-2.png differ
diff --git a/reference/phylosem-3.png b/reference/phylosem-3.png
index 524724c..fbd87eb 100644
Binary files a/reference/phylosem-3.png and b/reference/phylosem-3.png differ
diff --git a/reference/phylosem.html b/reference/phylosem.html
index 37e1791..193d56b 100644
--- a/reference/phylosem.html
+++ b/reference/phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Fit phylogenetic structural equation model</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/phylosem.R" class="external-link"><code>R/phylosem.R</code></a></small>
       <div class="d-none name"><code>phylosem.Rd</code></div>
     </div>
 
@@ -64,11 +70,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  estimate_lambda <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  estimate_kappa <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  data_labels <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span>,</span>
-<span>  quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
-<span>  newtonsteps <span class="op">=</span> <span class="fl">1</span>,</span>
 <span>  tmb_inputs <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  run_model <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  <span class="va">...</span></span>
+<span>  control <span class="op">=</span> <span class="fu"><a href="phylosem_control.html">phylosem_control</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
 
@@ -131,37 +134,14 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <code>tree$tip.label</code>.  Default pulls <code>data_labels</code> from <code>rownames(data)</code></p></dd>
 
 
-<dt>quiet</dt>
-<dd><p>if <code>FALSE</code>, the default, then the number of input lines is reported and
-    a message is printed suggesting that <code>specifyEquations</code> or <code>cfa</code> be used.</p></dd>
-
-
-<dt>newtonsteps</dt>
-<dd><p>Integer specifying the number of extra newton steps to take
-after optimization (alternative to <code>loopnum</code>).
-Each newtonstep requires calculating the Hessian matrix and is therefore slow.
-But for well-behaved models, each Newton step will typically
-decrease the maximum gradient of the loglikelihood with respect to each fixed effect,
-and therefore this option can be used to achieve an arbitrarily low final gradient
-given sufficient time for well-behaved models.  However, this option will also
-perform strangely or have unexpected consequences for poorly-behaved models, e.g.,
-when fixed effects are at upper or lower bounds. There is no need to increase the value
-of newtonsteps if the model appears to be converged (i.e., has low final_gradient and none of
-the standard errors are NA values)</p></dd>
-
-
 <dt>tmb_inputs</dt>
 <dd><p>optional tagged list that overrides the default constructor
 for TMB inputs (use at your own risk)</p></dd>
 
 
-<dt>run_model</dt>
-<dd><p>Boolean indicating whether to estimate parameters (the default), or
-instead to return the model inputs and compiled TMB object without running;</p></dd>
-
-
-<dt>...</dt>
-<dd><p>Additional parameters passed to <code><a href="fit_tmb.html">fit_tmb</a></code></p></dd>
+<dt>control</dt>
+<dd><p>Output from <code><a href="phylosem_control.html">phylosem_control</a></code>, used to define user
+settings, and see documentation for that function for details.</p></dd>
 
 </dl></div>
     <div class="section level2">
@@ -184,7 +164,10 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 <dd><p>The list of inputs passed to <code><a href="https://rdrr.io/pkg/TMB/man/MakeADFun.html" class="external-link">MakeADFun</a></code></p></dd>
 
 <dt>opt</dt>
-<dd><p>The output from <code><a href="fit_tmb.html">fit_tmb</a></code></p></dd>
+<dd><p>The output from <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code></p></dd>
+
+<dt>sdrep</dt>
+<dd><p>The output from <code><a href="https://rdrr.io/pkg/TMB/man/sdreport.html" class="external-link">sdreport</a></code></p></dd>
 
 <dt>report</dt>
 <dd><p>The output from <code>obj$report()</code></p></dd>
@@ -272,40 +255,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>   Coefficient_name Number_of_coefficients   Type</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1           beta_z                      9  Fixed</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2             x_vj                    495 Random</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   0:     218940.22: 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   1:     8397.8060: 0.0842226 0.130623 0.120621 0.124798 0.347153 0.487021 0.538215 0.426241 0.798883</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   2:     6354.4828: 0.0315557 0.151274 0.172831 0.173170 0.658033 0.551767 0.542706 0.578654 0.594083</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   3:     3672.8577: 0.000303728 0.221429 0.224967 0.235152 0.725274 0.724685 0.748919 0.705591 0.856342</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   4:     2740.3780: -0.102677 0.415193 0.403189 0.371336 0.731170 0.859963 0.790331 0.921711 0.951636</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   5:     1998.5720: -0.126539 0.503355 0.465231 0.444702 0.930180 0.997626  1.00743  1.03020  1.14979</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   6:     1603.6727: -0.156804 0.611920 0.546135 0.512778  1.10880  1.15370  1.19174  1.17670  1.34656</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   7:     1378.4437: -0.184978 0.735384 0.635855 0.574242  1.28215  1.30788  1.36879  1.33950  1.53299</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   8:     1246.1754: -0.205749 0.871125 0.727935 0.623959  1.45479  1.45790  1.54574  1.51056  1.71079</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   9:     1168.3619: -0.217139  1.01403 0.814506 0.657424  1.62857  1.60494  1.72664  1.68772  1.88166</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  10:     1123.9069: -0.220534  1.15457 0.885299 0.673319  1.80466  1.75160  1.91435  1.87091  2.04888</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  11:     1100.3689: -0.220150  1.27536 0.928361 0.675635  1.98358  1.90047  2.11097  2.06073  2.21911</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  12:     1089.9414: -0.220524  1.34559 0.935212 0.674388  2.16290  2.04937  2.31732  2.25655  2.40368</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  13:     1088.5461: -0.220084  1.33812 0.932369 0.675458  2.21370  2.08811  2.38334  2.31655  2.47029</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  14:     1087.8319: -0.220718  1.33618 0.933085 0.674475  2.26200  2.12267  2.45045  2.37612  2.54069</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  15:     1087.7787: -0.220253  1.33642 0.932854 0.675008  2.26795  2.12603  2.46060  2.38452  2.55226</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  16:     1087.7091: -0.220358  1.33673 0.932671 0.675146  2.27944  2.13226  2.48095  2.40115  2.57585</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  17:     1087.7069: -0.217349  1.33044 0.940994 0.668413  2.28729  2.11448  2.49234  2.41721  2.59797</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  18:     1087.6911: -0.222165  1.33489 0.932128 0.677383  2.28740  2.12316  2.49506  2.41681  2.59939</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  19:     1087.6907: -0.214887  1.33792 0.933697 0.669999  2.28758  2.13505  2.49955  2.41615  2.60180</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  20:     1087.6863: -0.221547  1.33726 0.932944 0.675110  2.28759  2.13517  2.49998  2.41611  2.60207</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  21:     1087.6861: -0.220478  1.33704 0.932837 0.675081  2.28760  2.13522  2.50021  2.41608  2.60222</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  22:     1087.6861: -0.220143  1.33645 0.932761 0.674901  2.28764  2.13538  2.50097  2.41602  2.60264</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  23:     1087.6861: -0.220221  1.33658 0.932819 0.675126  2.28770  2.13531  2.50117  2.41601  2.60276</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  24:     1087.6861: -0.220415  1.33670 0.932693 0.674998  2.28765  2.13538  2.50131  2.41596  2.60293</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  25:     1087.6861: -0.220192  1.33683 0.932842 0.675013  2.28773  2.13544  2.50141  2.41587  2.60309</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  26:     1087.6861: -0.220324  1.33674 0.932762 0.675074  2.28770  2.13543  2.50142  2.41588  2.60310</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  27:     1087.6861: -0.220275  1.33670 0.932749 0.675068  2.28767  2.13543  2.50143  2.41589  2.60311</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  28:     1087.6861: -0.220310  1.33668 0.932761 0.675067  2.28763  2.13543  2.50146  2.41592  2.60310</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  29:     1087.6861: -0.220287  1.33668 0.932751 0.675069  2.28763  2.13543  2.50146  2.41592  2.60311</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  30:     1087.6861: -0.220295  1.33668 0.932747 0.675069  2.28762  2.13542  2.50146  2.41592  2.60311</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  31:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   0:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   1:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Running nlminb_loop #1</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Running newton_loop #1</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Convert and plot using phylopath</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://Ax3man.github.io/phylopath/" class="external-link">phylopath</a></span><span class="op">)</span></span></span>
diff --git a/reference/phylosem_control.html b/reference/phylosem_control.html
new file mode 100644
index 0000000..5ad1493
--- /dev/null
+++ b/reference/phylosem_control.html
@@ -0,0 +1,154 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Define a list of control parameters.  Note that
+the format of this input is likely to change more rapidly than that of
+phylosem"><title>Detailed control for phylosem structure — phylosem_control • phylosem</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Detailed control for phylosem structure — phylosem_control"><meta property="og:description" content="Define a list of control parameters.  Note that
+the format of this input is likely to change more rapidly than that of
+phylosem"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
+
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
+    <a class="navbar-brand me-2" href="../index.html">phylosem</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
+
+    
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/comparison.html">Comparison with other packages</a>
+    <a class="dropdown-item" href="../articles/demonstration.html">Demonstration of selected features</a>
+    <a class="dropdown-item" href="../articles/fisheries.html">Phylogenetic comparative methods in fisheries science</a>
+    <a class="dropdown-item" href="../articles/phylopath.html">Detailed comparison with `phylopath`</a>
+  </div>
+</li>
+<li class="nav-item">
+  <a class="nav-link" href="../news/index.html">Changelog</a>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
+
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
+
+    
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="" class="logo" alt=""><h1>Detailed control for phylosem structure</h1>
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/phylosem.R" class="external-link"><code>R/phylosem.R</code></a></small>
+      <div class="d-none name"><code>phylosem_control.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Define a list of control parameters.  Note that
+the format of this input is likely to change more rapidly than that of
+<code><a href="phylosem.html">phylosem</a></code></p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">phylosem_control</span><span class="op">(</span></span>
+<span>  nlminb_loops <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  newton_loops <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  trace <span class="op">=</span> <span class="fl">0</span>,</span>
+<span>  eval.max <span class="op">=</span> <span class="fl">1000</span>,</span>
+<span>  iter.max <span class="op">=</span> <span class="fl">1000</span>,</span>
+<span>  getsd <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  run_model <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  getJointPrecision <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <dl><dt>nlminb_loops</dt>
+<dd><p>Integer number of times to call <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code>.</p></dd>
+
+
+<dt>newton_loops</dt>
+<dd><p>Integer number of Newton steps to do after running
+<code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code>.</p></dd>
+
+
+<dt>trace</dt>
+<dd><p>Parameter values are printed every `trace` iteration
+for the outer optimizer. Passed to
+`control` in <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code>.</p></dd>
+
+
+<dt>eval.max</dt>
+<dd><p>Maximum number of evaluations of the objective function
+allowed. Passed to `control` in <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code>.</p></dd>
+
+
+<dt>iter.max</dt>
+<dd><p>Maximum number of iterations allowed. Passed to `control` in
+<code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code>.</p></dd>
+
+
+<dt>getsd</dt>
+<dd><p>Boolean indicating whether to call <code><a href="https://rdrr.io/pkg/TMB/man/sdreport.html" class="external-link">sdreport</a></code></p></dd>
+
+
+<dt>quiet</dt>
+<dd><p>Boolean indicating whether to run model printing messages to terminal or not;</p></dd>
+
+
+<dt>run_model</dt>
+<dd><p>Boolean indicating whether to estimate parameters (the default), or
+instead to return the model inputs and compiled TMB object without running;</p></dd>
+
+
+<dt>getJointPrecision</dt>
+<dd><p>whether to get the joint precision matrix.  Passed
+to <code><a href="https://rdrr.io/pkg/TMB/man/sdreport.html" class="external-link">sdreport</a></code>.</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    
+
+<p>An S3 object of class "phylosem_control" that specifies detailed model settings,
+allowing user specification while also specifying default values</p>
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p><p>Developed by James Thorson.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/reference/print.phylosem.html b/reference/print.phylosem.html
index 9f6098d..4009565 100644
--- a/reference/print.phylosem.html
+++ b/reference/print.phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Print parameter estimates and standard errors.</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/phylosem.R" class="external-link"><code>R/phylosem.R</code></a></small>
       <div class="d-none name"><code>print.phylosem.Rd</code></div>
     </div>
 
@@ -72,7 +78,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>prints (and invisibly returns) output from <code><a href="fit_tmb.html">fit_tmb</a></code></p>
+<p>prints (and invisibly returns) output from <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">nlminb</a></code></p>
 
 
     </div>
diff --git a/reference/reinstalling.html b/reference/reinstalling.html
index be7fa17..145143f 100644
--- a/reference/reinstalling.html
+++ b/reference/reinstalling.html
@@ -70,7 +70,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -96,7 +96,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -104,7 +110,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Reinstalling binary dependencies</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>reinstalling.Rd</code></div>
     </div>
 
diff --git a/reference/summary.phylosem.html b/reference/summary.phylosem.html
index 1dfe159..12fb66b 100644
--- a/reference/summary.phylosem.html
+++ b/reference/summary.phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>summarize phylosem</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/phylosem.R" class="external-link"><code>R/phylosem.R</code></a></small>
       <div class="d-none name"><code>summary.phylosem.Rd</code></div>
     </div>
 
diff --git a/reference/vcov.phylosem.html b/reference/vcov.phylosem.html
index 0c8f104..968fa91 100644
--- a/reference/vcov.phylosem.html
+++ b/reference/vcov.phylosem.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phylosem</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.1.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,13 @@
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
-      <ul class="navbar-nav"></ul></div>
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/James-Thorson-NOAA/phylosem/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
 
     
   </div>
@@ -44,7 +50,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Extract Variance-Covariance Matrix</h1>
-      
+      <small class="dont-index">Source: <a href="https://github.com/James-Thorson-NOAA/phylosem/blob/HEAD/R/phylosem.R" class="external-link"><code>R/phylosem.R</code></a></small>
       <div class="d-none name"><code>vcov.phylosem.Rd</code></div>
     </div>
 
diff --git a/search.json b/search.json
index 803aa5a..69dcc0c 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"comparison-with-phylolm","dir":"Articles","previous_headings":"","what":"Comparison with phylolm","title":"Comparison with other packages","text":"first compare syntax run-times using simulated data phylolm. confirms runtimes phylosem within order magnitude results nearly identical BM, OU, delta, kappa models.","code":"# Settings Ntree = 100 sd_x = 0.3 sd_y = 0.3 b0_x = 1 b0_y = 0 b_xy = 1  # Simulate tree set.seed(1) tree = ape::rtree(n=Ntree)  # Simulate data x = b0_x + sd_x * phylolm::rTrait(n = 1, phy=tree) ybar = b0_y + b_xy*x y_normal = ybar + sd_y * phylolm::rTrait(n = 1, phy=tree)  # Construct, re-order, and reduce data Data = data.frame(x=x,y=y_normal)[]  # Compare using BM model start_time = Sys.time() plm_bm = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"BM\" ) Sys.time() - start_time #> Time difference of 0.00622654 secs knitr::kable(summary(plm_bm)$coefficients, digits=3) start_time = Sys.time() psem_bm = phylosem( sem = \"x -> y, p\",           data = Data,           tree = tree,           quiet = TRUE ) Sys.time() - start_time #> Time difference of 0.1971586 secs knitr::kable(summary(psem_bm)$coefficients, digits=3) # Compare using OU start_time = Sys.time() plm_ou = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"OUrandomRoot\" ) Sys.time() - start_time #> Time difference of 0.0199275 secs  start_time = Sys.time() psem_ou = phylosem( sem = \"x -> y, p\",           data = Data,           tree = tree,           estimate_ou = TRUE,           quiet = TRUE ) Sys.time() - start_time #> Time difference of 0.2294426 secs  knitr::kable(summary(psem_ou)$coefficients, digits=3) knitr::kable(summary(plm_ou)$coefficients, digits=3) knitr::kable(c( \"phylolm_alpha\"=plm_ou$optpar,                  \"phylosem_alpha\"=exp(psem_ou$parhat$lnalpha) ), digits=3) # Compare using Pagel's lambda start_time = Sys.time() plm_lambda = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"lambda\" ) Sys.time() - start_time #> Time difference of 0.04079676 secs  start_time = Sys.time() psem_lambda = phylosem( sem = \"x -> y, p\",           data = Data,           tree = tree,           estimate_lambda = TRUE,           quiet = TRUE ) Sys.time() - start_time #> Time difference of 0.1857631 secs  knitr::kable(summary(psem_lambda)$coefficients, digits=3) knitr::kable(summary(plm_lambda)$coefficients, digits=3) knitr::kable(c( \"phylolm_lambda\"=plm_lambda$optpar,                  \"phylosem_lambda\"=plogis(psem_lambda$parhat$logitlambda) ), digits=3) # Compare using Pagel's kappa start_time = Sys.time() plm_kappa = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"kappa\", lower.bound = 0, upper.bound = 3 ) Sys.time() - start_time #> Time difference of 0.01002622 secs  start_time = Sys.time() psem_kappa = phylosem( sem = \"x -> y, p\",           data = Data,           tree = tree,           estimate_kappa = TRUE,           quiet = TRUE ) Sys.time() - start_time #> Time difference of 0.1860392 secs  knitr::kable(summary(psem_kappa)$coefficients, digits=3) knitr::kable(summary(plm_kappa)$coefficients, digits=3) knitr::kable(c( \"phylolm_kappa\"=plm_kappa$optpar,                  \"phylosem_kappa\"=exp(psem_kappa$parhat$lnkappa) ), digits=3)"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"generalized-linear-models","dir":"Articles","previous_headings":"","what":"Generalized linear models","title":"Comparison with other packages","text":"also compare results among software fitting phylogenetic generalized linear models (PGLM).","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"poisson-distributed-response","dir":"Articles","previous_headings":"Generalized linear models","what":"Poisson-distributed response","title":"Comparison with other packages","text":"First, specifically explore Poisson-distributed PGLM, comparing phylosem phylolm::phyloglm (uses Generalized Estimating Equations) phyr::pglmm_compare (uses maximum likelihood). also compare results brms (fits Bayesian hierarchical model), although load results compiled run brms avoid users install STAN run vignettes phylosem:  instance (others explored), results phylolm::phyloglm generally different phylosem, phyr::pglmm_compare, brms close quite identical.","code":"# Settings Ntree = 100 sd_x = 0.3 sd_y = 0.3 b0_x = 1 b0_y = 0 b_xy = 1  # Simulate tree set.seed(1) tree = ape::rtree(n=Ntree)  # Simulate data x = b0_x + sd_x * phylolm::rTrait(n = 1, phy=tree) ybar = b0_y + b_xy*x y_normal = ybar + sd_y * phylolm::rTrait(n = 1, phy=tree) y_pois = rpois( n=Ntree, lambda=exp(y_normal) )  # Construct, re-order, and reduce data Data = data.frame(x=x,y=y_pois)  # Compare using phylolm::phyloglm pglm = phylolm::phyloglm(y ~ 1 + x, data=Data, phy=tree, method=\"poisson_GEE\" ) knitr::kable(summary(pglm)$coefficients, digits=3) # pglmm = phyr::pglmm_compare(   y ~ 1 + x,   family = \"poisson\",   data = Data,   phy = tree ) knitr::kable(summary(pglmm), digits=3) #> Generalized linear mixed model for poisson data fit by restricted maximum likelihood #>  #> Call:y ~ 1 + x #>  #> logLik    AIC    BIC  #> -173.4  354.7  360.6  #>  #> Phylogenetic random effects variance (s2): #>    Variance Std.Dev #> s2  0.05511  0.2348 #>  #> Fixed effects: #>                Value Std.Error  Zscore    Pvalue     #> (Intercept) -0.57009   0.30469 -1.8710   0.06134 .   #> x            1.18137   0.19807  5.9645 2.454e-09 *** #> --- #> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 # pgsem = phylosem( sem = \"x -> y, p\",           data = Data,           family = c(\"fixed\",\"poisson\"),           tree = tree,           quiet = TRUE ) knitr::kable(summary(pgsem)$coefficients, digits=3) # Comare using Bayesian implementation in brms library(brms) Amat <- ape::vcv.phylo(tree) Data$tips <- rownames(Data) mcmc <- brm(   y ~ 1 + x + (1 | gr(tips, cov = A)),   data = Data, data2 = list(A = Amat),   family = 'poisson',   cores = 4 ) knitr::kable(fixef(mcmc), digits = 3)  # Plot them together library(ggplot2) pdat <- rbind.data.frame(   coef(summary(pglm))[, 1:2],   data.frame(Estimate = pglmm$B, StdErr = pglmm$B.se),   setNames(as.data.frame(fixef(mcmc))[1:2], c('Estimate', 'StdErr')),   setNames(summary(pgsem)$coefficients[2:3, 3:4], c('Estimate', 'StdErr')) ) pdat$Param <- rep(c('Intercept', 'Slope'), 4) pdat$Method <- rep( c('phylolm::phyloglm', 'phyr::pglmm_compare',                      'brms::brm', 'phylosem::phylosem'), each = 2) figure = ggplot(pdat, aes(   x = Estimate, xmin = Estimate - StdErr,   xmax = Estimate + StdErr, y = Param, color = Method )) +   geom_pointrange(position = position_dodge(width = 0.6)) +   theme_classic() +   theme(panel.grid.major.x = element_line(), panel.grid.minor.x = element_line())"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"binomial-regression","dir":"Articles","previous_headings":"Generalized linear models","what":"Binomial regression","title":"Comparison with other packages","text":"also compare results Bernoulli-distributed response using PGLM. compare phylosem phyr::pglmm_compare, explore threshold models expect give different results due differences assumptions latent variables affect measurements. instance, phylosem phyr::pglmm_compare give similar estimates standard errors slope term.","code":"# Settings Ntree = 100 sd_x = 0.3 sd_y = 0.3 b0_x = 1 b0_y = 0 b_xy = 1  # Simulate tree set.seed(1) tree = ape::rtree(n=Ntree)  # Simulate data x = b0_x + sd_x * phylolm::rTrait(n = 1, phy=tree) ybar = b0_y + b_xy*x y_normal = ybar + sd_y * phylolm::rTrait(n = 1, phy=tree) y_binom = rbinom( n=Ntree, size=1, prob=plogis(y_normal) )  # Construct, re-order, and reduce data Data = data.frame(x=x,y=y_binom)  # pglmm = phyr::pglmm_compare(   y ~ 1 + x,   family = \"binomial\",   data = Data,   phy = tree ) knitr::kable(summary(pglmm), digits=3) #> Generalized linear mixed model for binomial data fit by restricted maximum likelihood #>  #> Call:y ~ 1 + x #>  #> logLik    AIC    BIC  #> -63.74 135.47 141.32  #>  #> Phylogenetic random effects variance (s2): #>    Variance Std.Dev #> s2   0.1076   0.328 #>  #> Fixed effects: #>               Value Std.Error Zscore Pvalue #> (Intercept) 0.23179   0.60507 0.3831 0.7017 #> x           0.44548   0.45708 0.9746 0.3297 # pgsem = phylosem( sem = \"x -> y, p\",           data = Data,           family = c(\"fixed\",\"binomial\"),           tree = tree,           quiet = TRUE ) knitr::kable(summary(pgsem)$coefficients, digits=3)"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"summary-of-pglm-results","dir":"Articles","previous_headings":"Generalized linear models","what":"Summary of PGLM results","title":"Comparison with other packages","text":"Based two comparisons, conclude phylosem provides interface maximum-likelihood estimate phylogenetic generalized linear models (PGLM), extends class include mixed data (.e., combination different measurement types), missing data, non-recursive structural linkages. However, also encourage cross-testing different software fitting phylogenetic generalized linear models.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"compare-with-phylopath","dir":"Articles","previous_headings":"","what":"Compare with phylopath","title":"Comparison with other packages","text":"next compare single run phylopath. confirms runtimes within order magnitude results identical standardized unstandardized coefficients.","code":"library(phylopath) library(phylosem)  # make copy of data that's rescaled rhino_scaled = rhino   rhino_scaled[,c(\"BM\",\"NL\",\"LS\",\"DD\",\"RS\")] = scale(rhino_scaled[,c(\"BM\",\"NL\",\"LS\",\"DD\",\"RS\")])  # Fit and plot using phylopath dag <- DAG(RS ~ DD, LS ~ BM, NL ~ BM, DD ~ NL) start_time = Sys.time() result <- est_DAG( DAG = dag,                     data = rhino,                     tree = rhino_tree,                     model = \"BM\",                     measurement_error = FALSE ) Sys.time() - start_time #> Time difference of 0.01152086 secs plot(result) # Fit and plot using phylosem model = \"   DD -> RS, p1   BM -> LS, p2   BM -> NL, p3   NL -> DD, p4 \" start_time = Sys.time() psem = phylosem( sem = model,           data = rhino_scaled[,c(\"BM\",\"NL\",\"DD\",\"RS\",\"LS\")],           tree = rhino_tree,           quiet = TRUE ) Sys.time() - start_time #> Time difference of 0.4174633 secs plot( as_fitted_DAG(psem) )"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"comparison-with-sem","dir":"Articles","previous_headings":"","what":"Comparison with sem","title":"Comparison with other packages","text":"next compare syntax runtime R-package sem. confirms runtimes within order magnitude specifying star-phylogeny phylosem match assumed structure sem compare estimated values standardized coefficients also compare values unstandardized coefficients:","code":"library(sem) library(TreeTools)  # Simulation parameters n_obs = 50 # Intercepts a1 = 1 a2 = 2 a3 = 3 a4 = 4 # Slopes b12 = 0.3 b23 = 0 b34 = 0.3 # Standard deviations s1 = 0.1 s2 = 0.2 s3 = 0.3 s4 = 0.4  # Simulate data E1 = rnorm(n_obs, sd=s1) E2 = rnorm(n_obs, sd=s2) E3 = rnorm(n_obs, sd=s3) E4 = rnorm(n_obs, sd=s4) Y1 = a1 + E1 Y2 = a2 + b12*Y1 + E2 Y3 = a3 + b23*Y2 + E3 Y4 = a4 + b34*Y3 + E4 Data = data.frame(Y1=Y1, Y2=Y2, Y3=Y3, Y4=Y4)  # Specify path diagram (in this case, using correct structure) equations = \"   Y2 = b12 * Y1   Y4 = b34 * Y3 \" model <- specifyEquations(text=equations, exog.variances=TRUE, endog.variances=TRUE)  # Fit using package:sem start_time = Sys.time() Sem <- sem(model, data=Data) Sys.time() - start_time #> Time difference of 0.01753688 secs  # Specify star phylogeny tree_null = TreeTools::StarTree(n_obs)   tree_null$edge.length = rep(1,nrow(tree_null$edge))   rownames(Data) = tree_null$tip.label  # Fit using phylosem start_time = Sys.time() psem = phylosem( data = Data,           sem = equations,           tree = tree_null,           quiet = TRUE ) Sys.time() - start_time #> Time difference of 0.07997537 secs"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"comparison-with-rphylopars","dir":"Articles","previous_headings":"","what":"Comparison with Rphylopars","title":"Comparison with other packages","text":"Finally, compare syntax runtime R-package Rphylopars. confirms can impute identical estimates using packages, specifying full-rank covariance phylosem note phylosem also allows parsimonious representations trait covariance via inputted SEM structure.","code":"library(Rphylopars)  # Format data, within no values for species t1 Data = rhino[,c(\"BM\",\"NL\",\"DD\",\"RS\",\"LS\")]   rownames(Data) = tree$tip.label Data['t1',] = NA  # fit using phylopars start_time = Sys.time() pars <- phylopars( trait_data = cbind(species=rownames(Data),Data),                   tree = tree,                   pheno_error = FALSE,                   phylo_correlated = TRUE,                   pheno_correlated = FALSE) Sys.time() - start_time #> Time difference of 0.1094489 secs  # Display estimates for missing values knitr::kable(cbind( \"Estimate\"=pars$anc_recon[\"t1\",], \"Var\"=pars$anc_var[\"t1\",] ), digits=3) # fit using phylosem start_time = Sys.time() psem = phylosem( data = Data,                  tree = tree,                  sem = \"\",                  covs = \"BM, NL, DD, RS, LS\",                  quiet = TRUE ) Sys.time() - start_time #> Time difference of 0.6932356 secs  # Display estimates for missing values knitr::kable(cbind(   \"Estimate\"=as.list(psem$opt$SD,\"Estimate\")$x_vj[ match(\"t1\",tree$tip.label), ],   \"Var\"=as.list(psem$opt$SD,\"Std. Error\")$x_vj[ match(\"t1\",tree$tip.label), ]^2 ), digits=3)"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/demonstration.html","id":"estimability-for-multiple-covariance-transformations","dir":"Articles","previous_headings":"","what":"Estimability for multiple covariance transformations","title":"Demonstration of selected features","text":"default, phylosem takes input phylogenetic tree constructs covariance Brownian motion evolutionary model. However, also allows combination following transformations: Ornstein-Uhlenbeck (OU); Pagel’s lambda; Pagel’s kappa; results eight possible covariance models formed including excluding transformation. first show transformations simultaneously estimable reference data set. see minimum eigenvalue precision matrix (corresponds maximum eigenvalue covariance matrix) greater zero, precision invertible Hessian matrix full rank. can see parameters estimable applying three transformations. also see transformation parameters perfectly correlated, although logit-lambda ln-alpha parameters correlation approximately 0.75. can also extract standard errors, calculated square-root diagonal elements covariance matrix. extract estimated values lnalpha, logitlambda, lnkappa plot plot 95% confidence interval estimates plus minus 1.96 times standard errors. values unbounded construction. However, also convert estimates, lower, upper confidence-interval bounds conventional parameters alpha, lambda, kappa, plot well. derived quantities bounded expected Ornstein-Uhlenbeck Pagel parameters:  confidence intervals suggest parameter lnkappa overlaps 0.0, suggesting Pagel’s kappa overlaps 1.0 instead turned thereby fixed default value.","code":"# Compare using Pagel's kappa library(phylopath)  # Run phylosem model = \"   DD -> RS, p1   BM -> LS, p2   BM -> NL, p3   NL -> DD, p4 \" psem = phylosem( sem = model,           data = rhino[,c(\"BM\",\"NL\",\"DD\",\"RS\",\"LS\")],           estimate_ou = TRUE,           estimate_lambda = TRUE,           estimate_kappa = TRUE,           tree = rhino_tree,           getJointPrecision = TRUE,           quiet = TRUE )  # V = psem$opt$SD$cov.fixed Rsub = cov2cor(V)[c('lnalpha','logitlambda','lnkappa'),c('lnalpha','logitlambda','lnkappa')]  knitr::kable(c(\"minimum_eigenvalue\"=min(eigen(psem$opt$SD$jointPrecision)$values),              \"maximum_eigenvalue\"=max(eigen(psem$opt$SD$jointPrecision)$values)), digits=3) knitr::kable(Rsub, digits=3) library(ggplot2) # Compile estimates and SEs pdat = data.frame( \"Estimate\" = psem$opt$SD$par.fixed[c('lnalpha','logitlambda','lnkappa')],               \"StdErr\" = sqrt(diag(V)[c('lnalpha','logitlambda','lnkappa')]) ) pdat = cbind( pdat, \"Param\" = rownames(pdat))  # pdat$lower = pdat$Estimate - 1.96*pdat$StdErr pdat$upper = pdat$Estimate + 1.96*pdat$StdErr pdat$type = \"estimated\"  # Transform from log / logit-space to natural space pdat2 = pdat pdat2$Param = c(\"alpha\", \"lambda\", \"kappa\") pdat2['lnalpha',c(\"Estimate\",\"lower\",\"upper\")] = exp(pdat2['lnalpha',c(\"Estimate\",\"lower\",\"upper\")]) pdat2['lnkappa',c(\"Estimate\",\"lower\",\"upper\")] = exp(pdat2['lnkappa',c(\"Estimate\",\"lower\",\"upper\")]) pdat2['logitlambda',c(\"Estimate\",\"lower\",\"upper\")] = plogis(as.numeric(pdat2['logitlambda',c(\"Estimate\",\"lower\",\"upper\")])) pdat2$type = \"derived\"  # Plot ggplot( rbind(pdat,pdat2), aes( x=Param, y = Estimate, ymin = lower, ymax = upper)) +   geom_pointrange(position = position_dodge(width = 0.6)) +   theme_classic() +   facet_grid( rows=vars(type), scales=\"free\" )"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/demonstration.html","id":"scaling-of-runtime-with-increased-tree-size","dir":"Articles","previous_headings":"","what":"Scaling of runtime with increased tree size","title":"Demonstration of selected features","text":"package phylolm expected “linear runtime”, .e., proportional increase runtime increasing tree size. therefore compare runtime phylosem phylolm using simulated tree across three orders magnitude (10, 100, 1000, 10000 tips).  Results show packages approximately linear runtime, phylolm approximately 10-100 times faster given tree size.","code":"# Settings Ntree_config = c( 1e1, 1e2, 1e3, 1e4 ) Nreplicates = 5 sd_x = 0.3 sd_y = 0.3 b0_x = 1 b0_y = 0 b_xy = 1  # Simulate tree set.seed(1) Time_rcz = array(NA, dim=c(Nreplicates,length(Ntree_config),2), dimnames=list(NULL,\"tree_size\"=Ntree_config,\"package\"=c(\"phylolm\",\"phylosem\")) )  for( rI in seq_len(Nreplicates) ){ for( cI in seq_along(Ntree_config) ){    # Simulate data   tree = ape::rtree(n=Ntree_config[cI])   x = b0_x + sd_x * phylolm::rTrait(n = 1, phy=tree)   ybar = b0_y + b_xy*x   y_normal = ybar + sd_y * phylolm::rTrait(n = 1, phy=tree)   Data = data.frame(x=x, y=y_normal)[]    # Run phylolm   start_time = Sys.time()   plm_bm = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"BM\" )   Time_rcz[rI,cI,\"phylolm\"] = Sys.time() - start_time    # Run phylosem   start_time = Sys.time()   psem_bm = phylosem( sem = \"x -> y, p\",             data = Data,             tree = tree,             quiet = TRUE,             newtonsteps = 0,             getsd = FALSE )   Time_rcz[rI,cI,\"phylosem\"] = Sys.time() - start_time }}  # Format df = apply( Time_rcz, MARGIN=2:3, FUN=mean ) df = cbind( expand.grid(dimnames(df)), \"time_seconds\"=as.vector(df) )  # Plot library(ggplot2) ggplot(data=df, aes(x=tree_size, y=time_seconds, group=package, color=package)) +   geom_line() +   geom_point() + scale_y_log10()"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/fisheries.html","id":"preparing-the-then-et-al--mortality-database","dir":"Articles","previous_headings":"","what":"Preparing the Then et al. mortality database","title":"Phylogenetic comparative methods in fisheries science","text":"demonstrate potential role PCM fisheries science, re-analyze foundational dataset compiled et al.. specifically download file “Mlifehist_ver1.0.csv” include copy data object package phylosem simplify following demonstration. demonstration provides basic syntax output PCM, showing relationship natural mortality rate, longevity, growth parameters. , first load phylogeny fishes using package fishtree, includes several versions phylogeny fishes develoepd Rabosky et al.. associate trait data tip label phylogeny, provide convenient names modeled variables.","code":"# Load packages library(phylosem) library(fishtree)  # Download tree out = fishtree_complete_phylogeny() tree = out[[1]]  # Load data object data( Mlifehist_ver1_0 ) Data = Mlifehist_ver1_0  # Reformat to match tree$tip.label Data$Genus_species = factor( paste0(Data$Genus, \"_\", Data$Species) )  # Drop duplicates ... not dealing with variation among stocks within species Data = Data[match(unique(Data$Genus_species),Data$Genus_species), ]  # log-transform to simplify later syuntax Data = cbind( Data, \"logM\" = log(Data[,'M']),                     \"logK\" = log(Data[,'K']),                     \"logtmax\" = log(Data[,'tmax']),                     \"logLinf\" = log(Data[,'Linf']) )  # Identify species in both datasets species_to_use = intersect( tree$tip.label, Data$Genus_species ) species_to_drop = setdiff( Data$Genus_species, tree$tip.label )  # Drop tips not present in trait-data # Not strictly necessary, but helpful to simplify later plots tree = ape::keep.tip( tree, tip=species_to_use )  # Drop trait-data not in phylogeny # Necessary to define correlation among data rows_to_use = which( Data$Genus_species %in% species_to_use ) Data = Data[rows_to_use,]  # Only include modeled variables in trait-data passed to phylosem rownames(Data) = Data$Genus_species Data = Data[,c('logM','logK','logtmax','logLinf')]"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/fisheries.html","id":"fitting-and-selecting-among-phylogenetic-structural-equation-models","dir":"Articles","previous_headings":"","what":"Fitting and selecting among phylogenetic structural equation models","title":"Phylogenetic comparative methods in fisheries science","text":"define path diagram specifying set linkages among variables. following, use path diagram ensures mortality rate statistically independent growth, conditional upon measurement longevity. specification ensures , longevity available, sole information used predict mortality rate. However, longevity available, model reverts predicting mortality growth parameters. fit model using phylogenetic structural equation models. specifically apply grid-search across eight models formed combination modeled transformations phylogenetic tree. use marginal AIC select model, list estimated path coefficients.","code":"# Specify SEM structure sem_structure = \"   logK -> logtmax, b1   logLinf -> logtmax, b2   logtmax -> logM, a \"  # Grid-search model selection using AIC for transformations Grid = expand.grid( \"OU\" = c(FALSE,TRUE),                     \"lambda\" = c(FALSE,TRUE),                     \"kappa\" = c(FALSE,TRUE) ) psem_grid = NULL for( i in 1:nrow(Grid)){   psem_grid[[i]] = phylosem( data=Data,                    tree = tree,                    sem = sem_structure,                    estimate_ou = Grid[i,'OU'],                    estimate_lambda = Grid[i,'lambda'],                    estimate_kappa = Grid[i,'kappa'],                    quiet = TRUE ) }  # Extract AIC for each model and rank-order by parsimony Grid$AIC = sapply( psem_grid, \\(m) m$opt$AIC ) Grid = Grid[order(Grid$AIC,decreasing=FALSE),]  # Select model with lowest AIC psem_best = psem_grid[[as.numeric(rownames(Grid[1,]))]]"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/fisheries.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing output","title":"Phylogenetic comparative methods in fisheries science","text":"Finally, can convert output formats packages, use existing third-party PCM packages plot, query, post-process output.  also show plot output using phylosignal, although currently unavailable CRAN therefore commented :","code":"# Plot path diagram my_fitted_DAG = as_fitted_DAG(psem_best) plot(my_fitted_DAG, type=\"color\") # Total, direct, and indirect effects my_sem = as_sem(psem_best) effects(my_sem) #>  #>  Total Effects (column on row) #>               logK   logtmax    logLinf #> logtmax -0.4480233  0.000000  0.4073488 #> logM     0.4579994 -1.022267 -0.4164192 #>  #>  Direct Effects #>               logK   logtmax   logLinf #> logtmax -0.4480233  0.000000 0.4073488 #> logM     0.0000000 -1.022267 0.0000000 #>  #>  Indirect Effects #>              logK logtmax    logLinf #> logtmax 0.0000000       0  0.0000000 #> logM    0.4579994       0 -0.4164192 # Load for plotting, # https://r-pkgs.org/vignettes.html#sec-vignettes-eval-option library(phylosignal)  # Plot using phylobase my_phylo4d = as_phylo4d( psem_best ) barplot(my_phylo4d)"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/fisheries.html","id":"sensitivity-to-using-taxonomic-tree","dir":"Articles","previous_headings":"","what":"Sensitivity to using taxonomic tree","title":"Phylogenetic comparative methods in fisheries science","text":"analysis, can also conduct sensivity analyses. , show construct taxonomic tree use place phylogenetic information. , requires code reformat data statistical analysis simple specify. estimated path coefficients similar estimates using phyogeny.","code":"library(ape) Data = Mlifehist_ver1_0  # Make taxonomic factors Data$Genus_species = factor( paste0(Data$Genus, \"_\", Data$Species) ) Data$Genus = factor( Data$Genus ) Data$Family = factor( Data$Family ) Data$Order = factor( Data$Order )  # Make taxonomic tree tree = ape::as.phylo( ~Order/Family/Genus/Genus_species, data=Data, collapse=FALSE) tree$edge.length = rep(1,nrow(tree$edge)) tree = collapse.singles(tree) tmp = root(tree, node=ape::Ntip(tree)+1 )  # Drop duplicates ... not dealing with variation among stocks within species Data = Data[match(unique(Data$Genus_species),Data$Genus_species), ]  # log-transform to simplify later syuntax Data = cbind( Data, \"logM\" = log(Data[,'M']),                     \"logK\" = log(Data[,'K']),                     \"logtmax\" = log(Data[,'tmax']),                     \"logLinf\" = log(Data[,'Linf']) )  # Only include modeled variables in trait-data passed to phylosem rownames(Data) = Data$Genus_species Data = Data[,c('logM','logK','logtmax','logLinf')]  # Fit model psem_taxon = phylosem( data=Data,                  tree = tree,                  sem = sem_structure,                  estimate_ou = TRUE,                  quiet = TRUE )  # Plot path diagram my_fitted_DAG = as_fitted_DAG(psem_taxon) plot(my_fitted_DAG, type=\"color\")"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/phylopath.html","id":"model-comparison-some-important-differences","dir":"Articles","previous_headings":"","what":"Model comparison: some important differences","title":"Detailed comparison with `phylopath`","text":"Let’s start loading Rhinogrades example data phylogeny. supply data model comparison functions, already two important differences flag . Firstly, phylo_path consciders columns data actually used models. compare_phylosem . rhino, first column contains copy species names, need exclude column (using rhino[-1]). , using phylosem, make sure data.frame contains variables ’d like inlcude analysis. Secondly, get standardized path coefficients, phylopath standardize data variable unit variance, phylosem keeps data original scale. make better comparison packages, ’ll standardize data manually . Now can define causal models want compare. First phylopath, use formulas can use DAG() define model, define_model_set() create list models: phylosem, can define models similarly, need use strings instead. Also note need write parameter front varialble (e.g. b1, b2, etc.). compare multiple models, collect models list: can now run model comparison. phylopath use d-separation , phylosem fitting structural equation model . Note phylo_path, specify want Brownian motion model (\"BM\"), default compare_phylosem. models perform? phylopath can use summary get table CICc values: phylosem, can extract AIC values model: Even though methodology used quite different, obtain similar result: model 5 fits much better models. However, methods somewhat differ ranking models. largely due different philosophies two approaches. phylopath uses PPA method described Von Hardenberg & Gonzalez-Voyer, uses Shipley’s d-separation. essence, method finds pairs variables causal model claims independent (conditionally independent), tests whether indeed case. phylosem hand directly evaluates fit casual model data. sense, phylosem analyzes paths included model phylopath analyzes paths included. Another source difference CICc metric used phylopath employs correction small sample sizes phylosem’s AIC metric . conclusion, cases one model clearly fits best (Brownian motion model) expect methods lead conclusion, don’t expect model comparison results match closely.","code":"data(rhino, rhino_tree, package = 'phylopath') rhino_std <- rhino[-1] rhino_std[] <- lapply(rhino_std, scale) models_pp <- phylopath::define_model_set(   one   = c(RS ~ DD),   two   = c(DD ~ NL, RS ~ LS + DD),   three = c(RS ~ NL),   four  = c(RS ~ BM + NL),   five  = c(RS ~ BM + NL + DD),   six   = c(NL ~ RS, RS ~ BM),   seven = c(NL ~ RS, RS ~ LS + BM),   eight = c(NL ~ RS),   nine  = c(NL ~ RS, RS ~ LS),   .common = c(LS ~ BM, NL ~ BM, DD ~ NL) ) models_ps <- list(   one   = 'RS = b1 * DD',   two   = 'DD = b1 * NL; RS = b2 * LS + b3 * DD',   three = 'RS = b1 * NL',   four  = 'RS = b * BM + b2 * NL',   five  = 'RS = b1 * BM + b2 * NL + b3 * DD',   six   = 'NL = b1 * RS; RS = b2 * BM',   seven = 'NL = b1 * RS; RS = b2 * LS + b3 * BM',   eight = 'NL = b1 * RS',   nine  = 'NL = b1 * RS; RS = b2 * LS' ) # we add the .common paths, by pasting them at the end of each of the model strings, e.g.: models_ps <- lapply(   models_ps,    \\(x) paste(x, c('LS = b1_ * BM; NL = b2_ * BM; DD = b3_ * NL'), sep = '; ') ) result_pp <- phylopath::phylo_path(   models_pp, data = rhino_std, tree = rhino_tree, model = 'BM' )  library(phylosem) result_ps <- phylosem::compare_phylosem(   models_ps, tree = rhino_tree, data = rhino_std ) summary(result_pp) #>       model k  q     C        p  CICc delta_CICc        l        w #> five   five 4 11  60.7 3.39e-10  85.7        0.0 1.00e+00 1.00e+00 #> eight eight 6  9 101.9 2.22e-16 121.9       36.2 1.38e-08 1.38e-08 #> three three 6  9 111.8 0.00e+00 131.8       46.0 1.00e-10 1.00e-10 #> nine   nine 5 10 110.7 0.00e+00 133.2       47.5 4.85e-11 4.85e-11 #> six     six 5 10 111.0 0.00e+00 133.5       47.8 4.25e-11 4.25e-11 #> one     one 6  9 113.9 0.00e+00 133.9       48.2 3.49e-11 3.49e-11 #> four   four 5 10 113.7 0.00e+00 136.2       50.5 1.08e-11 1.08e-11 #> two     two 5 10 115.2 0.00e+00 137.6       51.9 5.31e-12 5.31e-12 #> seven seven 4 11 114.2 0.00e+00 139.2       53.5 2.45e-12 2.45e-12 sapply(result_ps, AIC) |> sort() #>     five    eight     four      six     nine      two    seven      one  #> 1680.150 1730.808 1732.720 1732.720 1732.739 1733.104 1734.716 1735.057  #>    three  #> 1736.103"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/phylopath.html","id":"model-fitting-sometimes-different","dir":"Articles","previous_headings":"","what":"Model fitting: sometimes different","title":"Detailed comparison with `phylopath`","text":"take best model, particular model, perform model averaging, phylopath phylosem work largely way. packages implemented best(), choice() average() methods respective output types. can get best model (model 5) using best(). phylopath paths now fitted, phylosem already done model just extracted compare_phylosem object: compare two, can convert phylosem result DAG format phylopath uses, use included plot functionality:   phylopath now actually fitting causal model , performing d-separation procedure. makes methods much closely aligned, can see output matches closely. However, generally hold true assuming Brownian motion. deviate assumption using (example) Pagel’s lambda model, default phylopath, longer true:   reason happens phylosem implements additional parameters estimating single estimated parameter variables model. phylopath, hand, estimates separate lambda residuals regression ran. est_DAG() means one lambda variable modelled cause, phylo_path() means one lambda tested d-separation statement.","code":"best_pp <- phylopath::best(result_pp) best_ps <- phylosem::best(result_ps) plot(best_pp) plot(as_fitted_DAG(best_ps)) phylopath::est_DAG(   models_pp$five, data = rhino_std, tree = rhino_tree, model = 'lambda' ) |> plot() phylosem::phylosem(   models_ps$five, tree = rhino_tree, data = rhino_std, estimate_lambda = TRUE ) |> as_fitted_DAG() |> plot()"},{"path":"https://james-thorson-noaa.github.io/phylosem/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"James Thorson. Author, maintainer. Wouter van der Bijl. Contributor.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Thorson, J. T., Maureaud, . ., Frelat, R., Mérigot, B., Bigman, J. S., Friedman, S. T., Palomares, M. L. D., Pinsky, M. L., Price, S. ., & Wainwright, P. (2023). Identifying direct indirect associations among traits merging phylogenetic comparative methods structural equation models. Methods Ecology Evolution, 14(5), 1259–1275. https://doi.org/10.1111/2041-210X.14076 Thorson, J. T., & van der Bijl, W. (2023). phylosem: fast simple R package phylogenetic inference trait imputation using phylogenetic structural equation models. Journal Evolutionary Biology. 36(10): 1357-1364. https://doi.org/10.1111/jeb.14234","code":"@Article{,   title = {Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models},   journal = {Methods in Ecology and Evolution},   volume = {14},   number = {5},   pages = {1259–1275},   year = {2023},   doi = {10.1111/2041-210X.14076},   url = {https://doi.org/10.1111/2041-210X.14076},   author = {J. T. Thorson and A. A. Maureaud and R. Frelat and B. Mérigot and J. S. Bigman and S. T. Friedman and M. L. D. Palomares and M. L. Pinsky and S. A. Price and P. Wainwright}, } @Article{,   title = {phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equation models},   journal = {Journal of Evolutionary Biology},   volume = {36},   number = {10},   pages = {1357-1364},   year = {2023},   doi = {10.1111/jeb.14234},   url = {https://doi.org/10.1111/jeb.14234},   author = {James T. Thorson and & Wouter {van der Bijl}}, }"},{"path":"https://james-thorson-noaa.github.io/phylosem/index.html","id":"phylogenetic-structural-equation-models","dir":"","previous_headings":"","what":"Phylogenetic structural equation models","title":"Phylogenetic Structural Equation Model","text":"Package phylosem combines features structural equation models (SEM), phylogenetic comparative methods (PCM), generalized linear mixed models (GLMM). , incorporates broad feature-set: Comparing multiple evolutionary models similar phylopath Estimating trade-offs among multiple traits similar phylolm Predicting missing trait values (associated standard errors) similar Rphylopars Estimating tradeoffs including recursive (cyclic) dependencies similar package sem Applying ordination multiple traits, similar phylogenetic factor analysis package FishLife phylosem specifically intended minimal implementation, uses standard packages input/output formatting: Input: phylogenetic relatedness defined using class phylo package ape Input: structural trade-offs specified using syntax defined package sem Output: visualizing trade-offs using semPlot, diagrammeR, ggraph Output: assembling trait predictions standard errors using phylobase Output: plotting trait predictions using phylosignal Please see package vignettes details regarding syntax features.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/Mlifehist_ver1_0.html","id":null,"dir":"Reference","previous_headings":"","what":"Fisheries natural mortality example — Mlifehist_ver1_0","title":"Fisheries natural mortality example — Mlifehist_ver1_0","text":"Data used demonstrate phylogenetic comparative methods fisheries science.  Specifically copy et al. database doi:10.1093/icesjms/fsu136   using file \"Mlifehist_ver1.0.csv\" accessed  https://www.vims.edu/research/departments/fisheries/programs/mort_db/index.php","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/Mlifehist_ver1_0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fisheries natural mortality example — Mlifehist_ver1_0","text":"","code":"data(Mlifehist_ver1_0)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/TMBAIC.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate marginal AIC for a fitted model — TMBAIC","title":"Calculate marginal AIC for a fitted model — TMBAIC","text":"TMBAIC calculates AIC given model fit","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/TMBAIC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate marginal AIC for a fitted model — TMBAIC","text":"","code":"TMBAIC(opt, k = 2, n = Inf)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/TMBAIC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate marginal AIC for a fitted model — TMBAIC","text":"opt output nlminb optim k penalty additional fixed effects (default=2, AIC) n sample size, use AICc calculation (default=Inf, AICc=AIC)","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/TMBAIC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate marginal AIC for a fitted model — TMBAIC","text":"AIC, parsimonious model AIC relative candidate models","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert phylosem to phylopath output — as_fitted_DAG","title":"Convert phylosem to phylopath output — as_fitted_DAG","text":"Convert output package phylosem phylopath","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert phylosem to phylopath output — as_fitted_DAG","text":"","code":"as_fitted_DAG(object)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert phylosem to phylopath output — as_fitted_DAG","text":"object Output phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert phylosem to phylopath output — as_fitted_DAG","text":"Convert output format supplied est_DAG","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert phylosem to phylo4d — as_phylo4d","title":"Convert phylosem to phylo4d — as_phylo4d","text":"Convert output package phylosem phylo4d object package phylobase","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert phylosem to phylo4d — as_phylo4d","text":"","code":"as_phylo4d(object, what = c(\"Estimate\", \"Std. Error\"))"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert phylosem to phylo4d — as_phylo4d","text":"object Output phylosem Select convert (Estimate / Std. Error).","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert phylosem to phylo4d — as_phylo4d","text":"phylosem output converted format supplied phylo4d","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert phylosem to phylo4d — as_phylo4d","text":"package intended use using plots assocaited package sem, e.g., using package plotSEM semPlot::semPlotModel","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_sem.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert phylosem to sem output — as_sem","title":"Convert phylosem to sem output — as_sem","text":"Convert output package phylosem output package sem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_sem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert phylosem to sem output — as_sem","text":"","code":"as_sem(object)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_sem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert phylosem to sem output — as_sem","text":"object Output phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_sem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert phylosem to sem output — as_sem","text":"Output converted format supplied sem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.compare_phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose model — average.compare_phylosem","title":"Choose model — average.compare_phylosem","text":"Choose model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.compare_phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose model — average.compare_phylosem","text":"","code":"# S3 method for compare_phylosem average(x, cut_off = 2, avg_method = \"conditional\")"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.compare_phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose model — average.compare_phylosem","text":"x output compare_phylosem cut_off threshold model delta-AIC greater value excluded average avg_method see average_DAGs","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.compare_phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose model — average.compare_phylosem","text":"Returns AIC-weighted average fitted models compare_phylosem conversion format est_DAG","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose model — average","title":"Choose model — average","text":"Choose model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose model — average","text":"","code":"average(x, cut_off, avg_method)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose model — average","text":"x output compare_phylosem cut_off threshold model delta-AIC greater value excluded average avg_method see average_DAGs","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose model — average","text":"Returns AIC-weighted average fitted models compare_phylosem conversion format [phylopath::est_DAG]","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.compare_phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract best fitted model — best.compare_phylosem","title":"Extract best fitted model — best.compare_phylosem","text":"Extract best fitted model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.compare_phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract best fitted model — best.compare_phylosem","text":"","code":"# S3 method for compare_phylosem best(x)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.compare_phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract best fitted model — best.compare_phylosem","text":"x output compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.compare_phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract best fitted model — best.compare_phylosem","text":"Returns best model fitted using compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract best fitted model — best","title":"Extract best fitted model — best","text":"Extract best fitted model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract best fitted model — best","text":"","code":"best(x)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract best fitted model — best","text":"x output compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract best fitted model — best","text":"Returns best model fitted using compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/checkDepPackageVersion.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","title":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","text":"Copied glmmTMB permission","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/checkDepPackageVersion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","text":"","code":"checkDepPackageVersion(   dep_pkg = \"TMB\",   this_pkg = \"phylosem\",   write_file = FALSE,   warn = TRUE )"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/checkDepPackageVersion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","text":"dep_pkg upstream package this_pkg downstream package write_file (logical) write version file quit? warn give warning?","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/checkDepPackageVersion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","text":"logical: TRUE binary versions match","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.compare_phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose model — choice.compare_phylosem","title":"Choose model — choice.compare_phylosem","text":"Choose model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.compare_phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose model — choice.compare_phylosem","text":"","code":"# S3 method for compare_phylosem choice(x, choice)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.compare_phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose model — choice.compare_phylosem","text":"x output compare_phylosem choice Integer indicating model extract","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.compare_phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose model — choice.compare_phylosem","text":"Returns chosen model fitted using compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose model — choice","title":"Choose model — choice","text":"Choose model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose model — choice","text":"","code":"choice(x, choice)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose model — choice","text":"x output compare_phylosem choice Integer indicating model extract","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose model — choice","text":"Returns chosen model fitted using compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/coef.phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract path coefficients — coef.phylosem","title":"Extract path coefficients — coef.phylosem","text":"Extract path coefficients.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/coef.phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract path coefficients — coef.phylosem","text":"","code":"# S3 method for phylosem coef(object, standardized = FALSE, ...)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/coef.phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract path coefficients — coef.phylosem","text":"object Output phylosem standardized Whether standardize regression coefficients ... used","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/coef.phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract path coefficients — coef.phylosem","text":"Data-frame listing path coefficients, parameter index estimated values","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare phylogenetic structural equation models — compare_phylosem","title":"Compare phylogenetic structural equation models — compare_phylosem","text":"Fits several phylogenetic structural equation model comparison","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare phylogenetic structural equation models — compare_phylosem","text":"","code":"compare_phylosem(   sem_set,   tree,   data,   family = rep(\"fixed\", ncol(data)),   covs,   estimate_ou = FALSE,   estimate_lambda = FALSE,   estimate_kappa = FALSE,   ... )"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare phylogenetic structural equation models — compare_phylosem","text":"sem_set named list structural equation model specifications, element passed argument sem phylosem tree phylogenetic structure, using class .phylo data data-frame providing variables modeled.  Missing values inputted NA.  SEM includes latent variable (.e., variable available measurements) still must inputted column data entirely NA values. family Character-vector listing distribution used column data, element must fixed, normal, binomial, poisson. family=\"fixed\" default behavior assumes given variable measured exactly. options correspond different specifications measurement error. covs optional: character vector one elements, element   \tgiving string variable names, separated commas. Variances covariances   \tamong variables string added model. confirmatory   \tfactor analysis models specified via cfa, covs defaults   \tfactors model, thus specifying variances covariances among factors.   \tWarning: covs=\"x1, x2\" covs=c(\"x1\", \"x2\")   \tequivalent: covs=\"x1, x2\" specifies variance x1, variance   \tx2, covariance, covs=c(\"x1\", \"x2\") specifies   \tvariance x1 variance x2 covariance. estimate_ou Boolean indicating whether estimate autoregressive (Ornstein-Uhlenbeck) process using additional parameter lnalpha, corresponding model=\"OUrandomRoot\" parameterization phylolm listed doi:10.1093/sysbio/syu005 estimate_lambda Boolean indicating whether estimate additional branch lengths phylogenetic tips (.k.. Pagel-lambda term) using additional parameter logitlambda estimate_kappa Boolean indicating whether estimate nonlinear scaling branch lengths (.k.. Pagel-kappa term) using additional parameter lnkappa ... Additional arguments passed phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compare phylogenetic structural equation models — compare_phylosem","text":"object (list) class `compare_phylosem`, containing list         output phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/fit_tmb.html","id":null,"dir":"Reference","previous_headings":"","what":"Optimize a TMB model — fit_tmb","title":"Optimize a TMB model — fit_tmb","text":"fit_tmb runs TMB model generates standard diagnostics","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/fit_tmb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Optimize a TMB model — fit_tmb","text":"","code":"fit_tmb(   obj,   fn = obj$fn,   gr = obj$gr,   startpar = NULL,   lower = -Inf,   upper = Inf,   getsd = TRUE,   control = list(eval.max = 10000, iter.max = 10000, trace = 1),   bias.correct = FALSE,   bias.correct.control = list(sd = FALSE, split = NULL, nsplit = NULL, vars_to_correct =     NULL),   savedir = NULL,   loopnum = 2,   newtonsteps = 0,   n = Inf,   getReportCovariance = FALSE,   getJointPrecision = FALSE,   getHessian = FALSE,   quiet = FALSE,   start_time_elapsed = as.difftime(\"0:0:0\"),   ... )"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/fit_tmb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Optimize a TMB model — fit_tmb","text":"obj compiled TMB object fn Function minimized. Must return scalar value. . gr Optional function takes arguments objective evaluates gradient objective first argument. Must return vector long startpar startpar Starting values fixed effects (default NULL uses obj$par) lower, upper vectors lower upper bounds, replicated long     start.  unspecified, parameters assumed     unconstrained. getsd Boolean indicating whether run standard error calculation; see sdreport details control list control parameters. details see nlminb bias.correct Boolean indicating whether epsilon bias-correction; see sdreport fit_tmbfor details bias.correct.control tagged list options epsilon bias-correction, vars_to_correct character-vector ADREPORT variables bias-corrected savedir directory save results (savedir=NULL, results saved) loopnum number times re-start optimization (loopnum=3 sometimes achieves lower final gradient loopnum=1) newtonsteps Integer specifying number extra newton steps take optimization (alternative loopnum). newtonstep requires calculating Hessian matrix therefore slow. well-behaved models, Newton step typically decrease maximum gradient loglikelihood respect fixed effect, therefore option can used achieve arbitrarily low final gradient given sufficient time well-behaved models.  However, option also perform strangely unexpected consequences poorly-behaved models, e.g., fixed effects upper lower bounds. need increase value newtonsteps model appears converged (.e., low final_gradient none standard errors NA values) n sample sizes (n!=Inf n used calculate BIC AICc) getReportCovariance Get full covariance matrix ADREPORTed variables? getJointPrecision Optional. Return full joint precision matrix random effects parameters? getHessian return Hessian usage later code quiet Boolean whether print additional messages results terminal start_time_elapsed much time elapsed prior calling fit_tmb, use, e.g., calling fit_tmb multiple times sequence, start_time_elapsed = opt_previous$time_for_run ... list settings pass sdreport","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/fit_tmb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Optimize a TMB model — fit_tmb","text":"standard output nlminb, except additional diagnostics timing info,         new slot containing output sdreport","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/fit_tmb.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Optimize a TMB model — fit_tmb","text":"details see doi:10.1016/j.fishres.2015.11.016","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"List fixed and random effects — list_parameters","title":"List fixed and random effects — list_parameters","text":"list_parameters lists fixed random effects","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List fixed and random effects — list_parameters","text":"","code":"list_parameters(Obj, verbose = TRUE)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List fixed and random effects — list_parameters","text":"Obj Compiled TMB object verbose Boolean, whether print messages terminal","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List fixed and random effects — list_parameters","text":"Tagged-list fixed random effects, returned invisibly printed screen","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse path — parse_path","title":"Parse path — parse_path","text":"parse_path copied sem::parse.path","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse path — parse_path","text":"","code":"parse_path(path)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse path — parse_path","text":"path text parse","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse path — parse_path","text":"Tagged-list defining variables direction specified path coefficient","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Parse path — parse_path","text":"Copied permission John Fox licence GPL (>= 2)","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit phylogenetic structural equation model — phylosem","title":"Fit phylogenetic structural equation model — phylosem","text":"Fits phylogenetic structural equation model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit phylogenetic structural equation model — phylosem","text":"","code":"phylosem(   sem,   tree,   data,   family = rep(\"fixed\", ncol(data)),   covs = colnames(data),   estimate_ou = FALSE,   estimate_lambda = FALSE,   estimate_kappa = FALSE,   data_labels = rownames(data),   quiet = FALSE,   newtonsteps = 1,   tmb_inputs = NULL,   run_model = TRUE,   ... )"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit phylogenetic structural equation model — phylosem","text":"sem structural equation model structure, passed either specifyModel specifyEquations parsed control set path coefficients variance-covariance parameters tree phylogenetic structure, using class .phylo data data-frame providing variables modeled.  Missing values inputted NA.  SEM includes latent variable (.e., variable available measurements) still must inputted column data entirely NA values. family Character-vector listing distribution used column data, element must fixed, normal, binomial, poisson. family=\"fixed\" default behavior assumes given variable measured exactly. options correspond different specifications measurement error. covs optional: character vector one elements, element   \tgiving string variable names, separated commas. Variances covariances   \tamong variables string added model. confirmatory   \tfactor analysis models specified via cfa, covs defaults   \tfactors model, thus specifying variances covariances among factors.   \tWarning: covs=\"x1, x2\" covs=c(\"x1\", \"x2\")   \tequivalent: covs=\"x1, x2\" specifies variance x1, variance   \tx2, covariance, covs=c(\"x1\", \"x2\") specifies   \tvariance x1 variance x2 covariance. estimate_ou Boolean indicating whether estimate autoregressive (Ornstein-Uhlenbeck) process using additional parameter lnalpha, corresponding model=\"OUrandomRoot\" parameterization phylolm listed doi:10.1093/sysbio/syu005 estimate_lambda Boolean indicating whether estimate additional branch lengths phylogenetic tips (.k.. Pagel-lambda term) using additional parameter logitlambda estimate_kappa Boolean indicating whether estimate nonlinear scaling branch lengths (.k.. Pagel-kappa term) using additional parameter lnkappa data_labels row data, listing corresponding name tree$tip.label.  Default pulls data_labels rownames(data) quiet FALSE, default, number input lines reported     message printed suggesting specifyEquations cfa used. newtonsteps Integer specifying number extra newton steps take optimization (alternative loopnum). newtonstep requires calculating Hessian matrix therefore slow. well-behaved models, Newton step typically decrease maximum gradient loglikelihood respect fixed effect, therefore option can used achieve arbitrarily low final gradient given sufficient time well-behaved models.  However, option also perform strangely unexpected consequences poorly-behaved models, e.g., fixed effects upper lower bounds. need increase value newtonsteps model appears converged (.e., low final_gradient none standard errors NA values) tmb_inputs optional tagged list overrides default constructor TMB inputs (use risk) run_model Boolean indicating whether estimate parameters (default), instead return model inputs compiled TMB object without running; ... Additional parameters passed fit_tmb","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit phylogenetic structural equation model — phylosem","text":"object (list) class `phylosem`. Elements include: data Copy argument data SEM_model SEM model parsed sem using specifyModel specifyEquations obj TMB object MakeADFun tree Copy argument tree tmb_inputs list inputs passed MakeADFun opt output fit_tmb report output obj$report() parhat output obj$env$parList() containing maximum likelihood estimates empirical Bayes predictions","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit phylogenetic structural equation model — phylosem","text":"Note parameters logitlambda, lnkappa, lnalpha estimated estimated single value      applies modeled variables.      differs default behavior phylolm, parameters apply \"response\" \"predictor\" variables.      also differs default behavior phylopath, different value estimated      call phylolm d-separation estimate path coefficients. However,      consistent default behavior Rphylopars, estimates comparable case.      additional parameters estimated unbounded support, differs somewhat default      bounded estimates phylolm, although parameters match overriding phylolm defaults      use unbounded support.  Finally, phylosem allows three parameters estimated      combination, expanded functionality relative single-option functionality phylolm. Also note phylopath default uses standardized coefficients.  achieve matching parameter estimates      phylosem phylopath, standardize variable standard deviation 1.0 prior fitting phylosem.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Fit phylogenetic structural equation model — phylosem","text":"**Introducing package, features, comparison software (cite using phylosem):** Thorson, J. T., & van der Bijl, W. (press). phylosem: fast simple R package phylogenetic inference trait imputation using phylogenetic structural equation models. Journal Evolutionary Biology. doi:10.1111/jeb.14234 *Statistical methods phylogenetic structural equation models* Thorson, J. T., Maureaud, . ., Frelat, R., Merigot, B., Bigman, J. S., Friedman, S. T., Palomares, M. L. D., Pinsky, M. L., Price, S. ., & Wainwright, P. (2023). Identifying direct indirect associations among traits merging phylogenetic comparative methods structural equation models. Methods Ecology Evolution, 14(5), 1259-1275. doi:10.1111/2041-210X.14076 *Earlier development computational methods, originally used phlogenetic factor analysis:* Thorson, J. T. (2020). Predicting recruitment density dependence intrinsic growth rate fishes worldwide using data-integrated life-history model. Fish Fisheries, 21(2), 237-251. doi:10.1111/faf.12427 Thorson, J. T., Munch, S. B., Cope, J. M., & Gao, J. (2017). Predicting life history parameters fishes worldwide. Ecological Applications, 27(8), 2262-2276. doi:10.1002/eap.1606 *Earlier development phylogenetic path analysis:* van der Bijl, W. (2018). phylopath: Easy phylogenetic path analysis R. PeerJ, 6, e4718. doi:10.7717/peerj.4718 von Hardenberg, ., & Gonzalez-Voyer, . (2013). Disentangling evolutionary cause-effect relationships phylogenetic confirmatory path analysis. Evolution; International Journal Organic Evolution, 67(2), 378-387. doi:10.1111/j.1558-5646.2012.01790.x *Interface involving SEM `arrow notation` repurposed :* Fox, J., Nie, Z., & Byrnes, J. (2020). Sem: Structural equation models. R package version 3.1-11. https://CRAN.R-project.org/package=sem *Coercing output phylo4d depends upon:* Bolker, B., Butler, M., Cowan, P., de Vienne, D., Eddelbuettel, D., Holder, M., Jombart, T., Kembel, S., Michonneau, F., & Orme, B. (2015). phylobase: Base package phylogenetic structures comparative data. R Package Version 0.8.0. https://CRAN.R-project.org/package=phylobase *Laplace approximation parameter estimation depends upon:* Kristensen, K., Nielsen, ., Berg, C. W., Skaug, H., & Bell, B. M. (2016). TMB: Automatic differentiation Laplace approximation. Journal Statistical Software, 70(5), 1-21. doi:10.18637/jss.v070.i05","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit phylogenetic structural equation model — phylosem","text":"","code":"# Load data set data(rhino, rhino_tree, package=\"phylopath\")  # Run phylosem model = \"   DD -> RS, p1   BM -> LS, p2   BM -> NL, p3   NL -> DD, p4 \" psem = phylosem( sem = model,           data = rhino[,c(\"BM\",\"NL\",\"DD\",\"RS\",\"LS\")],           tree = rhino_tree ) #> NOTE: it is generally simpler to use specifyEquations() or cfa() #>       see ?specifyEquations #> List of estimated fixed and random effects: #>   Coefficient_name Number_of_coefficients   Type #> 1           beta_z                      9  Fixed #> 2             x_vj                    495 Random #>   0:     218940.22: 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 #>   1:     8397.8060: 0.0842226 0.130623 0.120621 0.124798 0.347153 0.487021 0.538215 0.426241 0.798883 #>   2:     6354.4828: 0.0315557 0.151274 0.172831 0.173170 0.658033 0.551767 0.542706 0.578654 0.594083 #>   3:     3672.8577: 0.000303728 0.221429 0.224967 0.235152 0.725274 0.724685 0.748919 0.705591 0.856342 #>   4:     2740.3780: -0.102677 0.415193 0.403189 0.371336 0.731170 0.859963 0.790331 0.921711 0.951636 #>   5:     1998.5720: -0.126539 0.503355 0.465231 0.444702 0.930180 0.997626  1.00743  1.03020  1.14979 #>   6:     1603.6727: -0.156804 0.611920 0.546135 0.512778  1.10880  1.15370  1.19174  1.17670  1.34656 #>   7:     1378.4437: -0.184978 0.735384 0.635855 0.574242  1.28215  1.30788  1.36879  1.33950  1.53299 #>   8:     1246.1754: -0.205749 0.871125 0.727935 0.623959  1.45479  1.45790  1.54574  1.51056  1.71079 #>   9:     1168.3619: -0.217139  1.01403 0.814506 0.657424  1.62857  1.60494  1.72664  1.68772  1.88166 #>  10:     1123.9069: -0.220534  1.15457 0.885299 0.673319  1.80466  1.75160  1.91435  1.87091  2.04888 #>  11:     1100.3689: -0.220150  1.27536 0.928361 0.675635  1.98358  1.90047  2.11097  2.06073  2.21911 #>  12:     1089.9414: -0.220524  1.34559 0.935212 0.674388  2.16290  2.04937  2.31732  2.25655  2.40368 #>  13:     1088.5461: -0.220084  1.33812 0.932369 0.675458  2.21370  2.08811  2.38334  2.31655  2.47029 #>  14:     1087.8319: -0.220718  1.33618 0.933085 0.674475  2.26200  2.12267  2.45045  2.37612  2.54069 #>  15:     1087.7787: -0.220253  1.33642 0.932854 0.675008  2.26795  2.12603  2.46060  2.38452  2.55226 #>  16:     1087.7091: -0.220358  1.33673 0.932671 0.675146  2.27944  2.13226  2.48095  2.40115  2.57585 #>  17:     1087.7069: -0.217349  1.33044 0.940994 0.668413  2.28729  2.11448  2.49234  2.41721  2.59797 #>  18:     1087.6911: -0.222165  1.33489 0.932128 0.677383  2.28740  2.12316  2.49506  2.41681  2.59939 #>  19:     1087.6907: -0.214887  1.33792 0.933697 0.669999  2.28758  2.13505  2.49955  2.41615  2.60180 #>  20:     1087.6863: -0.221547  1.33726 0.932944 0.675110  2.28759  2.13517  2.49998  2.41611  2.60207 #>  21:     1087.6861: -0.220478  1.33704 0.932837 0.675081  2.28760  2.13522  2.50021  2.41608  2.60222 #>  22:     1087.6861: -0.220143  1.33645 0.932761 0.674901  2.28764  2.13538  2.50097  2.41602  2.60264 #>  23:     1087.6861: -0.220221  1.33658 0.932819 0.675126  2.28770  2.13531  2.50117  2.41601  2.60276 #>  24:     1087.6861: -0.220415  1.33670 0.932693 0.674998  2.28765  2.13538  2.50131  2.41596  2.60293 #>  25:     1087.6861: -0.220192  1.33683 0.932842 0.675013  2.28773  2.13544  2.50141  2.41587  2.60309 #>  26:     1087.6861: -0.220324  1.33674 0.932762 0.675074  2.28770  2.13543  2.50142  2.41588  2.60310 #>  27:     1087.6861: -0.220275  1.33670 0.932749 0.675068  2.28767  2.13543  2.50143  2.41589  2.60311 #>  28:     1087.6861: -0.220310  1.33668 0.932761 0.675067  2.28763  2.13543  2.50146  2.41592  2.60310 #>  29:     1087.6861: -0.220287  1.33668 0.932751 0.675069  2.28763  2.13543  2.50146  2.41592  2.60311 #>  30:     1087.6861: -0.220295  1.33668 0.932747 0.675069  2.28762  2.13542  2.50146  2.41592  2.60311 #>  31:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312 #>   0:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312 #>   1:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312  # Convert and plot using phylopath library(phylopath) #>  #> Attaching package: ‘phylopath’ #> The following objects are masked from ‘package:phylosem’: #>  #>     average, best, choice my_fitted_DAG = as_fitted_DAG(psem) coef_plot( my_fitted_DAG ) #> The fitted model does not contain confidence intervals, so showing standard errors instead. Fit the model with `boot` larger than 0 to get confidence intervals, or set `error_bar = \"se\"` to avoid this warning.  plot( my_fitted_DAG )   # Convert to phylo4d to extract estimated traits and Standard errors # for all ancestors and tips in the tree. # In this rhino example, note that species are labeled s1-s100 # and ancestral nodes are not named. (traits_est = as_phylo4d(psem)) #>     label node ancestor  edge.length node.type          BM          NL #> 1      s1    1      107 0.5640308162       tip -0.76690456 -2.01757398 #> 2      s2    2      107 0.5640308162       tip -1.00970438 -1.74246592 #> 3      s3    3      106 0.6358275951       tip -1.22528123 -2.46855326 #> 4      s4    4      105 0.7144448083       tip  1.33053521  0.34055901 #> 5      s5    5      104 1.1830950600       tip  2.49234369  1.22400475 #> 6      s6    6      109 0.0361022107       tip  1.42514860  2.96922655 #> 7      s7    7      109 0.0361022107       tip  0.35610742  2.01122280 #> 8      s8    8      112 0.5022074646       tip -0.53161422  0.18490174 #> 9      s9    9      112 0.5022074646       tip -0.15373314  0.81809201 #> 10    s10   10      111 1.7871837580       tip  1.11171876  1.24302184 #> 11    s11   11      116 0.5913975424       tip  0.19579448  2.13282693 #> 12    s12   12      119 0.0477228892       tip  0.20125048  3.08972748 #> 13    s13   13      119 0.0477228892       tip  1.52219709  2.96228199 #> 14    s14   14      120 0.1142573039       tip -1.00338251  1.86652322 #> 15    s15   15      120 0.1142573039       tip  1.07689653  1.52906374 #> 16    s16   16      121 0.2756963162       tip  1.61531748  3.57241266 #> 17    s17   17      121 0.2756963162       tip -0.17420285  0.43146654 #> 18    s18   18      122 0.5512595516       tip  2.90711896  3.25268633 #> 19    s19   19      123 0.0349638989       tip  2.40453010  2.24981247 #> 20    s20   20      123 0.0349638989       tip  0.82895203  1.20324781 #> 21    s21   21      114 0.8767527377       tip  2.64255460  3.86427495 #> 22    s22   22      113 1.7461743450       tip -0.07719953  3.19026617 #> 23    s23   23      125 0.9075157185       tip -0.30484408  3.51060091 #> 24    s24   24      125 0.9075157185       tip  1.52258759  3.21435348 #> 25    s25   25      126 0.5415591015       tip  1.23860573  2.04363009 #> 26    s26   26      127 0.1089356405       tip  1.95343200  3.06738965 #> 27    s27   27      127 0.1089356405       tip  1.68648719  4.22039397 #> 28    s28   28      130 3.0857795440       tip  1.23934345  2.26507981 #> 29    s29   29      131 1.6399242000       tip -1.10263719 -1.63892351 #> 30    s30   30      132 0.8944032869       tip  0.08301170  0.42665712 #> 31    s31   31      133 0.7715950937       tip  1.01879042  0.03819250 #> 32    s32   32      133 0.7715950937       tip  0.02167732 -0.37157709 #> 33    s33   33      136 0.8699913472       tip  0.73065935  1.95289384 #> 34    s34   34      137 0.8479589114       tip  2.72407349  3.49784027 #> 35    s35   35      137 0.8479589114       tip  3.76646555  4.49878875 #> 36    s36   36      138 0.4591954289       tip -2.33729326  1.74995773 #> 37    s37   37      139 0.1736071099       tip  0.30205947  2.68777644 #> 38    s38   38      139 0.1736071099       tip -1.33960415  1.76434408 #> 39    s39   39      141 2.0905969730       tip  4.27686830  3.21806190 #> 40    s40   40      143 0.0744131178       tip  1.25068016 -0.71254314 #> 41    s41   41      143 0.0744131178       tip  1.41155371 -0.43526905 #> 42    s42   42      144 0.9370864528       tip  0.08393879  0.23591102 #> 43    s43   43      145 0.0881684468       tip  2.84964114  0.68816551 #> 44    s44   44      145 0.0881684468       tip  2.99095373  1.80145127 #> 45    s45   45      147 1.7204295900       tip  5.13749665  4.26473497 #> 46    s46   46      149 1.1842473100       tip  2.58859925  1.56946821 #> 47    s47   47      149 1.1842473100       tip  1.43384898  1.65242204 #> 48    s48   48      150 1.0253154590       tip  2.80876268  3.24344386 #> 49    s49   49      152 0.7195368746       tip  1.22593514  5.02896634 #> 50    s50   50      152 0.7195368746       tip  2.61927222  0.67351377 #> 51    s51   51      153 0.3613256451       tip  2.30223945  1.34901806 #> 52    s52   52      153 0.3613256451       tip  2.56528288  1.45099218 #> 53    s53   53      155 0.3002640020       tip  0.40340933 -1.65526609 #> 54    s54   54      155 0.3002640020       tip  0.88479865 -1.98334601 #> 55    s55   55      154 0.5937157619       tip  0.46893874 -0.62261098 #> 56    s56   56      156 3.2486997580       tip  2.95039314  4.03454344 #> 57    s57   57      161 0.4215356986       tip  1.53656023  0.46891422 #> 58    s58   58      161 0.4215356986       tip  2.50142020  0.45568152 #> 59    s59   59      162 0.0698869058       tip  2.33417280 -0.61028405 #> 60    s60   60      162 0.0698869058       tip  2.39854268  0.90424064 #> 61    s61   61      164 0.9090035873       tip  1.15944783  0.14368777 #> 62    s62   62      165 0.7237639845       tip  0.59250982 -1.00793024 #> 63    s63   63      167 0.3390345394       tip -0.70393275 -1.59874559 #> 64    s64   64      167 0.3390345394       tip  1.58394613  0.45296021 #> 65    s65   65      168 0.3269574705       tip  1.59263345  0.56850859 #> 66    s66   66      168 0.3269574705       tip  2.15658024 -0.88396728 #> 67    s67   67      170 0.4816150364       tip  5.26743199  2.18963416 #> 68    s68   68      171 0.0359279485       tip  1.34622701 -1.84421537 #> 69    s69   69      171 0.0359279485       tip  2.18241698 -0.76580964 #> 70    s70   70      173 0.6413136611       tip  2.93983039 -0.11351013 #> 71    s71   71      175 0.0945133814       tip  3.01129396  1.25866166 #> 72    s72   72      176 0.0006422211       tip  2.59398228  1.21303645 #> 73    s73   73      176 0.0006422211       tip  2.71938915  1.62942984 #> 74    s74   74      174 0.3139612126       tip  2.60745101  0.91920273 #> 75    s75   75      177 0.0359670563       tip  4.86547665  0.44478185 #> 76    s76   76      177 0.0359670563       tip  5.43684487  0.22107243 #> 77    s77   77      180 0.8668137583       tip  1.58687164  1.50654438 #> 78    s78   78      181 0.5981367654       tip  0.09365673  0.40527336 #> 79    s79   79      182 0.0727809267       tip  0.27286020  0.21689207 #> 80    s80   80      182 0.0727809267       tip  2.25220200 -1.07873909 #> 81    s81   81      179 1.5434906440       tip  1.05736541 -0.05289912 #> 82    s82   82      183 0.8078943991       tip  4.69785604  0.33163484 #> 83    s83   83      184 0.4661635151       tip  3.52231773  1.69620670 #> 84    s84   84      185 0.1900157199       tip  1.60779377  2.53614523 #> 85    s85   85      185 0.1900157199       tip  1.90789841  2.74261353 #> 86    s86   86      188 0.2378751898       tip  3.94393984 -1.28344814 #> 87    s87   87      190 0.0040209131       tip  2.67507049 -0.72928762 #> 88    s88   88      190 0.0040209131       tip  4.02248087  1.27038228 #> 89    s89   89      189 0.0295310172       tip  4.11611390  0.89924275 #> 90    s90   90      195 0.3502461608       tip  2.45594624  0.51529773 #> 91    s91   91      196 0.1859710332       tip  4.14053815  2.17333172 #> 92    s92   92      196 0.1859710332       tip  3.16070940 -0.62189645 #> 93    s93   93      194 0.8106943515       tip  2.97788577 -0.22596947 #> 94    s94   94      193 0.8259283637       tip  3.93086602  1.00077297 #> 95    s95   95      197 0.4469879611       tip  1.54045681  0.11089573 #> 96    s96   96      197 0.4469879611       tip  1.04974779  2.05813396 #> 97    s97   97      198 0.2644025504       tip  4.08564283  1.22297875 #> 98    s98   98      198 0.2644025504       tip  3.47019109  1.80421473 #> 99    s99   99      199 0.0717127012       tip -1.51698326 -2.66773226 #> 100  s100  100      199 0.0717127012       tip -1.55493000 -1.25446488 #> 101  <NA>  101        0           NA      root  1.37537396  1.29911665 #> 102  <NA>  102      101 0.3278789676  internal  1.16700652  1.46268576 #> 103  <NA>  103      102 0.0448143702  internal  1.14127151  1.44843940 #> 104  <NA>  104      103 1.7536273230  internal  0.80116123 -0.04630783 #> 105  <NA>  105      104 0.4686502517  internal  0.04035308 -0.94897241 #> 106  <NA>  106      105 0.0786172132  internal -0.22924544 -1.24229608 #> 107  <NA>  107      106 0.0717967789  internal -0.36298395 -1.37170519 #> 108  <NA>  108      103 0.5388417629  internal  0.93634388  1.73643821 #> 109  <NA>  109      108 2.3617784090  internal  0.89097477  2.48450717 #> 110  <NA>  110      108 0.1838847379  internal  0.86994281  1.77647687 #> 111  <NA>  111      110 0.4268121240  internal  0.68585957  1.45889941 #> 112  <NA>  112      111 1.2849762930  internal -0.17453886  0.65800392 #> 113  <NA>  113      110 0.4678215366  internal  0.90278222  2.22643059 #> 114  <NA>  114      113 0.8694216075  internal  1.45174623  2.58275128 #> 115  <NA>  115      114 0.0071530214  internal  1.44654748  2.57522749 #> 116  <NA>  116      115 0.2782021739  internal  0.86447464  2.32881108 #> 117  <NA>  117      116 0.1696001798  internal  0.70138920  2.23479250 #> 118  <NA>  118      117 0.1745800373  internal  0.52173009  2.28117789 #> 119  <NA>  119      118 0.1994944362  internal  0.82540175  2.94643376 #> 120  <NA>  120      118 0.1329600215  internal  0.18250929  1.87312200 #> 121  <NA>  121      117 0.1461010464  internal  0.71125182  2.11498215 #> 122  <NA>  122      115 0.3183401648  internal  1.88123312  2.52235493 #> 123  <NA>  123      122 0.5162956527  internal  1.62540354  1.75259450 #> 124  <NA>  124      102 1.5076279270  internal  1.07467482  2.69406705 #> 125  <NA>  125      124 0.5663931071  internal  0.81605854  3.06517183 #> 126  <NA>  126      124 0.9323497240  internal  1.44328773  2.84469772 #> 127  <NA>  127      126 0.4326234610  internal  1.77783916  3.55452384 #> 128  <NA>  128      101 0.0206999989  internal  1.38852884  1.28879004 #> 129  <NA>  129      128 0.2000464880  internal  1.33869173  1.25256763 #> 130  <NA>  130      129 0.0028896898  internal  1.33645716  1.25093770 #> 131  <NA>  131      130 1.4458553430  internal  0.26389060 -0.03977885 #> 132  <NA>  132      131 0.7455209135  internal  0.33208018  0.02167613 #> 133  <NA>  133      132 0.1228081933  internal  0.37751187 -0.02380741 #> 134  <NA>  134      129 0.6949407786  internal  1.70295554  1.51871663 #> 135  <NA>  135      134 0.9138552433  internal  1.13478525  2.30724483 #> 136  <NA>  136      135 0.6098818644  internal  1.98297090  2.97989486 #> 137  <NA>  137      136 0.0220324358  internal  2.04532689  3.03020353 #> 138  <NA>  138      135 1.0206777830  internal -0.91929472  2.06222134 #> 139  <NA>  139      138 0.2855883190  internal -0.61213304  2.18786984 #> 140  <NA>  140      134 0.0802496379  internal  1.79491314  1.48020658 #> 141  <NA>  141      140 0.2228818440  internal  1.93611785  1.40251215 #> 142  <NA>  142      141 0.2076500851  internal  1.83517586  1.14979654 #> 143  <NA>  143      142 1.8085337700  internal  1.34127779 -0.53915958 #> 144  <NA>  144      142 0.9458604351  internal  1.63368609  0.88198103 #> 145  <NA>  145      144 0.8489180060  internal  2.85678218  1.22689695 #> 146  <NA>  146      140 0.1770607381  internal  1.88563084  1.45696065 #> 147  <NA>  147      146 0.4159884892  internal  2.40357460  2.04245093 #> 148  <NA>  148      147 0.1695261804  internal  2.34525741  2.06207604 #> 149  <NA>  149      148 0.3666560998  internal  2.21751655  1.88955477 #> 150  <NA>  150      148 0.5255879506  internal  2.34756636  2.37022333 #> 151  <NA>  151      150 0.2079515725  internal  2.25494138  2.31503928 #> 152  <NA>  152      151 0.0978270115  internal  2.18389259  2.42967093 #> 153  <NA>  153      151 0.4560382411  internal  2.38302136  1.65964448 #> 154  <NA>  154      146 1.5427023170  internal  0.75523426 -0.91688085 #> 155  <NA>  155      154 0.2934517599  internal  0.68171630 -1.51387805 #> 156  <NA>  156      128 0.0400159638  internal  1.42392811  1.27607295 #> 157  <NA>  157      156 0.4026925133  internal  1.59094851  0.80617095 #> 158  <NA>  158      157 0.7951233038  internal  1.94014906  0.57576258 #> 159  <NA>  159      158 0.3736798197  internal  2.09528413  0.38387613 #> 160  <NA>  160      159 1.1492712710  internal  2.14639670  0.34532781 #> 161  <NA>  161      160 0.1063971509  internal  2.10365653  0.38456695 #> 162  <NA>  162      160 0.4580459438  internal  2.35076674  0.16103746 #> 163  <NA>  163      159 0.2335971502  internal  2.18187420  0.27175804 #> 164  <NA>  164      163 0.5346033834  internal  1.43309091 -0.13103237 #> 165  <NA>  165      164 0.1852396028  internal  1.22940201 -0.32658223 #> 166  <NA>  166      165 0.1474062575  internal  1.19702794 -0.34342541 #> 167  <NA>  167      166 0.2373231876  internal  0.75543298 -0.47728109 #> 168  <NA>  168      166 0.2494002564  internal  1.60632063 -0.23125539 #> 169  <NA>  169      163 0.4262080943  internal  2.93682275  0.38831503 #> 170  <NA>  170      169 0.5357838400  internal  3.31558918  0.40274303 #> 171  <NA>  171      170 0.4456870879  internal  1.82442522 -1.23884620 #> 172  <NA>  172      169 0.3680846598  internal  3.32860306  0.47906468 #> 173  <NA>  173      172 0.0080005555  internal  3.31402225  0.48288912 #> 174  <NA>  174      173 0.3273524485  internal  2.90843309  0.94379679 #> 175  <NA>  175      174 0.2194478311  internal  2.84691345  1.26996664 #> 176  <NA>  176      175 0.0938711603  internal  2.65733422  1.42071746 #> 177  <NA>  177      172 0.6133471602  internal  5.09924499  0.33708989 #> 178  <NA>  178      158 0.3661103260  internal  1.94894404  0.65767175 #> 179  <NA>  179      178 0.1412829703  internal  1.78053559  0.59541556 #> 180  <NA>  180      179 0.6766768859  internal  1.29098355  0.58146426 #> 181  <NA>  181      180 0.2686769929  internal  1.00489189  0.28918765 #> 182  <NA>  182      181 0.5253558386  internal  1.24584098 -0.38427402 #> 183  <NA>  183      178 0.8768792154  internal  3.01524389  1.24025010 #> 184  <NA>  184      183 0.3417308840  internal  2.71906704  1.85162298 #> 185  <NA>  185      184 0.2761477952  internal  2.00389796  2.43773069 #> 186  <NA>  186      157 0.4967710625  internal  1.57881801  0.37044145 #> 187  <NA>  187      186 0.8026320886  internal  2.63989652  0.47536690 #> 188  <NA>  188      187 1.3087289040  internal  3.73176237 -0.25942644 #> 189  <NA>  189      188 0.2083441725  internal  3.71974615  0.52049204 #> 190  <NA>  190      189 0.0255101041  internal  3.37587615  0.28880652 #> 191  <NA>  191      187 0.3703056422  internal  2.82049596  0.73168597 #> 192  <NA>  192      191 0.1968950188  internal  2.73597270  0.72052113 #> 193  <NA>  193      192 0.1534750686  internal  2.96263400  0.63791542 #> 194  <NA>  194      193 0.0152340122  internal  2.96727375  0.62302314 #> 195  <NA>  195      194 0.4604481907  internal  3.10148300  0.65510394 #> 196  <NA>  196      195 0.1642751276  internal  3.45213971  0.73212244 #> 197  <NA>  197      192 0.5324154713  internal  1.72111346  0.97689560 #> 198  <NA>  198      191 0.9118959007  internal  3.65669043  1.41459293 #> 199  <NA>  199      186 2.2775234810  internal -1.48767902 -1.92496075 #>               DD           RS           LS #> 1   -0.792261887 -3.392696532 -0.094767133 #> 2    1.764320772 -1.046718911 -2.146334945 #> 3   -1.806155037 -2.859660611 -0.632068429 #> 4    0.948874128 -0.278689412 -0.134264890 #> 5    1.624151256  0.220814157  0.608236202 #> 6    2.252422051  2.426804694  3.085533985 #> 7    4.108146451  1.633655726  1.223147978 #> 8   -1.160995541  0.999431600  0.517537813 #> 9    1.341758025  1.304985166  1.521502859 #> 10   0.570073147  0.720705268  1.017846421 #> 11   2.828030732  2.001705516 -0.919563025 #> 12   2.980595831  1.521314671  0.131015359 #> 13   1.359162717  2.162885763  1.163026706 #> 14   1.848692884  1.583433981  0.927126010 #> 15   2.141254323  0.189198068  1.812639133 #> 16   1.560178083  2.781747914  3.347392203 #> 17  -0.073939690  0.027354662  0.900742360 #> 18   3.402771712 -0.457261541 -0.106852864 #> 19   2.876235296  0.463291813  1.744751921 #> 20   2.660581053  0.222790773 -0.532153665 #> 21   2.299374032  3.217700305 -1.138669460 #> 22   1.993843377  2.765155326 -0.621091021 #> 23   2.443433385  2.335835676  0.469978073 #> 24   3.979027350  3.226436578  2.780465714 #> 25   2.034137013  0.942969691  3.576663764 #> 26   3.027626293  1.238032443  3.065084710 #> 27   3.714825776  1.176979136  1.534261968 #> 28   0.675597786  2.317952086 -0.218626950 #> 29  -2.974709277 -1.760554760 -1.239583231 #> 30   0.867846728  2.592129904  0.021198341 #> 31  -1.320245499  0.237320570 -0.105135494 #> 32  -1.143376610  0.425657695  0.271740269 #> 33   3.123728954  1.116995185  3.162476646 #> 34   1.753272053  2.688262363  4.250866454 #> 35   1.210588042  1.223837757  2.943572655 #> 36   0.909660193  2.451038343  1.895478114 #> 37   1.859861867  0.828466484  2.481719676 #> 38   2.717730773  0.796806294  1.126178674 #> 39   4.477326061  2.610442179  1.465738306 #> 40   2.277574874  0.484494584  1.791592125 #> 41   1.593822132  1.454823177  0.729183055 #> 42   2.322463839  0.204364321 -0.885061737 #> 43   2.292615149 -1.418461690  3.138543805 #> 44   2.146223656 -0.184209303  3.099199564 #> 45   2.055324236  2.083887955  2.952789127 #> 46   2.486684424  1.457198741  4.701207454 #> 47   1.420995810  1.601339097  1.396442779 #> 48   3.405244971  1.876423665  4.818320993 #> 49   2.446367879  4.942733281  1.918220026 #> 50   0.373382213 -0.811619200  2.145960417 #> 51   0.858730865  2.844229971  2.215893641 #> 52   2.048278126  1.876438183  2.253066255 #> 53  -0.979401859  0.066992787  1.239294862 #> 54  -1.520667823 -0.517780882  0.002562199 #> 55   0.649664697  0.296776545  0.993825267 #> 56   4.379073801  2.422662868  0.795863984 #> 57  -0.328722937  1.480830939 -1.445882168 #> 58   0.646239216  0.424770897 -1.916304907 #> 59   0.835999391  0.217055270 -0.355409430 #> 60   0.142267982  2.659357457 -0.333557662 #> 61   1.587819101  2.699486648 -0.405668792 #> 62   1.082524348 -0.011507182  0.161447095 #> 63  -1.299067758  1.555475543 -0.651822690 #> 64   0.351846112  0.605027979  2.046577980 #> 65  -0.279595862  1.236295365 -0.684431280 #> 66   0.115635072 -0.342677375 -0.311295514 #> 67   2.599415169 -0.513369614  2.115479969 #> 68  -0.943343694 -0.906440767  0.753327404 #> 69  -0.891525122 -0.467958901  1.752160922 #> 70  -0.375173649  1.154414206  0.965969722 #> 71  -0.592328994 -0.336852088  1.329634282 #> 72   0.719152392  1.226426188  0.316414278 #> 73   1.599438191  0.789638349  0.899306546 #> 74  -0.332396124 -0.433700522  0.629458828 #> 75   0.175928921  0.707616811  2.808930860 #> 76  -0.311789389 -1.996944450  3.564422436 #> 77   2.868493105  0.326425814 -0.441878566 #> 78  -0.250515866  1.272618452  0.526962588 #> 79   0.398301132  0.929595781  2.317926260 #> 80   0.382728205 -0.729808449  2.075454233 #> 81   1.380853148 -0.655486117  1.238821897 #> 82   1.096240272  0.151342211  1.187553629 #> 83   0.794919057  3.466323051  1.677363592 #> 84   0.659773370  3.554223820 -1.116737022 #> 85   1.416964480  3.808228110 -0.272035393 #> 86   0.430344619 -0.918540236  3.601938769 #> 87  -1.503773245 -0.173989015  2.884114421 #> 88  -0.529029913  0.420256120  5.698224578 #> 89   1.230771112 -0.287094234  2.761662804 #> 90   0.560078571  2.048855290  1.138288790 #> 91   1.959411459  0.763497433  1.756392549 #> 92   0.698357920  0.787654206  1.640998942 #> 93   0.678480280 -0.093837593  1.648291943 #> 94   0.840604819  0.001959162  3.568538018 #> 95   0.992731804  2.524498697  2.340271301 #> 96   1.033125330  3.258153919  2.484460337 #> 97   0.270032796  3.015785994  2.745792037 #> 98   0.144785071  4.052392486  1.909532374 #> 99  -1.029371553 -1.760670551 -1.074155886 #> 100 -0.954367914  1.702235497 -0.555582075 #> 101  1.308843827  1.116983364  0.941671321 #> 102  1.500843440  1.095518802  0.946854714 #> 103  1.494577889  1.072951763  0.919909252 #> 104  0.798558133 -0.636985822  0.003413918 #> 105  0.285513704 -1.433753796 -0.481099535 #> 106  0.126453352 -1.694516361 -0.600543380 #> 107  0.199419762 -1.801089988 -0.706065112 #> 108  1.633109628  1.327025910  0.877534736 #> 109  3.168548867  2.024896376  2.144656353 #> 110  1.560837730  1.359395853  0.764417737 #> 111  1.135439910  1.220869473  0.851058307 #> 112  0.261217479  1.163432444  0.991981768 #> 113  1.843241992  1.593584710  0.381671289 #> 114  2.293090839  1.445486375  0.169633396 #> 115  2.296740634  1.429809245  0.178562730 #> 116  2.068841007  1.518722645  0.489558785 #> 117  1.712187338  1.434417686  1.083257103 #> 118  1.940872105  1.366000045  1.054468126 #> 119  2.145414094  1.791237720  0.690549218 #> 120  1.978714109  1.030478751  1.275088906 #> 121  1.213570447  1.419050458  1.618787592 #> 122  2.719952322  0.630368111  0.220090980 #> 123  2.766821179  0.352451641  0.593650281 #> 124  2.594464616  1.756013836  1.877177529 #> 125  2.936896160  2.325167049  1.737290454 #> 126  2.707100980  1.227585072  2.682779876 #> 127  3.296961835  1.209751107  2.342513313 #> 128  1.296722306  1.118338487  0.941344078 #> 129  1.164383097  1.118495599  0.943855518 #> 130  1.160313003  1.118077898  0.940846150 #> 131 -0.649041547  0.346875063 -0.021614045 #> 132 -0.524727502  0.907274878  0.035813489 #> 133 -0.695460246  0.768245367  0.047280182 #> 134  1.683466167  1.219494219  1.676302177 #> 135  1.810253231  1.473661832  2.372100281 #> 136  1.964019245  1.607147790  3.098631717 #> 137  1.940204635  1.624383130  3.123261340 #> 138  1.694523083  1.534142041  1.933333163 #> 139  2.150272810  0.980817437  1.834108238 #> 140  1.732274565  1.208837658  1.699781795 #> 141  2.018227402  1.159933763  1.598592939 #> 142  2.040386417  0.970299146  1.517515220 #> 143  1.937808809  0.969671787  1.265570786 #> 144  2.194970191  0.106828516  1.279967184 #> 145  2.218212435 -0.756502792  3.028091758 #> 146  1.612798864  1.224175296  1.831972593 #> 147  1.806870188  1.544144043  2.386029080 #> 148  1.861477377  1.621354858  2.555974674 #> 149  1.896798692  1.586139397  2.744450307 #> 150  1.980146158  1.911214308  2.812690102 #> 151  1.738063572  2.032954829  2.507484513 #> 152  1.667901811  2.039924690  2.405852377 #> 153  1.534247640  2.267440783  2.311944520 #> 154 -0.147891799  0.171198695  0.928999717 #> 155 -0.877011852 -0.091166271  0.725195972 #> 156  1.299761980  1.120926701  0.940209099 #> 157  0.948655082  0.985615977  0.946679770 #> 158  0.826966290  0.854360177  0.652302687 #> 159  0.621612795  0.779146856  0.439322451 #> 160  0.336050797  1.090538403 -0.928180900 #> 161  0.276575654  1.044332560 -1.180755300 #> 162  0.478283058  1.413563401 -0.385856446 #> 163  0.551283293  0.668836582  0.584137161 #> 164  0.594216305  1.017376552  0.175590443 #> 165  0.406613061  0.795359672  0.152480195 #> 166  0.119665632  0.783019034  0.132263730 #> 167 -0.226411699  0.956404490  0.461912941 #> 168 -0.002138993  0.579930789 -0.248365631 #> 169  0.388736091  0.189700133  1.174068323 #> 170  0.679411860 -0.359701226  1.522352945 #> 171 -0.855565241 -0.674511032  1.263190047 #> 172  0.048661117  0.153345062  1.444276295 #> 173  0.042746877  0.162667651  1.428068822 #> 174  0.014082113  0.037885115  1.000794444 #> 175  0.237042152  0.283856183  0.973912293 #> 176  1.156151241  1.005563482  0.609108318 #> 177 -0.064609116 -0.621932444  3.137044171 #> 178  0.972129054  0.867613889  0.725424288 #> 179  1.025171086  0.716639048  0.757475405 #> 180  1.123283232  0.595091884  0.699959101 #> 181  0.621294968  0.630106695  1.031045258 #> 182  0.405464837  0.134241374  2.121178648 #> 183  0.990603910  1.836390418  0.701632784 #> 184  0.953120717  2.926692616  0.486821499 #> 185  1.016547218  3.488081666 -0.392022456 #> 186  0.591549056  0.900698445  1.138580809 #> 187  0.563944049  1.086133686  2.126388552 #> 188  0.268872389 -0.355935806  3.459696990 #> 189  0.080471955 -0.092747344  3.547370950 #> 190 -0.936271794  0.107362828  4.236832864 #> 191  0.634698796  1.579721293  2.204867160 #> 192  0.752897750  1.473613342  2.223438386 #> 193  0.792236063  1.103061208  2.199555594 #> 194  0.795248656  1.086589529  2.171934487 #> 195  0.952624971  1.259177316  1.634498265 #> 196  1.192887579  0.950371055  1.675491901 #> 197  0.936047239  2.472161931  2.356507086 #> 198  0.261511431  3.286631493  2.312114168 #> 199 -0.967327452 -0.014804246 -0.784591384 (traits_SE = as_phylo4d(psem, what=\"Std. Error\")) #>     label node ancestor  edge.length node.type         BM         NL         DD #> 1      s1    1      107 0.5640308162       tip         NA         NA         NA #> 2      s2    2      107 0.5640308162       tip         NA         NA         NA #> 3      s3    3      106 0.6358275951       tip         NA         NA         NA #> 4      s4    4      105 0.7144448083       tip         NA         NA         NA #> 5      s5    5      104 1.1830950600       tip         NA         NA         NA #> 6      s6    6      109 0.0361022107       tip         NA         NA         NA #> 7      s7    7      109 0.0361022107       tip         NA         NA         NA #> 8      s8    8      112 0.5022074646       tip         NA         NA         NA #> 9      s9    9      112 0.5022074646       tip         NA         NA         NA #> 10    s10   10      111 1.7871837580       tip         NA         NA         NA #> 11    s11   11      116 0.5913975424       tip         NA         NA         NA #> 12    s12   12      119 0.0477228892       tip         NA         NA         NA #> 13    s13   13      119 0.0477228892       tip         NA         NA         NA #> 14    s14   14      120 0.1142573039       tip         NA         NA         NA #> 15    s15   15      120 0.1142573039       tip         NA         NA         NA #> 16    s16   16      121 0.2756963162       tip         NA         NA         NA #> 17    s17   17      121 0.2756963162       tip         NA         NA         NA #> 18    s18   18      122 0.5512595516       tip         NA         NA         NA #> 19    s19   19      123 0.0349638989       tip         NA         NA         NA #> 20    s20   20      123 0.0349638989       tip         NA         NA         NA #> 21    s21   21      114 0.8767527377       tip         NA         NA         NA #> 22    s22   22      113 1.7461743450       tip         NA         NA         NA #> 23    s23   23      125 0.9075157185       tip         NA         NA         NA #> 24    s24   24      125 0.9075157185       tip         NA         NA         NA #> 25    s25   25      126 0.5415591015       tip         NA         NA         NA #> 26    s26   26      127 0.1089356405       tip         NA         NA         NA #> 27    s27   27      127 0.1089356405       tip         NA         NA         NA #> 28    s28   28      130 3.0857795440       tip         NA         NA         NA #> 29    s29   29      131 1.6399242000       tip         NA         NA         NA #> 30    s30   30      132 0.8944032869       tip         NA         NA         NA #> 31    s31   31      133 0.7715950937       tip         NA         NA         NA #> 32    s32   32      133 0.7715950937       tip         NA         NA         NA #> 33    s33   33      136 0.8699913472       tip         NA         NA         NA #> 34    s34   34      137 0.8479589114       tip         NA         NA         NA #> 35    s35   35      137 0.8479589114       tip         NA         NA         NA #> 36    s36   36      138 0.4591954289       tip         NA         NA         NA #> 37    s37   37      139 0.1736071099       tip         NA         NA         NA #> 38    s38   38      139 0.1736071099       tip         NA         NA         NA #> 39    s39   39      141 2.0905969730       tip         NA         NA         NA #> 40    s40   40      143 0.0744131178       tip         NA         NA         NA #> 41    s41   41      143 0.0744131178       tip         NA         NA         NA #> 42    s42   42      144 0.9370864528       tip         NA         NA         NA #> 43    s43   43      145 0.0881684468       tip         NA         NA         NA #> 44    s44   44      145 0.0881684468       tip         NA         NA         NA #> 45    s45   45      147 1.7204295900       tip         NA         NA         NA #> 46    s46   46      149 1.1842473100       tip         NA         NA         NA #> 47    s47   47      149 1.1842473100       tip         NA         NA         NA #> 48    s48   48      150 1.0253154590       tip         NA         NA         NA #> 49    s49   49      152 0.7195368746       tip         NA         NA         NA #> 50    s50   50      152 0.7195368746       tip         NA         NA         NA #> 51    s51   51      153 0.3613256451       tip         NA         NA         NA #> 52    s52   52      153 0.3613256451       tip         NA         NA         NA #> 53    s53   53      155 0.3002640020       tip         NA         NA         NA #> 54    s54   54      155 0.3002640020       tip         NA         NA         NA #> 55    s55   55      154 0.5937157619       tip         NA         NA         NA #> 56    s56   56      156 3.2486997580       tip         NA         NA         NA #> 57    s57   57      161 0.4215356986       tip         NA         NA         NA #> 58    s58   58      161 0.4215356986       tip         NA         NA         NA #> 59    s59   59      162 0.0698869058       tip         NA         NA         NA #> 60    s60   60      162 0.0698869058       tip         NA         NA         NA #> 61    s61   61      164 0.9090035873       tip         NA         NA         NA #> 62    s62   62      165 0.7237639845       tip         NA         NA         NA #> 63    s63   63      167 0.3390345394       tip         NA         NA         NA #> 64    s64   64      167 0.3390345394       tip         NA         NA         NA #> 65    s65   65      168 0.3269574705       tip         NA         NA         NA #> 66    s66   66      168 0.3269574705       tip         NA         NA         NA #> 67    s67   67      170 0.4816150364       tip         NA         NA         NA #> 68    s68   68      171 0.0359279485       tip         NA         NA         NA #> 69    s69   69      171 0.0359279485       tip         NA         NA         NA #> 70    s70   70      173 0.6413136611       tip         NA         NA         NA #> 71    s71   71      175 0.0945133814       tip         NA         NA         NA #> 72    s72   72      176 0.0006422211       tip         NA         NA         NA #> 73    s73   73      176 0.0006422211       tip         NA         NA         NA #> 74    s74   74      174 0.3139612126       tip         NA         NA         NA #> 75    s75   75      177 0.0359670563       tip         NA         NA         NA #> 76    s76   76      177 0.0359670563       tip         NA         NA         NA #> 77    s77   77      180 0.8668137583       tip         NA         NA         NA #> 78    s78   78      181 0.5981367654       tip         NA         NA         NA #> 79    s79   79      182 0.0727809267       tip         NA         NA         NA #> 80    s80   80      182 0.0727809267       tip         NA         NA         NA #> 81    s81   81      179 1.5434906440       tip         NA         NA         NA #> 82    s82   82      183 0.8078943991       tip         NA         NA         NA #> 83    s83   83      184 0.4661635151       tip         NA         NA         NA #> 84    s84   84      185 0.1900157199       tip         NA         NA         NA #> 85    s85   85      185 0.1900157199       tip         NA         NA         NA #> 86    s86   86      188 0.2378751898       tip         NA         NA         NA #> 87    s87   87      190 0.0040209131       tip         NA         NA         NA #> 88    s88   88      190 0.0040209131       tip         NA         NA         NA #> 89    s89   89      189 0.0295310172       tip         NA         NA         NA #> 90    s90   90      195 0.3502461608       tip         NA         NA         NA #> 91    s91   91      196 0.1859710332       tip         NA         NA         NA #> 92    s92   92      196 0.1859710332       tip         NA         NA         NA #> 93    s93   93      194 0.8106943515       tip         NA         NA         NA #> 94    s94   94      193 0.8259283637       tip         NA         NA         NA #> 95    s95   95      197 0.4469879611       tip         NA         NA         NA #> 96    s96   96      197 0.4469879611       tip         NA         NA         NA #> 97    s97   97      198 0.2644025504       tip         NA         NA         NA #> 98    s98   98      198 0.2644025504       tip         NA         NA         NA #> 99    s99   99      199 0.0717127012       tip         NA         NA         NA #> 100  s100  100      199 0.0717127012       tip         NA         NA         NA #> 101  <NA>  101        0           NA      root 1.22322635 1.61418789 1.72525631 #> 102  <NA>  102      101 0.3278789676  internal 1.30071498 1.71644304 1.83454740 #> 103  <NA>  103      102 0.0448143702  internal 1.31380257 1.73371363 1.85300633 #> 104  <NA>  104      103 1.7536273230  internal 1.37288352 1.81167774 1.93633497 #> 105  <NA>  105      104 0.4686502517  internal 0.97714845 1.28945978 1.37818444 #> 106  <NA>  106      105 0.0786172132  internal 0.91260141 1.20428254 1.28714636 #> 107  <NA>  107      106 0.0717967789  internal 0.91028188 1.20122166 1.28387486 #> 108  <NA>  108      103 0.5388417629  internal 1.39262282 1.83772602 1.96417557 #> 109  <NA>  109      108 2.3617784090  internal 0.30636597 0.40428514 0.43210304 #> 110  <NA>  110      108 0.1838847379  internal 1.36644386 1.80317986 1.92725237 #> 111  <NA>  111      110 0.4268121240  internal 1.51142111 1.99449403 2.13173041 #> 112  <NA>  112      111 1.2849762930  internal 1.07717612 1.42145781 1.51926493 #> 113  <NA>  113      110 0.4678215366  internal 1.44312706 1.90437217 2.03540748 #> 114  <NA>  114      113 0.8694216075  internal 0.97715330 1.28946619 1.37819129 #> 115  <NA>  115      114 0.0071530214  internal 0.97044019 1.28060746 1.36872301 #> 116  <NA>  116      115 0.2782021739  internal 0.88470104 1.16746480 1.24779527 #> 117  <NA>  117      116 0.1696001798  internal 0.74979954 0.98944675 1.05752823 #> 118  <NA>  118      117 0.1745800373  internal 0.64458322 0.85060171 0.90912959 #> 119  <NA>  119      118 0.1994944362  internal 0.34098890 0.44997408 0.48093573 #> 120  <NA>  120      118 0.1329600215  internal 0.49663196 0.65536300 0.70045697 #> 121  <NA>  121      117 0.1461010464  internal 0.70970095 0.93653205 1.00097259 #> 122  <NA>  122      115 0.3183401648  internal 0.98266488 1.29673935 1.38596490 #> 123  <NA>  123      122 0.5162956527  internal 0.29920899 0.39484068 0.42200872 #> 124  <NA>  124      102 1.5076279270  internal 1.49221553 1.96915006 2.10464258 #> 125  <NA>  125      124 0.5663931071  internal 1.32624680 1.75013522 1.87055785 #> 126  <NA>  126      124 0.9323497240  internal 1.07523634 1.41889804 1.51652903 #> 127  <NA>  127      126 0.4326234610  internal 0.51732351 0.68266788 0.72964063 #> 128  <NA>  128      101 0.0206999989  internal 1.20634454 1.59191040 1.70144596 #> 129  <NA>  129      128 0.2000464880  internal 1.25574263 1.65709685 1.77111774 #> 130  <NA>  130      129 0.0028896898  internal 1.25884677 1.66119313 1.77549587 #> 131  <NA>  131      130 1.4458553430  internal 1.57854250 2.08306843 2.22639940 #> 132  <NA>  132      131 0.7455209135  internal 1.18802246 1.56773230 1.67560422 #> 133  <NA>  133      132 0.1228081933  internal 1.13999603 1.50435591 1.60786705 #> 134  <NA>  134      129 0.6949407786  internal 1.20257065 1.58693032 1.69612321 #> 135  <NA>  135      134 0.9138552433  internal 1.38787894 1.83146592 1.95748473 #> 136  <NA>  136      135 0.6098818644  internal 1.11567674 1.47226380 1.57356677 #> 137  <NA>  137      136 0.0220324358  internal 1.11103546 1.46613910 1.56702064 #> 138  <NA>  138      135 1.0206777830  internal 0.97459019 1.28608387 1.37457624 #> 139  <NA>  139      138 0.2855883190  internal 0.63244106 0.83457873 0.89200411 #> 140  <NA>  140      134 0.0802496379  internal 1.16877200 1.54232911 1.64845310 #> 141  <NA>  141      140 0.2228818440  internal 1.28533627 1.69614907 1.81285704 #> 142  <NA>  142      141 0.2076500851  internal 1.37909625 1.81987615 1.94509749 #> 143  <NA>  143      142 1.8085337700  internal 0.43767253 0.57755925 0.61729973 #> 144  <NA>  144      142 0.9458604351  internal 1.34725029 1.77785174 1.90018148 #> 145  <NA>  145      144 0.8489180060  internal 0.47300751 0.62418782 0.66713669 #> 146  <NA>  146      140 0.1770607381  internal 1.23211080 1.62591193 1.73778706 #> 147  <NA>  147      146 0.4159884892  internal 1.24623965 1.64455658 1.75771460 #> 148  <NA>  148      147 0.1695261804  internal 1.21017992 1.59697162 1.70685543 #> 149  <NA>  149      148 0.3666560998  internal 1.32044920 1.74248462 1.86238084 #> 150  <NA>  150      148 0.5255879506  internal 1.12365874 1.48279697 1.58482469 #> 151  <NA>  151      150 0.2079515725  internal 1.00451302 1.32557048 1.41677983 #> 152  <NA>  152      151 0.0978270115  internal 1.01302888 1.33680815 1.42879073 #> 153  <NA>  153      151 0.4560382411  internal 0.87087189 1.14921565 1.22829044 #> 154  <NA>  154      146 1.5427023170  internal 1.08223037 1.42812747 1.52639352 #> 155  <NA>  155      154 0.2934517599  internal 0.80865458 1.06711274 1.14053822 #> 156  <NA>  156      128 0.0400159638  internal 1.23140386 1.62497905 1.73678999 #> 157  <NA>  157      156 0.4026925133  internal 1.35918408 1.79359975 1.91701308 #> 158  <NA>  158      157 0.7951233038  internal 1.27358140 1.68063717 1.79627781 #> 159  <NA>  159      158 0.3736798197  internal 1.22652022 1.61853452 1.72990203 #> 160  <NA>  160      159 1.1492712710  internal 0.94650940 1.24902804 1.33497069 #> 161  <NA>  161      160 0.1063971509  internal 0.87500944 1.15467562 1.23412609 #> 162  <NA>  162      160 0.4580459438  internal 0.41761870 0.55109591 0.58901551 #> 163  <NA>  163      159 0.2335971502  internal 1.16536491 1.53783306 1.64364769 #> 164  <NA>  164      163 0.5346033834  internal 1.07091058 1.41318971 1.51042792 #> 165  <NA>  165      164 0.1852396028  internal 0.95150270 1.25561727 1.34201330 #> 166  <NA>  166      165 0.1474062575  internal 0.86886630 1.14656904 1.22546172 #> 167  <NA>  167      166 0.2373231876  internal 0.80532548 1.06271962 1.13584282 #> 168  <NA>  168      166 0.2494002564  internal 0.79695072 1.05166816 1.12403094 #> 169  <NA>  169      163 0.4262080943  internal 1.10440718 1.45739233 1.55767202 #> 170  <NA>  170      169 0.5357838400  internal 0.98598517 1.30112086 1.39064788 #> 171  <NA>  171      170 0.4456870879  internal 0.30302820 0.39988057 0.42739540 #> 172  <NA>  172      169 0.3680846598  internal 0.89979805 1.18738704 1.26908831 #> 173  <NA>  173      172 0.0080005555  internal 0.89702741 1.18373086 1.26518056 #> 174  <NA>  174      173 0.3273524485  internal 0.77398260 1.02135908 1.09163636 #> 175  <NA>  175      174 0.2194478311  internal 0.47112032 0.62169745 0.66447497 #> 176  <NA>  176      175 0.0938711603  internal 0.04095469 0.05404443 0.05776309 #> 177  <NA>  177      172 0.6133471602  internal 0.30345934 0.40044951 0.42800348 #> 178  <NA>  178      158 0.3661103260  internal 1.25575706 1.65711591 1.77113810 #> 179  <NA>  179      178 0.1412829703  internal 1.28149047 1.69107409 1.80743287 #> 180  <NA>  180      179 0.6766768859  internal 1.16906592 1.54271697 1.64886765 #> 181  <NA>  181      180 0.2686769929  internal 1.04754240 1.38235271 1.47746911 #> 182  <NA>  182      181 0.5253558386  internal 0.42744225 0.56405922 0.60287079 #> 183  <NA>  183      178 0.8768792154  internal 1.16688879 1.53984400 1.64579700 #> 184  <NA>  184      183 0.3417308840  internal 0.93124907 1.22889027 1.31344729 #> 185  <NA>  185      184 0.2761477952  internal 0.65326012 0.86205188 0.92136761 #> 186  <NA>  186      157 0.4967710625  internal 1.52763597 2.01589140 2.15460008 #> 187  <NA>  187      186 0.8026320886  internal 1.36167014 1.79688039 1.92051945 #> 188  <NA>  188      187 1.3087289040  internal 0.75183416 0.99213166 1.06039788 #> 189  <NA>  189      188 0.2083441725  internal 0.26849975 0.35431631 0.37869597 #> 190  <NA>  190      189 0.0255101041  internal 0.10068396 0.13286406 0.14200612 #> 191  <NA>  191      187 0.3703056422  internal 1.13842365 1.50228097 1.60564934 #> 192  <NA>  192      191 0.1968950188  internal 1.00764393 1.32970209 1.42119572 #> 193  <NA>  193      192 0.1534750686  internal 0.94424288 1.24603711 1.33177395 #> 194  <NA>  194      193 0.0152340122  internal 0.94588044 1.24819805 1.33408359 #> 195  <NA>  195      194 0.4604481907  internal 0.80011381 1.05584222 1.12849221 #> 196  <NA>  196      195 0.1642751276  internal 0.62798360 0.82869660 0.88571724 #> 197  <NA>  197      192 0.5324154713  internal 0.95527123 1.26059028 1.34732849 #> 198  <NA>  198      191 0.9118959007  internal 0.79057873 1.04325957 1.11504378 #> 199  <NA>  199      186 2.2775234810  internal 0.43045988 0.56804132 0.60712690 #>             RS         LS #> 1           NA         NA #> 2           NA         NA #> 3           NA         NA #> 4           NA         NA #> 5           NA         NA #> 6           NA         NA #> 7           NA         NA #> 8           NA         NA #> 9           NA         NA #> 10          NA         NA #> 11          NA         NA #> 12          NA         NA #> 13          NA         NA #> 14          NA         NA #> 15          NA         NA #> 16          NA         NA #> 17          NA         NA #> 18          NA         NA #> 19          NA         NA #> 20          NA         NA #> 21          NA         NA #> 22          NA         NA #> 23          NA         NA #> 24          NA         NA #> 25          NA         NA #> 26          NA         NA #> 27          NA         NA #> 28          NA         NA #> 29          NA         NA #> 30          NA         NA #> 31          NA         NA #> 32          NA         NA #> 33          NA         NA #> 34          NA         NA #> 35          NA         NA #> 36          NA         NA #> 37          NA         NA #> 38          NA         NA #> 39          NA         NA #> 40          NA         NA #> 41          NA         NA #> 42          NA         NA #> 43          NA         NA #> 44          NA         NA #> 45          NA         NA #> 46          NA         NA #> 47          NA         NA #> 48          NA         NA #> 49          NA         NA #> 50          NA         NA #> 51          NA         NA #> 52          NA         NA #> 53          NA         NA #> 54          NA         NA #> 55          NA         NA #> 56          NA         NA #> 57          NA         NA #> 58          NA         NA #> 59          NA         NA #> 60          NA         NA #> 61          NA         NA #> 62          NA         NA #> 63          NA         NA #> 64          NA         NA #> 65          NA         NA #> 66          NA         NA #> 67          NA         NA #> 68          NA         NA #> 69          NA         NA #> 70          NA         NA #> 71          NA         NA #> 72          NA         NA #> 73          NA         NA #> 74          NA         NA #> 75          NA         NA #> 76          NA         NA #> 77          NA         NA #> 78          NA         NA #> 79          NA         NA #> 80          NA         NA #> 81          NA         NA #> 82          NA         NA #> 83          NA         NA #> 84          NA         NA #> 85          NA         NA #> 86          NA         NA #> 87          NA         NA #> 88          NA         NA #> 89          NA         NA #> 90          NA         NA #> 91          NA         NA #> 92          NA         NA #> 93          NA         NA #> 94          NA         NA #> 95          NA         NA #> 96          NA         NA #> 97          NA         NA #> 98          NA         NA #> 99          NA         NA #> 100         NA         NA #> 101 1.34657639 2.14730314 #> 102 1.43187897 2.28332994 #> 103 1.44628631 2.30630446 #> 104 1.51132499 2.41001765 #> 105 1.07568402 1.71532760 #> 106 1.00462806 1.60201901 #> 107 1.00207463 1.59794722 #> 108 1.53305479 2.44466885 #> 109 0.33725989 0.53780774 #> 110 1.50423594 2.39871319 #> 111 1.66383269 2.65321238 #> 112 1.18579847 1.89092040 #> 113 1.58865188 2.53332612 #> 114 1.07568936 1.71533613 #> 115 1.06829930 1.70355164 #> 116 0.97391422 1.55304153 #> 117 0.82540927 1.31622975 #> 118 0.70958294 1.13152858 #> 119 0.37537419 0.59858630 #> 120 0.54671228 0.87180869 #> 121 0.78126714 1.24583899 #> 122 1.08175673 1.72501138 #> 123 0.32938120 0.52524408 #> 124 1.64269043 2.61949810 #> 125 1.45998542 2.32814958 #> 126 1.18366308 1.88751522 #> 127 0.56949037 0.90813151 #> 128 1.32799223 2.11766810 #> 129 1.38237161 2.20438358 #> 130 1.38578878 2.20983273 #> 131 1.73772260 2.77104010 #> 132 1.30782254 2.08550473 #> 133 1.25495314 2.00119713 #> 134 1.32383778 2.11104325 #> 135 1.52783254 2.43634124 #> 136 1.22818149 1.95850601 #> 137 1.22307219 1.95035852 #> 138 1.07286779 1.71083674 #> 139 0.69621637 1.11021372 #> 140 1.28663087 2.05171168 #> 141 1.41494947 2.25633350 #> 142 1.51816420 2.42092373 #> 143 0.48180739 0.76830882 #> 144 1.48310690 2.36501999 #> 145 0.52070554 0.83033733 #> 146 1.35635675 2.16289927 #> 147 1.37191036 2.18770166 #> 148 1.33221436 2.12440088 #> 149 1.45360319 2.31797223 #> 150 1.23696839 1.97251795 #> 151 1.10580803 1.76336452 #> 152 1.11518263 1.77831364 #> 153 0.95869054 1.52876526 #> 154 1.19136239 1.89979285 #> 155 0.89019924 1.41954636 #> 156 1.35557853 2.16165828 #> 157 1.49624409 2.38596907 #> 158 1.40200925 2.23569852 #> 159 1.35020242 2.15308533 #> 160 1.04195534 1.66154254 #> 161 0.96324532 1.53602848 #> 162 0.45973133 0.73310547 #> 163 1.28288021 2.04573073 #> 164 1.17890112 1.87992161 #> 165 1.04745215 1.67030797 #> 166 0.95648271 1.52524456 #> 167 0.88653444 1.41370232 #> 168 0.87731517 1.39900092 #> 169 1.21577551 1.93872296 #> 170 1.08541183 1.73083996 #> 171 0.33358554 0.53194849 #> 172 0.99053361 1.57954346 #> 173 0.98748358 1.57467976 #> 174 0.85203094 1.35868171 #> 175 0.51862805 0.82702448 #> 176 0.04508456 0.07189359 #> 177 0.33406015 0.53270532 #> 178 1.38238750 2.20440892 #> 179 1.41071586 2.24958242 #> 180 1.28695443 2.05222763 #> 181 1.15317650 1.83890013 #> 182 0.47054549 0.75035015 #> 183 1.28455776 2.04840581 #> 184 1.02515615 1.63475390 #> 185 0.71913482 1.14676037 #> 186 1.68168266 2.68167663 #> 187 1.49898084 2.39033320 #> 188 0.82764906 1.31980140 #> 189 0.29557524 0.47133579 #> 190 0.11083692 0.17674487 #> 191 1.25322220 1.99843690 #> 192 1.10925466 1.76886067 #> 193 1.03946026 1.65756379 #> 194 1.04126295 1.66043843 #> 195 0.88079722 1.40455354 #> 196 0.69130942 1.10238891 #> 197 1.05160070 1.67692341 #> 198 0.87030062 1.38781525 #> 199 0.47386741 0.75564742  # Convert to sem and plot library(sem) my_sem = as_sem(psem) pathDiagram( model = my_sem,                   style = \"traditional\",                   edge.labels = \"values\" ) #> Loading required namespace: DiagrammeR effects( my_sem ) #>  #>  Total Effects (column on row) #>            BM         NL         DD #> DD  0.6296696  0.6750692  0.0000000 #> RS -0.1387108 -0.1487120 -0.2202914 #> LS  1.3366815  0.0000000  0.0000000 #> NL  0.9327482  0.0000000  0.0000000 #>  #>  Direct Effects #>           BM        NL         DD #> DD 0.0000000 0.6750692  0.0000000 #> RS 0.0000000 0.0000000 -0.2202914 #> LS 1.3366815 0.0000000  0.0000000 #> NL 0.9327482 0.0000000  0.0000000 #>  #>  Indirect Effects #>            BM        NL DD #> DD  0.6296696  0.000000  0 #> RS -0.1387108 -0.148712  0 #> LS  0.0000000  0.000000  0 #> NL  0.0000000  0.000000  0  # Plot using semPlot if( require(semPlot) ){   myplot = semPlotModel( my_sem )   semPaths( my_sem,                    nodeLabels = myplot@Vars$name ) } #> Loading required package: semPlot"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Print parameter estimates and standard errors. — print.phylosem","title":"Print parameter estimates and standard errors. — print.phylosem","text":"Print parameter estimates","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print parameter estimates and standard errors. — print.phylosem","text":"","code":"# S3 method for phylosem print(x, ...)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print parameter estimates and standard errors. — print.phylosem","text":"x Output phylosem ... used","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print parameter estimates and standard errors. — print.phylosem","text":"prints (invisibly returns) output fit_tmb","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/reinstalling.html","id":null,"dir":"Reference","previous_headings":"","what":"Reinstalling binary dependencies — reinstalling","title":"Reinstalling binary dependencies — reinstalling","text":"phylosem package depends several upstream packages, uses way depends heavily internal (binary) structure. Sometimes, therefore, installing update one packages require re-install binary-compatible version phylosem, .e. version compiled updated version upstream package. development tools (compilers etc.) installed, able re-install binary-compatible version package running install.packages(\"phylosem\", type=\"source\"). want install development version phylosem instead, can use remotes::install_github(\"James-Thorson-NOAA/phylosem\"). (Windows, can install development tools following instructions https://cran.r-project.org/bin/windows/Rtools/; MacOS, see https://mac.r-project.org/tools/.) development tools /want install (install packages compiled code source), can revert upstream package(s) previous binary version. example, using checkpoint package: similar recipe (substituting Matrix TMB TMB phylosem) can used get warnings incompatibility TMB Matrix.","code":"## load (installing if necessary) the checkpoint package while (!require(\"checkpoint\")) install.packages(\"checkpoint\") ## retrieve build date of installed version of phylosem bd <- as.character(asDateBuilt(       packageDescription(\"phylosem\",fields=\"Built\"))) oldrepo <- getOption(\"repos\") use_mran_snapshot(bd) ## was setSnapshot() pre-checkpoint v1.0.0 install.packages(\"TMB\") options(repos=oldrepo) ## restore original repo"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/reinstalling.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reinstalling binary dependencies — reinstalling","text":"Copied glmmTMB permission","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/summary.phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize phylosem — summary.phylosem","title":"summarize phylosem — summary.phylosem","text":"Summarize phylosem output phylosem, including calculating intercepts tree root","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/summary.phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize phylosem — summary.phylosem","text":"","code":"# S3 method for phylosem summary(object, ...)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/summary.phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize phylosem — summary.phylosem","text":"object Output phylosem ... used","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/summary.phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize phylosem — summary.phylosem","text":"Data-frame containing estimated intercepts, path coefficients, variance-covariance parameters         well standard errors","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/vcov.phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract Variance-Covariance Matrix — vcov.phylosem","title":"Extract Variance-Covariance Matrix — vcov.phylosem","text":"extract covariance fixed effects, fixed random effects.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/vcov.phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract Variance-Covariance Matrix — vcov.phylosem","text":"","code":"# S3 method for phylosem vcov(object, which = c(\"fixed\", \"random\", \"both\"), ...)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/vcov.phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract Variance-Covariance Matrix — vcov.phylosem","text":"object output phylosem whether extract covariance among fixed effects, random effects, ... ignored, method compatibility","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-112","dir":"Changelog","previous_headings":"","what":"phylosem 1.1.2","title":"phylosem 1.1.2","text":"CRAN release: 2023-12-20 Adding new functions provide warning Matrix version doesn’t match ’s expected TMB","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-111","dir":"Changelog","previous_headings":"","what":"phylosem 1.1.1","title":"phylosem 1.1.1","text":"CRAN release: 2023-11-26 Re-adding phylosignal SUGGESTS Re-adding phylosignal Fisheries vignette adding arguemnt as_phylo4d allow easy extraction standard errors","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-110","dir":"Changelog","previous_headings":"","what":"phylosem 1.1.0","title":"phylosem 1.1.0","text":"CRAN release: 2023-10-06 Adding new S3 generic functions: logLik vcov Adding vignette “fisheries” associated paper “Trees fishes: neglected role phylogenetic comparative methods fisheries science” accepted Fish Fisheries","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-102","dir":"Changelog","previous_headings":"","what":"phylosem 1.0.2","title":"phylosem 1.0.2","text":"CRAN release: 2023-09-22 Fixed bug arising data missing observations earliest tips first inputted variable Updating vignette show confidence intervals alpha/kappa/lambda well lnalppha/lnkappa/logitlambda","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-101","dir":"Changelog","previous_headings":"","what":"phylosem 1.0.1","title":"phylosem 1.0.1","text":"CRAN release: 2023-09-19 Address request CRAN use Suggests packages conditionally examples Continuing use Suggests packages unconditionally vignettes based Wickham guidance online","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-100","dir":"Changelog","previous_headings":"","what":"phylosem 1.0.0","title":"phylosem 1.0.0","text":"CRAN release: 2023-08-25 Attempting fix warnings","code":""}]
+[{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"comparison-with-phylolm","dir":"Articles","previous_headings":"","what":"Comparison with phylolm","title":"Comparison with other packages","text":"first compare syntax run-times using simulated data phylolm. confirms runtimes phylosem within order magnitude results nearly identical BM, OU, delta, kappa models.","code":"# Settings Ntree = 100 sd_x = 0.3 sd_y = 0.3 b0_x = 1 b0_y = 0 b_xy = 1  # Simulate tree set.seed(1) tree = ape::rtree(n=Ntree)  # Simulate data x = b0_x + sd_x * phylolm::rTrait(n = 1, phy=tree) ybar = b0_y + b_xy*x y_normal = ybar + sd_y * phylolm::rTrait(n = 1, phy=tree)  # Construct, re-order, and reduce data Data = data.frame(x=x,y=y_normal)[]  # Compare using BM model start_time = Sys.time() plm_bm = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"BM\" ) Sys.time() - start_time #> Time difference of 0.00464797 secs knitr::kable(summary(plm_bm)$coefficients, digits=3) start_time = Sys.time() psem_bm = phylosem( sem = \"x -> y, p\",           data = Data,           tree = tree,           control = phylosem_control(quiet = TRUE) ) Sys.time() - start_time #> Time difference of 0.09037399 secs knitr::kable(summary(psem_bm)$coefficients, digits=3) # Compare using OU start_time = Sys.time() plm_ou = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"OUrandomRoot\" ) Sys.time() - start_time #> Time difference of 0.008813143 secs  start_time = Sys.time() psem_ou = phylosem( sem = \"x -> y, p\",           data = Data,           tree = tree,           estimate_ou = TRUE,           control = phylosem_control(quiet = TRUE) ) Sys.time() - start_time #> Time difference of 0.1400571 secs  knitr::kable(summary(psem_ou)$coefficients, digits=3) knitr::kable(summary(plm_ou)$coefficients, digits=3) knitr::kable(c( \"phylolm_alpha\"=plm_ou$optpar,                  \"phylosem_alpha\"=exp(psem_ou$parhat$lnalpha) ), digits=3) # Compare using Pagel's lambda start_time = Sys.time() plm_lambda = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"lambda\" ) Sys.time() - start_time #> Time difference of 0.01395488 secs  start_time = Sys.time() psem_lambda = phylosem( sem = \"x -> y, p\",           data = Data,           tree = tree,           estimate_lambda = TRUE,           control = phylosem_control(quiet = TRUE) ) Sys.time() - start_time #> Time difference of 0.07518101 secs  knitr::kable(summary(psem_lambda)$coefficients, digits=3) knitr::kable(summary(plm_lambda)$coefficients, digits=3) knitr::kable(c( \"phylolm_lambda\"=plm_lambda$optpar,                  \"phylosem_lambda\"=plogis(psem_lambda$parhat$logitlambda) ), digits=3) # Compare using Pagel's kappa start_time = Sys.time() plm_kappa = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"kappa\", lower.bound = 0, upper.bound = 3 ) Sys.time() - start_time #> Time difference of 0.1530089 secs  start_time = Sys.time() psem_kappa = phylosem( sem = \"x -> y, p\",           data = Data,           tree = tree,           estimate_kappa = TRUE,           control = phylosem_control(quiet = TRUE) ) Sys.time() - start_time #> Time difference of 0.07159591 secs  knitr::kable(summary(psem_kappa)$coefficients, digits=3) knitr::kable(summary(plm_kappa)$coefficients, digits=3) knitr::kable(c( \"phylolm_kappa\"=plm_kappa$optpar,                  \"phylosem_kappa\"=exp(psem_kappa$parhat$lnkappa) ), digits=3)"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"generalized-linear-models","dir":"Articles","previous_headings":"","what":"Generalized linear models","title":"Comparison with other packages","text":"also compare results among software fitting phylogenetic generalized linear models (PGLM).","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"poisson-distributed-response","dir":"Articles","previous_headings":"Generalized linear models","what":"Poisson-distributed response","title":"Comparison with other packages","text":"First, specifically explore Poisson-distributed PGLM, comparing phylosem phylolm::phyloglm (uses Generalized Estimating Equations) phyr::pglmm_compare (uses maximum likelihood). also compare results brms (fits Bayesian hierarchical model), although load results compiled run brms avoid users install STAN run vignettes phylosem:  instance (others explored), results phylolm::phyloglm generally different phylosem, phyr::pglmm_compare, brms close quite identical.","code":"# Settings Ntree = 100 sd_x = 0.3 sd_y = 0.3 b0_x = 1 b0_y = 0 b_xy = 1  # Simulate tree set.seed(1) tree = ape::rtree(n=Ntree)  # Simulate data x = b0_x + sd_x * phylolm::rTrait(n = 1, phy=tree) ybar = b0_y + b_xy*x y_normal = ybar + sd_y * phylolm::rTrait(n = 1, phy=tree) y_pois = rpois( n=Ntree, lambda=exp(y_normal) )  # Construct, re-order, and reduce data Data = data.frame(x=x,y=y_pois)  # Compare using phylolm::phyloglm pglm = phylolm::phyloglm(y ~ 1 + x, data=Data, phy=tree, method=\"poisson_GEE\" ) knitr::kable(summary(pglm)$coefficients, digits=3) # pglmm = phyr::pglmm_compare(   y ~ 1 + x,   family = \"poisson\",   data = Data,   phy = tree ) knitr::kable(summary(pglmm), digits=3) #> Generalized linear mixed model for poisson data fit by restricted maximum likelihood #>  #> Call:y ~ 1 + x #>  #> logLik    AIC    BIC  #> -173.4  354.7  360.6  #>  #> Phylogenetic random effects variance (s2): #>    Variance Std.Dev #> s2  0.05511  0.2348 #>  #> Fixed effects: #>                Value Std.Error  Zscore    Pvalue     #> (Intercept) -0.57009   0.30469 -1.8710   0.06134 .   #> x            1.18137   0.19807  5.9645 2.454e-09 *** #> --- #> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 # pgsem = phylosem( sem = \"x -> y, p\",           data = Data,           family = c(\"fixed\",\"poisson\"),           tree = tree,           control = phylosem_control(quiet = TRUE) ) knitr::kable(summary(pgsem)$coefficients, digits=3) # Comare using Bayesian implementation in brms library(brms) Amat <- ape::vcv.phylo(tree) Data$tips <- rownames(Data) mcmc <- brm(   y ~ 1 + x + (1 | gr(tips, cov = A)),   data = Data, data2 = list(A = Amat),   family = 'poisson',   cores = 4 ) knitr::kable(fixef(mcmc), digits = 3)  # Plot them together library(ggplot2) pdat <- rbind.data.frame(   coef(summary(pglm))[, 1:2],   data.frame(Estimate = pglmm$B, StdErr = pglmm$B.se),   setNames(as.data.frame(fixef(mcmc))[1:2], c('Estimate', 'StdErr')),   setNames(summary(pgsem)$coefficients[2:3, 3:4], c('Estimate', 'StdErr')) ) pdat$Param <- rep(c('Intercept', 'Slope'), 4) pdat$Method <- rep( c('phylolm::phyloglm', 'phyr::pglmm_compare',                      'brms::brm', 'phylosem::phylosem'), each = 2) figure = ggplot(pdat, aes(   x = Estimate, xmin = Estimate - StdErr,   xmax = Estimate + StdErr, y = Param, color = Method )) +   geom_pointrange(position = position_dodge(width = 0.6)) +   theme_classic() +   theme(panel.grid.major.x = element_line(), panel.grid.minor.x = element_line())"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"binomial-regression","dir":"Articles","previous_headings":"Generalized linear models","what":"Binomial regression","title":"Comparison with other packages","text":"also compare results Bernoulli-distributed response using PGLM. compare phylosem phyr::pglmm_compare, explore threshold models expect give different results due differences assumptions latent variables affect measurements. instance, phylosem phyr::pglmm_compare give similar estimates standard errors slope term.","code":"# Settings Ntree = 100 sd_x = 0.3 sd_y = 0.3 b0_x = 1 b0_y = 0 b_xy = 1  # Simulate tree set.seed(1) tree = ape::rtree(n=Ntree)  # Simulate data x = b0_x + sd_x * phylolm::rTrait(n = 1, phy=tree) ybar = b0_y + b_xy*x y_normal = ybar + sd_y * phylolm::rTrait(n = 1, phy=tree) y_binom = rbinom( n=Ntree, size=1, prob=plogis(y_normal) )  # Construct, re-order, and reduce data Data = data.frame(x=x,y=y_binom)  # pglmm = phyr::pglmm_compare(   y ~ 1 + x,   family = \"binomial\",   data = Data,   phy = tree ) knitr::kable(summary(pglmm), digits=3) #> Generalized linear mixed model for binomial data fit by restricted maximum likelihood #>  #> Call:y ~ 1 + x #>  #> logLik    AIC    BIC  #> -63.74 135.47 141.32  #>  #> Phylogenetic random effects variance (s2): #>    Variance Std.Dev #> s2   0.1076   0.328 #>  #> Fixed effects: #>               Value Std.Error Zscore Pvalue #> (Intercept) 0.23179   0.60507 0.3831 0.7017 #> x           0.44548   0.45708 0.9746 0.3297 # pgsem = phylosem( sem = \"x -> y, p\",           data = Data,           family = c(\"fixed\",\"binomial\"),           tree = tree,           control = phylosem_control(quiet = TRUE) ) knitr::kable(summary(pgsem)$coefficients, digits=3)"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"summary-of-pglm-results","dir":"Articles","previous_headings":"Generalized linear models","what":"Summary of PGLM results","title":"Comparison with other packages","text":"Based two comparisons, conclude phylosem provides interface maximum-likelihood estimate phylogenetic generalized linear models (PGLM), extends class include mixed data (.e., combination different measurement types), missing data, non-recursive structural linkages. However, also encourage cross-testing different software fitting phylogenetic generalized linear models.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"compare-with-phylopath","dir":"Articles","previous_headings":"","what":"Compare with phylopath","title":"Comparison with other packages","text":"next compare single run phylopath. confirms runtimes within order magnitude results identical standardized unstandardized coefficients.","code":"library(phylopath) library(phylosem)  # make copy of data that's rescaled rhino_scaled = rhino   rhino_scaled[,c(\"BM\",\"NL\",\"LS\",\"DD\",\"RS\")] = scale(rhino_scaled[,c(\"BM\",\"NL\",\"LS\",\"DD\",\"RS\")])  # Fit and plot using phylopath dag <- DAG(RS ~ DD, LS ~ BM, NL ~ BM, DD ~ NL) start_time = Sys.time() result <- est_DAG( DAG = dag,                     data = rhino,                     tree = rhino_tree,                     model = \"BM\",                     measurement_error = FALSE ) Sys.time() - start_time #> Time difference of 0.00779891 secs plot(result) # Fit and plot using phylosem model = \"   DD -> RS, p1   BM -> LS, p2   BM -> NL, p3   NL -> DD, p4 \" start_time = Sys.time() psem = phylosem( sem = model,           data = rhino_scaled[,c(\"BM\",\"NL\",\"DD\",\"RS\",\"LS\")],           tree = rhino_tree,           control = phylosem_control(quiet = TRUE) ) Sys.time() - start_time #> Time difference of 0.1682889 secs plot( as_fitted_DAG(psem) )"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"comparison-with-sem","dir":"Articles","previous_headings":"","what":"Comparison with sem","title":"Comparison with other packages","text":"next compare syntax runtime R-package sem. confirms runtimes within order magnitude specifying star-phylogeny phylosem match assumed structure sem compare estimated values standardized coefficients also compare values unstandardized coefficients:","code":"library(sem) library(TreeTools)  # Simulation parameters n_obs = 50 # Intercepts a1 = 1 a2 = 2 a3 = 3 a4 = 4 # Slopes b12 = 0.3 b23 = 0 b34 = 0.3 # Standard deviations s1 = 0.1 s2 = 0.2 s3 = 0.3 s4 = 0.4  # Simulate data E1 = rnorm(n_obs, sd=s1) E2 = rnorm(n_obs, sd=s2) E3 = rnorm(n_obs, sd=s3) E4 = rnorm(n_obs, sd=s4) Y1 = a1 + E1 Y2 = a2 + b12*Y1 + E2 Y3 = a3 + b23*Y2 + E3 Y4 = a4 + b34*Y3 + E4 Data = data.frame(Y1=Y1, Y2=Y2, Y3=Y3, Y4=Y4)  # Specify path diagram (in this case, using correct structure) equations = \"   Y2 = b12 * Y1   Y4 = b34 * Y3 \" model <- specifyEquations(text=equations, exog.variances=TRUE, endog.variances=TRUE)  # Fit using package:sem start_time = Sys.time() Sem <- sem(model, data=Data) Sys.time() - start_time #> Time difference of 0.01031017 secs  # Specify star phylogeny tree_null = TreeTools::StarTree(n_obs)   tree_null$edge.length = rep(1,nrow(tree_null$edge))   rownames(Data) = tree_null$tip.label  # Fit using phylosem start_time = Sys.time() psem = phylosem( data = Data,           sem = equations,           tree = tree_null,           control = phylosem_control(quiet = TRUE) ) Sys.time() - start_time #> Time difference of 0.02785897 secs"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/comparison.html","id":"comparison-with-rphylopars","dir":"Articles","previous_headings":"","what":"Comparison with Rphylopars","title":"Comparison with other packages","text":"Finally, compare syntax runtime R-package Rphylopars. confirms can impute identical estimates using packages, specifying full-rank covariance phylosem note phylosem also allows parsimonious representations trait covariance via inputted SEM structure.","code":"library(Rphylopars)  # Format data, within no values for species t1 Data = rhino[,c(\"BM\",\"NL\",\"DD\",\"RS\",\"LS\")]   rownames(Data) = tree$tip.label Data['t1',] = NA  # fit using phylopars start_time = Sys.time() pars <- phylopars( trait_data = cbind(species=rownames(Data),Data),                   tree = tree,                   pheno_error = FALSE,                   phylo_correlated = TRUE,                   pheno_correlated = FALSE) Sys.time() - start_time #> Time difference of 0.0825429 secs  # Display estimates for missing values knitr::kable(cbind( \"Estimate\"=pars$anc_recon[\"t1\",], \"Var\"=pars$anc_var[\"t1\",] ), digits=3) # fit using phylosem start_time = Sys.time() psem = phylosem( data = Data,                  tree = tree,                  sem = \"\",                  covs = \"BM, NL, DD, RS, LS\",                  control = phylosem_control(quiet = TRUE) ) Sys.time() - start_time #> Time difference of 0.2777879 secs  # Display estimates for missing values knitr::kable(cbind(   \"Estimate\"=as.list(psem$sdrep,\"Estimate\")$x_vj[ match(\"t1\",tree$tip.label), ],   \"Var\"=as.list(psem$sdrep,\"Std. Error\")$x_vj[ match(\"t1\",tree$tip.label), ]^2 ), digits=3)"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/demonstration.html","id":"estimability-for-multiple-covariance-transformations","dir":"Articles","previous_headings":"","what":"Estimability for multiple covariance transformations","title":"Demonstration of selected features","text":"default, phylosem takes input phylogenetic tree constructs covariance Brownian motion evolutionary model. However, also allows combination following transformations: Ornstein-Uhlenbeck (OU); Pagel’s lambda; Pagel’s kappa; results eight possible covariance models formed including excluding transformation. first show transformations simultaneously estimable reference data set. see minimum eigenvalue precision matrix (corresponds maximum eigenvalue covariance matrix) greater zero, precision invertible Hessian matrix full rank. can see parameters estimable applying three transformations. also see transformation parameters perfectly correlated, although logit-lambda ln-alpha parameters correlation approximately 0.75. can also extract standard errors, calculated square-root diagonal elements covariance matrix. extract estimated values lnalpha, logitlambda, lnkappa plot plot 95% confidence interval estimates plus minus 1.96 times standard errors. values unbounded construction. However, also convert estimates, lower, upper confidence-interval bounds conventional parameters alpha, lambda, kappa, plot well. derived quantities bounded expected Ornstein-Uhlenbeck Pagel parameters:  confidence intervals suggest parameter lnkappa overlaps 0.0, suggesting Pagel’s kappa overlaps 1.0 instead turned thereby fixed default value.","code":"# Compare using Pagel's kappa library(phylopath)  # Run phylosem model = \"   DD -> RS, p1   BM -> LS, p2   BM -> NL, p3   NL -> DD, p4 \" psem = phylosem( sem = model,           data = rhino[,c(\"BM\",\"NL\",\"DD\",\"RS\",\"LS\")],           estimate_ou = TRUE,           estimate_lambda = TRUE,           estimate_kappa = TRUE,           tree = rhino_tree,           control = phylosem_control(             getJointPrecision = TRUE,             quiet = TRUE) )  # V = psem$sdrep$cov.fixed Rsub = cov2cor(V)[c('lnalpha','logitlambda','lnkappa'),c('lnalpha','logitlambda','lnkappa')]  knitr::kable(c(\"minimum_eigenvalue\"=min(eigen(psem$sdrep$jointPrecision)$values),              \"maximum_eigenvalue\"=max(eigen(psem$sdrep$jointPrecision)$values)), digits=3) knitr::kable(Rsub, digits=3) library(ggplot2) # Compile estimates and SEs pdat = data.frame( \"Estimate\" = psem$sdrep$par.fixed[c('lnalpha','logitlambda','lnkappa')],               \"StdErr\" = sqrt(diag(V)[c('lnalpha','logitlambda','lnkappa')]) ) pdat = cbind( pdat, \"Param\" = rownames(pdat))  # pdat$lower = pdat$Estimate - 1.96*pdat$StdErr pdat$upper = pdat$Estimate + 1.96*pdat$StdErr pdat$type = \"estimated\"  # Transform from log / logit-space to natural space pdat2 = pdat pdat2$Param = c(\"alpha\", \"lambda\", \"kappa\") pdat2['lnalpha',c(\"Estimate\",\"lower\",\"upper\")] = exp(pdat2['lnalpha',c(\"Estimate\",\"lower\",\"upper\")]) pdat2['lnkappa',c(\"Estimate\",\"lower\",\"upper\")] = exp(pdat2['lnkappa',c(\"Estimate\",\"lower\",\"upper\")]) pdat2['logitlambda',c(\"Estimate\",\"lower\",\"upper\")] = plogis(as.numeric(pdat2['logitlambda',c(\"Estimate\",\"lower\",\"upper\")])) pdat2$type = \"derived\"  # Plot ggplot( rbind(pdat,pdat2), aes( x=Param, y = Estimate, ymin = lower, ymax = upper)) +   geom_pointrange(position = position_dodge(width = 0.6)) +   theme_classic() +   facet_grid( rows=vars(type), scales=\"free\" )"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/demonstration.html","id":"scaling-of-runtime-with-increased-tree-size","dir":"Articles","previous_headings":"","what":"Scaling of runtime with increased tree size","title":"Demonstration of selected features","text":"package phylolm expected “linear runtime”, .e., proportional increase runtime increasing tree size. therefore compare runtime phylosem phylolm using simulated tree across three orders magnitude (10, 100, 1000, 10000 tips).  Results show packages approximately linear runtime, phylolm approximately 10-100 times faster given tree size.","code":"# Settings Ntree_config = c( 1e1, 1e2, 1e3, 1e4 ) Nreplicates = 5 sd_x = 0.3 sd_y = 0.3 b0_x = 1 b0_y = 0 b_xy = 1  # Simulate tree set.seed(1) Time_rcz = array(NA, dim=c(Nreplicates,length(Ntree_config),2), dimnames=list(NULL,\"tree_size\"=Ntree_config,\"package\"=c(\"phylolm\",\"phylosem\")) )  for( rI in seq_len(Nreplicates) ){ for( cI in seq_along(Ntree_config) ){    # Simulate data   tree = ape::rtree(n=Ntree_config[cI])   x = b0_x + sd_x * phylolm::rTrait(n = 1, phy=tree)   ybar = b0_y + b_xy*x   y_normal = ybar + sd_y * phylolm::rTrait(n = 1, phy=tree)   Data = data.frame(x=x, y=y_normal)[]    # Run phylolm   start_time = Sys.time()   plm_bm = phylolm::phylolm(y ~ 1 + x, data=Data, phy=tree, model=\"BM\" )   Time_rcz[rI,cI,\"phylolm\"] = Sys.time() - start_time    # Run phylosem   start_time = Sys.time()   psem_bm = phylosem( sem = \"x -> y, p\",             data = Data,             tree = tree,             control = phylosem_control(               quiet = TRUE,               newton_loops = 0,               getsd = FALSE) )   Time_rcz[rI,cI,\"phylosem\"] = Sys.time() - start_time }}  # Format df = apply( Time_rcz, MARGIN=2:3, FUN=mean ) df = cbind( expand.grid(dimnames(df)), \"time_seconds\"=as.vector(df) )  # Plot library(ggplot2) ggplot(data=df, aes(x=tree_size, y=time_seconds, group=package, color=package)) +   geom_line() +   geom_point() + scale_y_log10()"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/fisheries.html","id":"preparing-the-then-et-al--mortality-database","dir":"Articles","previous_headings":"","what":"Preparing the Then et al. mortality database","title":"Phylogenetic comparative methods in fisheries science","text":"demonstrate potential role PCM fisheries science, re-analyze foundational dataset compiled et al.. specifically download file “Mlifehist_ver1.0.csv” include copy data object package phylosem simplify following demonstration. demonstration provides basic syntax output PCM, showing relationship natural mortality rate, longevity, growth parameters. , first load phylogeny fishes using package fishtree, includes several versions phylogeny fishes develoepd Rabosky et al.. associate trait data tip label phylogeny, provide convenient names modeled variables.","code":"# Load packages library(phylosem) library(fishtree)  # Download tree out = fishtree_complete_phylogeny() tree = out[[1]]  # Load data object data( Mlifehist_ver1_0 ) Data = Mlifehist_ver1_0  # Reformat to match tree$tip.label Data$Genus_species = factor( paste0(Data$Genus, \"_\", Data$Species) )  # Drop duplicates ... not dealing with variation among stocks within species Data = Data[match(unique(Data$Genus_species),Data$Genus_species), ]  # log-transform to simplify later syuntax Data = cbind( Data, \"logM\" = log(Data[,'M']),                     \"logK\" = log(Data[,'K']),                     \"logtmax\" = log(Data[,'tmax']),                     \"logLinf\" = log(Data[,'Linf']) )  # Identify species in both datasets species_to_use = intersect( tree$tip.label, Data$Genus_species ) species_to_drop = setdiff( Data$Genus_species, tree$tip.label )  # Drop tips not present in trait-data # Not strictly necessary, but helpful to simplify later plots tree = ape::keep.tip( tree, tip=species_to_use )  # Drop trait-data not in phylogeny # Necessary to define correlation among data rows_to_use = which( Data$Genus_species %in% species_to_use ) Data = Data[rows_to_use,]  # Only include modeled variables in trait-data passed to phylosem rownames(Data) = Data$Genus_species Data = Data[,c('logM','logK','logtmax','logLinf')]"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/fisheries.html","id":"fitting-and-selecting-among-phylogenetic-structural-equation-models","dir":"Articles","previous_headings":"","what":"Fitting and selecting among phylogenetic structural equation models","title":"Phylogenetic comparative methods in fisheries science","text":"define path diagram specifying set linkages among variables. following, use path diagram ensures mortality rate statistically independent growth, conditional upon measurement longevity. specification ensures , longevity available, sole information used predict mortality rate. However, longevity available, model reverts predicting mortality growth parameters. fit model using phylogenetic structural equation models. specifically apply grid-search across eight models formed combination modeled transformations phylogenetic tree. use marginal AIC select model, list estimated path coefficients.","code":"# Specify SEM structure sem_structure = \"   logK -> logtmax, b1   logLinf -> logtmax, b2   logtmax -> logM, a \"  # Grid-search model selection using AIC for transformations Grid = expand.grid( \"OU\" = c(FALSE,TRUE),                     \"lambda\" = c(FALSE,TRUE),                     \"kappa\" = c(FALSE,TRUE) ) psem_grid = NULL for( i in 1:nrow(Grid)){   psem_grid[[i]] = phylosem( data=Data,                    tree = tree,                    sem = sem_structure,                    estimate_ou = Grid[i,'OU'],                    estimate_lambda = Grid[i,'lambda'],                    estimate_kappa = Grid[i,'kappa'],                    control = phylosem_control(quiet = TRUE) ) }  # Extract AIC for each model and rank-order by parsimony Grid$AIC = sapply( psem_grid, \\(m) AIC(m) ) Grid = Grid[order(Grid$AIC,decreasing=FALSE),]  # Select model with lowest AIC psem_best = psem_grid[[as.numeric(rownames(Grid[1,]))]]"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/fisheries.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing output","title":"Phylogenetic comparative methods in fisheries science","text":"Finally, can convert output formats packages, use existing third-party PCM packages plot, query, post-process output.  also show plot output using phylosignal, although currently unavailable CRAN therefore commented :","code":"# Plot path diagram my_fitted_DAG = as_fitted_DAG(psem_best) plot(my_fitted_DAG, type=\"color\") # Total, direct, and indirect effects my_sem = as_sem(psem_best) effects(my_sem) #>  #>  Total Effects (column on row) #>               logK   logtmax    logLinf #> logtmax -0.4480233  0.000000  0.4073488 #> logM     0.4579994 -1.022267 -0.4164192 #>  #>  Direct Effects #>               logK   logtmax   logLinf #> logtmax -0.4480233  0.000000 0.4073488 #> logM     0.0000000 -1.022267 0.0000000 #>  #>  Indirect Effects #>              logK logtmax    logLinf #> logtmax 0.0000000       0  0.0000000 #> logM    0.4579994       0 -0.4164192 # Load for plotting, # https://r-pkgs.org/vignettes.html#sec-vignettes-eval-option library(phylosignal)  # Plot using phylobase my_phylo4d = as_phylo4d( psem_best ) barplot(my_phylo4d)"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/fisheries.html","id":"sensitivity-to-using-taxonomic-tree","dir":"Articles","previous_headings":"","what":"Sensitivity to using taxonomic tree","title":"Phylogenetic comparative methods in fisheries science","text":"analysis, can also conduct sensivity analyses. , show construct taxonomic tree use place phylogenetic information. , requires code reformat data statistical analysis simple specify. estimated path coefficients similar estimates using phyogeny.","code":"library(ape) Data = Mlifehist_ver1_0  # Make taxonomic factors Data$Genus_species = factor( paste0(Data$Genus, \"_\", Data$Species) ) Data$Genus = factor( Data$Genus ) Data$Family = factor( Data$Family ) Data$Order = factor( Data$Order )  # Make taxonomic tree tree = ape::as.phylo( ~Order/Family/Genus/Genus_species, data=Data, collapse=FALSE) tree$edge.length = rep(1,nrow(tree$edge)) tree = collapse.singles(tree) tmp = root(tree, node=ape::Ntip(tree)+1 )  # Drop duplicates ... not dealing with variation among stocks within species Data = Data[match(unique(Data$Genus_species),Data$Genus_species), ]  # log-transform to simplify later syuntax Data = cbind( Data, \"logM\" = log(Data[,'M']),                     \"logK\" = log(Data[,'K']),                     \"logtmax\" = log(Data[,'tmax']),                     \"logLinf\" = log(Data[,'Linf']) )  # Only include modeled variables in trait-data passed to phylosem rownames(Data) = Data$Genus_species Data = Data[,c('logM','logK','logtmax','logLinf')]  # Fit model psem_taxon = phylosem( data=Data,                  tree = tree,                  sem = sem_structure,                  estimate_ou = TRUE,                  control = phylosem_control(quiet = TRUE) )  # Plot path diagram my_fitted_DAG = as_fitted_DAG(psem_taxon) plot(my_fitted_DAG, type=\"color\")"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/phylopath.html","id":"model-comparison-some-important-differences","dir":"Articles","previous_headings":"","what":"Model comparison: some important differences","title":"Detailed comparison with `phylopath`","text":"Let’s start loading Rhinogrades example data phylogeny. supply data model comparison functions, already two important differences flag . Firstly, phylo_path consciders columns data actually used models. compare_phylosem . rhino, first column contains copy species names, need exclude column (using rhino[-1]). , using phylosem, make sure data.frame contains variables ’d like inlcude analysis. Secondly, get standardized path coefficients, phylopath standardize data variable unit variance, phylosem keeps data original scale. make better comparison packages, ’ll standardize data manually . Now can define causal models want compare. First phylopath, use formulas can use DAG() define model, define_model_set() create list models: phylosem, can define models similarly, need use strings instead. Also note need write parameter front varialble (e.g. b1, b2, etc.). compare multiple models, collect models list: can now run model comparison. phylopath use d-separation , phylosem fitting structural equation model . Note phylo_path, specify want Brownian motion model (\"BM\"), default compare_phylosem. models perform? phylopath can use summary get table CICc values: phylosem, can extract AIC values model: Even though methodology used quite different, obtain similar result: model 5 fits much better models. However, methods somewhat differ ranking models. largely due different philosophies two approaches. phylopath uses PPA method described Von Hardenberg & Gonzalez-Voyer, uses Shipley’s d-separation. essence, method finds pairs variables causal model claims independent (conditionally independent), tests whether indeed case. phylosem hand directly evaluates fit casual model data. sense, phylosem analyzes paths included model phylopath analyzes paths included. Another source difference CICc metric used phylopath employs correction small sample sizes phylosem’s AIC metric . conclusion, cases one model clearly fits best (Brownian motion model) expect methods lead conclusion, don’t expect model comparison results match closely.","code":"data(rhino, rhino_tree, package = 'phylopath') rhino_std <- rhino[-1] rhino_std[] <- lapply(rhino_std, scale) models_pp <- phylopath::define_model_set(   one   = c(RS ~ DD),   two   = c(DD ~ NL, RS ~ LS + DD),   three = c(RS ~ NL),   four  = c(RS ~ BM + NL),   five  = c(RS ~ BM + NL + DD),   six   = c(NL ~ RS, RS ~ BM),   seven = c(NL ~ RS, RS ~ LS + BM),   eight = c(NL ~ RS),   nine  = c(NL ~ RS, RS ~ LS),   .common = c(LS ~ BM, NL ~ BM, DD ~ NL) ) models_ps <- list(   one   = 'RS = b1 * DD',   two   = 'DD = b1 * NL; RS = b2 * LS + b3 * DD',   three = 'RS = b1 * NL',   four  = 'RS = b * BM + b2 * NL',   five  = 'RS = b1 * BM + b2 * NL + b3 * DD',   six   = 'NL = b1 * RS; RS = b2 * BM',   seven = 'NL = b1 * RS; RS = b2 * LS + b3 * BM',   eight = 'NL = b1 * RS',   nine  = 'NL = b1 * RS; RS = b2 * LS' ) # we add the .common paths, by pasting them at the end of each of the model strings, e.g.: models_ps <- lapply(   models_ps,    \\(x) paste(x, c('LS = b1_ * BM; NL = b2_ * BM; DD = b3_ * NL'), sep = '; ') ) result_pp <- phylopath::phylo_path(   models_pp, data = rhino_std, tree = rhino_tree, model = 'BM' )  library(phylosem) result_ps <- phylosem::compare_phylosem(   models_ps, tree = rhino_tree, data = rhino_std ) summary(result_pp) #>       model k  q     C        p  CICc delta_CICc        l        w #> five   five 4 11  60.7 3.39e-10  85.7        0.0 1.00e+00 1.00e+00 #> eight eight 6  9 101.9 2.22e-16 121.9       36.2 1.38e-08 1.38e-08 #> three three 6  9 111.8 0.00e+00 131.8       46.0 1.00e-10 1.00e-10 #> nine   nine 5 10 110.7 0.00e+00 133.2       47.5 4.85e-11 4.85e-11 #> six     six 5 10 111.0 0.00e+00 133.5       47.8 4.25e-11 4.25e-11 #> one     one 6  9 113.9 0.00e+00 133.9       48.2 3.49e-11 3.49e-11 #> four   four 5 10 113.7 0.00e+00 136.2       50.5 1.08e-11 1.08e-11 #> two     two 5 10 115.2 0.00e+00 137.6       51.9 5.31e-12 5.31e-12 #> seven seven 4 11 114.2 0.00e+00 139.2       53.5 2.45e-12 2.45e-12 sapply(result_ps, AIC) |> sort() #>     five    eight     four      six     nine      two    seven      one  #> 1680.150 1730.808 1732.720 1732.720 1732.739 1733.104 1734.716 1735.057  #>    three  #> 1736.103"},{"path":"https://james-thorson-noaa.github.io/phylosem/articles/phylopath.html","id":"model-fitting-sometimes-different","dir":"Articles","previous_headings":"","what":"Model fitting: sometimes different","title":"Detailed comparison with `phylopath`","text":"take best model, particular model, perform model averaging, phylopath phylosem work largely way. packages implemented best(), choice() average() methods respective output types. can get best model (model 5) using best(). phylopath paths now fitted, phylosem already done model just extracted compare_phylosem object: compare two, can convert phylosem result DAG format phylopath uses, use included plot functionality:   phylopath now actually fitting causal model , performing d-separation procedure. makes methods much closely aligned, can see output matches closely. However, generally hold true assuming Brownian motion. deviate assumption using (example) Pagel’s lambda model, default phylopath, longer true:   reason happens phylosem implements additional parameters estimating single estimated parameter variables model. phylopath, hand, estimates separate lambda residuals regression ran. est_DAG() means one lambda variable modelled cause, phylo_path() means one lambda tested d-separation statement.","code":"best_pp <- phylopath::best(result_pp) best_ps <- phylosem::best(result_ps) plot(best_pp) plot(as_fitted_DAG(best_ps)) phylopath::est_DAG(   models_pp$five, data = rhino_std, tree = rhino_tree, model = 'lambda' ) |> plot() phylosem::phylosem(   models_ps$five, tree = rhino_tree, data = rhino_std, estimate_lambda = TRUE ) |> as_fitted_DAG() |> plot()"},{"path":"https://james-thorson-noaa.github.io/phylosem/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"James Thorson. Author, maintainer. Wouter van der Bijl. Contributor.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Thorson, J. T., Maureaud, . ., Frelat, R., Mérigot, B., Bigman, J. S., Friedman, S. T., Palomares, M. L. D., Pinsky, M. L., Price, S. ., & Wainwright, P. (2023). Identifying direct indirect associations among traits merging phylogenetic comparative methods structural equation models. Methods Ecology Evolution, 14(5), 1259–1275. https://doi.org/10.1111/2041-210X.14076 Thorson, J. T., & van der Bijl, W. (2023). phylosem: fast simple R package phylogenetic inference trait imputation using phylogenetic structural equation models. Journal Evolutionary Biology. 36(10): 1357-1364. https://doi.org/10.1111/jeb.14234","code":"@Article{,   title = {Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models},   journal = {Methods in Ecology and Evolution},   volume = {14},   number = {5},   pages = {1259–1275},   year = {2023},   doi = {10.1111/2041-210X.14076},   url = {https://doi.org/10.1111/2041-210X.14076},   author = {J. T. Thorson and A. A. Maureaud and R. Frelat and B. Mérigot and J. S. Bigman and S. T. Friedman and M. L. D. Palomares and M. L. Pinsky and S. A. Price and P. Wainwright}, } @Article{,   title = {phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equation models},   journal = {Journal of Evolutionary Biology},   volume = {36},   number = {10},   pages = {1357-1364},   year = {2023},   doi = {10.1111/jeb.14234},   url = {https://doi.org/10.1111/jeb.14234},   author = {James T. Thorson and & Wouter {van der Bijl}}, }"},{"path":"https://james-thorson-noaa.github.io/phylosem/index.html","id":"phylogenetic-structural-equation-models","dir":"","previous_headings":"","what":"Phylogenetic structural equation models","title":"Phylogenetic Structural Equation Model","text":"Package phylosem combines features structural equation models (SEM), phylogenetic comparative methods (PCM), generalized linear mixed models (GLMM). , incorporates broad feature-set: Comparing multiple evolutionary models similar phylopath Estimating trade-offs among multiple traits similar phylolm Predicting missing trait values (associated standard errors) similar Rphylopars Estimating tradeoffs including recursive (cyclic) dependencies similar package sem Applying ordination multiple traits, similar phylogenetic factor analysis package FishLife phylosem specifically intended minimal implementation, uses standard packages input/output formatting: Input: phylogenetic relatedness defined using class phylo package ape Input: structural trade-offs specified using syntax defined package sem Output: visualizing trade-offs using semPlot, diagrammeR, ggraph Output: assembling trait predictions standard errors using phylobase Output: plotting trait predictions using phylosignal Please see package vignettes details regarding syntax features.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert phylosem to phylopath output — as_fitted_DAG","title":"Convert phylosem to phylopath output — as_fitted_DAG","text":"Convert output package phylosem phylopath","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert phylosem to phylopath output — as_fitted_DAG","text":"","code":"as_fitted_DAG(object)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert phylosem to phylopath output — as_fitted_DAG","text":"object Output phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert phylosem to phylopath output — as_fitted_DAG","text":"Convert output format supplied est_DAG","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert phylosem to phylo4d — as_phylo4d","title":"Convert phylosem to phylo4d — as_phylo4d","text":"Convert output package phylosem phylo4d object package phylobase","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert phylosem to phylo4d — as_phylo4d","text":"","code":"as_phylo4d(object, what = c(\"Estimate\", \"Std. Error\"))"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert phylosem to phylo4d — as_phylo4d","text":"object Output phylosem Select convert (Estimate / Std. Error).","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert phylosem to phylo4d — as_phylo4d","text":"phylosem output converted format supplied phylo4d","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_phylo4d.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert phylosem to phylo4d — as_phylo4d","text":"package intended use using plots assocaited package sem, e.g., using package plotSEM semPlot::semPlotModel","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_sem.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert phylosem to sem output — as_sem","title":"Convert phylosem to sem output — as_sem","text":"Convert output package phylosem output package sem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_sem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert phylosem to sem output — as_sem","text":"","code":"as_sem(object)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_sem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert phylosem to sem output — as_sem","text":"object Output phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/as_sem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert phylosem to sem output — as_sem","text":"Output converted format supplied sem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.compare_phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose model — average.compare_phylosem","title":"Choose model — average.compare_phylosem","text":"Choose model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.compare_phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose model — average.compare_phylosem","text":"","code":"# S3 method for compare_phylosem average(x, cut_off = 2, avg_method = \"conditional\")"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.compare_phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose model — average.compare_phylosem","text":"x output compare_phylosem cut_off threshold model delta-AIC greater value excluded average avg_method see average_DAGs","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.compare_phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose model — average.compare_phylosem","text":"Returns AIC-weighted average fitted models compare_phylosem conversion format est_DAG","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose model — average","title":"Choose model — average","text":"Choose model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose model — average","text":"","code":"average(x, cut_off, avg_method)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose model — average","text":"x output compare_phylosem cut_off threshold model delta-AIC greater value excluded average avg_method see average_DAGs","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/average.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose model — average","text":"Returns AIC-weighted average fitted models compare_phylosem conversion format [phylopath::est_DAG]","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.compare_phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract best fitted model — best.compare_phylosem","title":"Extract best fitted model — best.compare_phylosem","text":"Extract best fitted model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.compare_phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract best fitted model — best.compare_phylosem","text":"","code":"# S3 method for compare_phylosem best(x)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.compare_phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract best fitted model — best.compare_phylosem","text":"x output compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.compare_phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract best fitted model — best.compare_phylosem","text":"Returns best model fitted using compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract best fitted model — best","title":"Extract best fitted model — best","text":"Extract best fitted model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract best fitted model — best","text":"","code":"best(x)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract best fitted model — best","text":"x output compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/best.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract best fitted model — best","text":"Returns best model fitted using compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/checkDepPackageVersion.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","title":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","text":"Copied glmmTMB permission","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/checkDepPackageVersion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","text":"","code":"checkDepPackageVersion(   dep_pkg = \"TMB\",   this_pkg = \"phylosem\",   write_file = FALSE,   warn = TRUE )"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/checkDepPackageVersion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","text":"dep_pkg upstream package this_pkg downstream package write_file (logical) write version file quit? warn give warning?","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/checkDepPackageVersion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check for version mismatch in dependent binary packages — checkDepPackageVersion","text":"logical: TRUE binary versions match","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.compare_phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose model — choice.compare_phylosem","title":"Choose model — choice.compare_phylosem","text":"Choose model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.compare_phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose model — choice.compare_phylosem","text":"","code":"# S3 method for compare_phylosem choice(x, choice)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.compare_phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose model — choice.compare_phylosem","text":"x output compare_phylosem choice Integer indicating model extract","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.compare_phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose model — choice.compare_phylosem","text":"Returns chosen model fitted using compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.html","id":null,"dir":"Reference","previous_headings":"","what":"Choose model — choice","title":"Choose model — choice","text":"Choose model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Choose model — choice","text":"","code":"choice(x, choice)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Choose model — choice","text":"x output compare_phylosem choice Integer indicating model extract","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/choice.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Choose model — choice","text":"Returns chosen model fitted using compare_phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/coef.phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract path coefficients — coef.phylosem","title":"Extract path coefficients — coef.phylosem","text":"Extract path coefficients.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/coef.phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract path coefficients — coef.phylosem","text":"","code":"# S3 method for phylosem coef(object, standardized = FALSE, ...)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/coef.phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract path coefficients — coef.phylosem","text":"object Output phylosem standardized Whether standardize regression coefficients ... used","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/coef.phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract path coefficients — coef.phylosem","text":"Data-frame listing path coefficients, parameter index estimated values","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare phylogenetic structural equation models — compare_phylosem","title":"Compare phylogenetic structural equation models — compare_phylosem","text":"Fits several phylogenetic structural equation model comparison","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare phylogenetic structural equation models — compare_phylosem","text":"","code":"compare_phylosem(   sem_set,   tree,   data,   family = rep(\"fixed\", ncol(data)),   covs,   estimate_ou = FALSE,   estimate_lambda = FALSE,   estimate_kappa = FALSE,   control = phylosem_control(),   ... )"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare phylogenetic structural equation models — compare_phylosem","text":"sem_set named list structural equation model specifications, element passed argument sem phylosem tree phylogenetic structure, using class .phylo data data-frame providing variables modeled.  Missing values inputted NA.  SEM includes latent variable (.e., variable available measurements) still must inputted column data entirely NA values. family Character-vector listing distribution used column data, element must fixed, normal, binomial, poisson. family=\"fixed\" default behavior assumes given variable measured exactly. options correspond different specifications measurement error. covs optional: character vector one elements, element   \tgiving string variable names, separated commas. Variances covariances   \tamong variables string added model. confirmatory   \tfactor analysis models specified via cfa, covs defaults   \tfactors model, thus specifying variances covariances among factors.   \tWarning: covs=\"x1, x2\" covs=c(\"x1\", \"x2\")   \tequivalent: covs=\"x1, x2\" specifies variance x1, variance   \tx2, covariance, covs=c(\"x1\", \"x2\") specifies   \tvariance x1 variance x2 covariance. estimate_ou Boolean indicating whether estimate autoregressive (Ornstein-Uhlenbeck) process using additional parameter lnalpha, corresponding model=\"OUrandomRoot\" parameterization phylolm listed doi:10.1093/sysbio/syu005 estimate_lambda Boolean indicating whether estimate additional branch lengths phylogenetic tips (.k.. Pagel-lambda term) using additional parameter logitlambda estimate_kappa Boolean indicating whether estimate nonlinear scaling branch lengths (.k.. Pagel-kappa term) using additional parameter lnkappa control Output phylosem_control, used define user settings, see documentation function details. ... Additional arguments passed phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compare phylogenetic structural equation models — compare_phylosem","text":"object (list) class `compare_phylosem`, containing list         output phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html","id":null,"dir":"Reference","previous_headings":"","what":"List fixed and random effects — list_parameters","title":"List fixed and random effects — list_parameters","text":"list_parameters lists fixed random effects","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List fixed and random effects — list_parameters","text":"","code":"list_parameters(Obj, verbose = TRUE)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List fixed and random effects — list_parameters","text":"Obj Compiled TMB object verbose Boolean, whether print messages terminal","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List fixed and random effects — list_parameters","text":"Tagged-list fixed random effects, returned invisibly printed screen","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/Mlifehist_ver1_0.html","id":null,"dir":"Reference","previous_headings":"","what":"Fisheries natural mortality example — Mlifehist_ver1_0","title":"Fisheries natural mortality example — Mlifehist_ver1_0","text":"Data used demonstrate phylogenetic comparative methods fisheries science.  Specifically copy et al. database doi:10.1093/icesjms/fsu136   using file \"Mlifehist_ver1.0.csv\" accessed  https://www.vims.edu/research/departments/fisheries/programs/mort_db/","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/Mlifehist_ver1_0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fisheries natural mortality example — Mlifehist_ver1_0","text":"","code":"data(Mlifehist_ver1_0)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse path — parse_path","title":"Parse path — parse_path","text":"parse_path copied sem::parse.path","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse path — parse_path","text":"","code":"parse_path(path)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse path — parse_path","text":"path text parse","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse path — parse_path","text":"Tagged-list defining variables direction specified path coefficient","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Parse path — parse_path","text":"Copied permission John Fox licence GPL (>= 2)","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit phylogenetic structural equation model — phylosem","title":"Fit phylogenetic structural equation model — phylosem","text":"Fits phylogenetic structural equation model","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit phylogenetic structural equation model — phylosem","text":"","code":"phylosem(   sem,   tree,   data,   family = rep(\"fixed\", ncol(data)),   covs = colnames(data),   estimate_ou = FALSE,   estimate_lambda = FALSE,   estimate_kappa = FALSE,   data_labels = rownames(data),   tmb_inputs = NULL,   control = phylosem_control() )"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit phylogenetic structural equation model — phylosem","text":"sem structural equation model structure, passed either specifyModel specifyEquations parsed control set path coefficients variance-covariance parameters tree phylogenetic structure, using class .phylo data data-frame providing variables modeled.  Missing values inputted NA.  SEM includes latent variable (.e., variable available measurements) still must inputted column data entirely NA values. family Character-vector listing distribution used column data, element must fixed, normal, binomial, poisson. family=\"fixed\" default behavior assumes given variable measured exactly. options correspond different specifications measurement error. covs optional: character vector one elements, element   \tgiving string variable names, separated commas. Variances covariances   \tamong variables string added model. confirmatory   \tfactor analysis models specified via cfa, covs defaults   \tfactors model, thus specifying variances covariances among factors.   \tWarning: covs=\"x1, x2\" covs=c(\"x1\", \"x2\")   \tequivalent: covs=\"x1, x2\" specifies variance x1, variance   \tx2, covariance, covs=c(\"x1\", \"x2\") specifies   \tvariance x1 variance x2 covariance. estimate_ou Boolean indicating whether estimate autoregressive (Ornstein-Uhlenbeck) process using additional parameter lnalpha, corresponding model=\"OUrandomRoot\" parameterization phylolm listed doi:10.1093/sysbio/syu005 estimate_lambda Boolean indicating whether estimate additional branch lengths phylogenetic tips (.k.. Pagel-lambda term) using additional parameter logitlambda estimate_kappa Boolean indicating whether estimate nonlinear scaling branch lengths (.k.. Pagel-kappa term) using additional parameter lnkappa data_labels row data, listing corresponding name tree$tip.label.  Default pulls data_labels rownames(data) tmb_inputs optional tagged list overrides default constructor TMB inputs (use risk) control Output phylosem_control, used define user settings, see documentation function details.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit phylogenetic structural equation model — phylosem","text":"object (list) class `phylosem`. Elements include: data Copy argument data SEM_model SEM model parsed sem using specifyModel specifyEquations obj TMB object MakeADFun tree Copy argument tree tmb_inputs list inputs passed MakeADFun opt output nlminb sdrep output sdreport report output obj$report() parhat output obj$env$parList() containing maximum likelihood estimates empirical Bayes predictions","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit phylogenetic structural equation model — phylosem","text":"Note parameters logitlambda, lnkappa, lnalpha estimated estimated single value      applies modeled variables.      differs default behavior phylolm, parameters apply \"response\" \"predictor\" variables.      also differs default behavior phylopath, different value estimated      call phylolm d-separation estimate path coefficients. However,      consistent default behavior Rphylopars, estimates comparable case.      additional parameters estimated unbounded support, differs somewhat default      bounded estimates phylolm, although parameters match overriding phylolm defaults      use unbounded support.  Finally, phylosem allows three parameters estimated      combination, expanded functionality relative single-option functionality phylolm. Also note phylopath default uses standardized coefficients.  achieve matching parameter estimates      phylosem phylopath, standardize variable standard deviation 1.0 prior fitting phylosem.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Fit phylogenetic structural equation model — phylosem","text":"**Introducing package, features, comparison software (cite using phylosem):** Thorson, J. T., & van der Bijl, W. (press). phylosem: fast simple R package phylogenetic inference trait imputation using phylogenetic structural equation models. Journal Evolutionary Biology. doi:10.1111/jeb.14234 *Statistical methods phylogenetic structural equation models* Thorson, J. T., Maureaud, . ., Frelat, R., Merigot, B., Bigman, J. S., Friedman, S. T., Palomares, M. L. D., Pinsky, M. L., Price, S. ., & Wainwright, P. (2023). Identifying direct indirect associations among traits merging phylogenetic comparative methods structural equation models. Methods Ecology Evolution, 14(5), 1259-1275. doi:10.1111/2041-210X.14076 *Earlier development computational methods, originally used phlogenetic factor analysis:* Thorson, J. T. (2020). Predicting recruitment density dependence intrinsic growth rate fishes worldwide using data-integrated life-history model. Fish Fisheries, 21(2), 237-251. doi:10.1111/faf.12427 Thorson, J. T., Munch, S. B., Cope, J. M., & Gao, J. (2017). Predicting life history parameters fishes worldwide. Ecological Applications, 27(8), 2262-2276. doi:10.1002/eap.1606 *Earlier development phylogenetic path analysis:* van der Bijl, W. (2018). phylopath: Easy phylogenetic path analysis R. PeerJ, 6, e4718. doi:10.7717/peerj.4718 von Hardenberg, ., & Gonzalez-Voyer, . (2013). Disentangling evolutionary cause-effect relationships phylogenetic confirmatory path analysis. Evolution; International Journal Organic Evolution, 67(2), 378-387. doi:10.1111/j.1558-5646.2012.01790.x *Interface involving SEM `arrow notation` repurposed :* Fox, J., Nie, Z., & Byrnes, J. (2020). Sem: Structural equation models. R package version 3.1-11. https://CRAN.R-project.org/package=sem *Coercing output phylo4d depends upon:* Bolker, B., Butler, M., Cowan, P., de Vienne, D., Eddelbuettel, D., Holder, M., Jombart, T., Kembel, S., Michonneau, F., & Orme, B. (2015). phylobase: Base package phylogenetic structures comparative data. R Package Version 0.8.0. https://CRAN.R-project.org/package=phylobase *Laplace approximation parameter estimation depends upon:* Kristensen, K., Nielsen, ., Berg, C. W., Skaug, H., & Bell, B. M. (2016). TMB: Automatic differentiation Laplace approximation. Journal Statistical Software, 70(5), 1-21. doi:10.18637/jss.v070.i05","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit phylogenetic structural equation model — phylosem","text":"","code":"# Load data set data(rhino, rhino_tree, package=\"phylopath\")  # Run phylosem model = \"   DD -> RS, p1   BM -> LS, p2   BM -> NL, p3   NL -> DD, p4 \" psem = phylosem( sem = model,           data = rhino[,c(\"BM\",\"NL\",\"DD\",\"RS\",\"LS\")],           tree = rhino_tree ) #> NOTE: it is generally simpler to use specifyEquations() or cfa() #>       see ?specifyEquations #> List of estimated fixed and random effects: #>   Coefficient_name Number_of_coefficients   Type #> 1           beta_z                      9  Fixed #> 2             x_vj                    495 Random #> Running nlminb_loop #1 #> Running newton_loop #1  # Convert and plot using phylopath library(phylopath) #>  #> Attaching package: ‘phylopath’ #> The following objects are masked from ‘package:phylosem’: #>  #>     average, best, choice my_fitted_DAG = as_fitted_DAG(psem) coef_plot( my_fitted_DAG ) #> The fitted model does not contain confidence intervals, so showing standard errors instead. Fit the model with `boot` larger than 0 to get confidence intervals, or set `error_bar = \"se\"` to avoid this warning.  plot( my_fitted_DAG )   # Convert to phylo4d to extract estimated traits and Standard errors # for all ancestors and tips in the tree. # In this rhino example, note that species are labeled s1-s100 # and ancestral nodes are not named. (traits_est = as_phylo4d(psem)) #>     label node ancestor  edge.length node.type          BM          NL #> 1      s1    1      107 0.5640308162       tip -0.76690456 -2.01757398 #> 2      s2    2      107 0.5640308162       tip -1.00970438 -1.74246592 #> 3      s3    3      106 0.6358275951       tip -1.22528123 -2.46855326 #> 4      s4    4      105 0.7144448083       tip  1.33053521  0.34055901 #> 5      s5    5      104 1.1830950600       tip  2.49234369  1.22400475 #> 6      s6    6      109 0.0361022107       tip  1.42514860  2.96922655 #> 7      s7    7      109 0.0361022107       tip  0.35610742  2.01122280 #> 8      s8    8      112 0.5022074646       tip -0.53161422  0.18490174 #> 9      s9    9      112 0.5022074646       tip -0.15373314  0.81809201 #> 10    s10   10      111 1.7871837580       tip  1.11171876  1.24302184 #> 11    s11   11      116 0.5913975424       tip  0.19579448  2.13282693 #> 12    s12   12      119 0.0477228892       tip  0.20125048  3.08972748 #> 13    s13   13      119 0.0477228892       tip  1.52219709  2.96228199 #> 14    s14   14      120 0.1142573039       tip -1.00338251  1.86652322 #> 15    s15   15      120 0.1142573039       tip  1.07689653  1.52906374 #> 16    s16   16      121 0.2756963162       tip  1.61531748  3.57241266 #> 17    s17   17      121 0.2756963162       tip -0.17420285  0.43146654 #> 18    s18   18      122 0.5512595516       tip  2.90711896  3.25268633 #> 19    s19   19      123 0.0349638989       tip  2.40453010  2.24981247 #> 20    s20   20      123 0.0349638989       tip  0.82895203  1.20324781 #> 21    s21   21      114 0.8767527377       tip  2.64255460  3.86427495 #> 22    s22   22      113 1.7461743450       tip -0.07719953  3.19026617 #> 23    s23   23      125 0.9075157185       tip -0.30484408  3.51060091 #> 24    s24   24      125 0.9075157185       tip  1.52258759  3.21435348 #> 25    s25   25      126 0.5415591015       tip  1.23860573  2.04363009 #> 26    s26   26      127 0.1089356405       tip  1.95343200  3.06738965 #> 27    s27   27      127 0.1089356405       tip  1.68648719  4.22039397 #> 28    s28   28      130 3.0857795440       tip  1.23934345  2.26507981 #> 29    s29   29      131 1.6399242000       tip -1.10263719 -1.63892351 #> 30    s30   30      132 0.8944032869       tip  0.08301170  0.42665712 #> 31    s31   31      133 0.7715950937       tip  1.01879042  0.03819250 #> 32    s32   32      133 0.7715950937       tip  0.02167732 -0.37157709 #> 33    s33   33      136 0.8699913472       tip  0.73065935  1.95289384 #> 34    s34   34      137 0.8479589114       tip  2.72407349  3.49784027 #> 35    s35   35      137 0.8479589114       tip  3.76646555  4.49878875 #> 36    s36   36      138 0.4591954289       tip -2.33729326  1.74995773 #> 37    s37   37      139 0.1736071099       tip  0.30205947  2.68777644 #> 38    s38   38      139 0.1736071099       tip -1.33960415  1.76434408 #> 39    s39   39      141 2.0905969730       tip  4.27686830  3.21806190 #> 40    s40   40      143 0.0744131178       tip  1.25068016 -0.71254314 #> 41    s41   41      143 0.0744131178       tip  1.41155371 -0.43526905 #> 42    s42   42      144 0.9370864528       tip  0.08393879  0.23591102 #> 43    s43   43      145 0.0881684468       tip  2.84964114  0.68816551 #> 44    s44   44      145 0.0881684468       tip  2.99095373  1.80145127 #> 45    s45   45      147 1.7204295900       tip  5.13749665  4.26473497 #> 46    s46   46      149 1.1842473100       tip  2.58859925  1.56946821 #> 47    s47   47      149 1.1842473100       tip  1.43384898  1.65242204 #> 48    s48   48      150 1.0253154590       tip  2.80876268  3.24344386 #> 49    s49   49      152 0.7195368746       tip  1.22593514  5.02896634 #> 50    s50   50      152 0.7195368746       tip  2.61927222  0.67351377 #> 51    s51   51      153 0.3613256451       tip  2.30223945  1.34901806 #> 52    s52   52      153 0.3613256451       tip  2.56528288  1.45099218 #> 53    s53   53      155 0.3002640020       tip  0.40340933 -1.65526609 #> 54    s54   54      155 0.3002640020       tip  0.88479865 -1.98334601 #> 55    s55   55      154 0.5937157619       tip  0.46893874 -0.62261098 #> 56    s56   56      156 3.2486997580       tip  2.95039314  4.03454344 #> 57    s57   57      161 0.4215356986       tip  1.53656023  0.46891422 #> 58    s58   58      161 0.4215356986       tip  2.50142020  0.45568152 #> 59    s59   59      162 0.0698869058       tip  2.33417280 -0.61028405 #> 60    s60   60      162 0.0698869058       tip  2.39854268  0.90424064 #> 61    s61   61      164 0.9090035873       tip  1.15944783  0.14368777 #> 62    s62   62      165 0.7237639845       tip  0.59250982 -1.00793024 #> 63    s63   63      167 0.3390345394       tip -0.70393275 -1.59874559 #> 64    s64   64      167 0.3390345394       tip  1.58394613  0.45296021 #> 65    s65   65      168 0.3269574705       tip  1.59263345  0.56850859 #> 66    s66   66      168 0.3269574705       tip  2.15658024 -0.88396728 #> 67    s67   67      170 0.4816150364       tip  5.26743199  2.18963416 #> 68    s68   68      171 0.0359279485       tip  1.34622701 -1.84421537 #> 69    s69   69      171 0.0359279485       tip  2.18241698 -0.76580964 #> 70    s70   70      173 0.6413136611       tip  2.93983039 -0.11351013 #> 71    s71   71      175 0.0945133814       tip  3.01129396  1.25866166 #> 72    s72   72      176 0.0006422211       tip  2.59398228  1.21303645 #> 73    s73   73      176 0.0006422211       tip  2.71938915  1.62942984 #> 74    s74   74      174 0.3139612126       tip  2.60745101  0.91920273 #> 75    s75   75      177 0.0359670563       tip  4.86547665  0.44478185 #> 76    s76   76      177 0.0359670563       tip  5.43684487  0.22107243 #> 77    s77   77      180 0.8668137583       tip  1.58687164  1.50654438 #> 78    s78   78      181 0.5981367654       tip  0.09365673  0.40527336 #> 79    s79   79      182 0.0727809267       tip  0.27286020  0.21689207 #> 80    s80   80      182 0.0727809267       tip  2.25220200 -1.07873909 #> 81    s81   81      179 1.5434906440       tip  1.05736541 -0.05289912 #> 82    s82   82      183 0.8078943991       tip  4.69785604  0.33163484 #> 83    s83   83      184 0.4661635151       tip  3.52231773  1.69620670 #> 84    s84   84      185 0.1900157199       tip  1.60779377  2.53614523 #> 85    s85   85      185 0.1900157199       tip  1.90789841  2.74261353 #> 86    s86   86      188 0.2378751898       tip  3.94393984 -1.28344814 #> 87    s87   87      190 0.0040209131       tip  2.67507049 -0.72928762 #> 88    s88   88      190 0.0040209131       tip  4.02248087  1.27038228 #> 89    s89   89      189 0.0295310172       tip  4.11611390  0.89924275 #> 90    s90   90      195 0.3502461608       tip  2.45594624  0.51529773 #> 91    s91   91      196 0.1859710332       tip  4.14053815  2.17333172 #> 92    s92   92      196 0.1859710332       tip  3.16070940 -0.62189645 #> 93    s93   93      194 0.8106943515       tip  2.97788577 -0.22596947 #> 94    s94   94      193 0.8259283637       tip  3.93086602  1.00077297 #> 95    s95   95      197 0.4469879611       tip  1.54045681  0.11089573 #> 96    s96   96      197 0.4469879611       tip  1.04974779  2.05813396 #> 97    s97   97      198 0.2644025504       tip  4.08564283  1.22297875 #> 98    s98   98      198 0.2644025504       tip  3.47019109  1.80421473 #> 99    s99   99      199 0.0717127012       tip -1.51698326 -2.66773226 #> 100  s100  100      199 0.0717127012       tip -1.55493000 -1.25446488 #> 101  <NA>  101        0           NA      root  1.37537396  1.29911665 #> 102  <NA>  102      101 0.3278789676  internal  1.16700652  1.46268576 #> 103  <NA>  103      102 0.0448143702  internal  1.14127151  1.44843940 #> 104  <NA>  104      103 1.7536273230  internal  0.80116123 -0.04630783 #> 105  <NA>  105      104 0.4686502517  internal  0.04035308 -0.94897241 #> 106  <NA>  106      105 0.0786172132  internal -0.22924544 -1.24229608 #> 107  <NA>  107      106 0.0717967789  internal -0.36298395 -1.37170519 #> 108  <NA>  108      103 0.5388417629  internal  0.93634388  1.73643821 #> 109  <NA>  109      108 2.3617784090  internal  0.89097477  2.48450717 #> 110  <NA>  110      108 0.1838847379  internal  0.86994281  1.77647687 #> 111  <NA>  111      110 0.4268121240  internal  0.68585957  1.45889941 #> 112  <NA>  112      111 1.2849762930  internal -0.17453886  0.65800392 #> 113  <NA>  113      110 0.4678215366  internal  0.90278222  2.22643059 #> 114  <NA>  114      113 0.8694216075  internal  1.45174623  2.58275128 #> 115  <NA>  115      114 0.0071530214  internal  1.44654748  2.57522749 #> 116  <NA>  116      115 0.2782021739  internal  0.86447464  2.32881108 #> 117  <NA>  117      116 0.1696001798  internal  0.70138920  2.23479250 #> 118  <NA>  118      117 0.1745800373  internal  0.52173009  2.28117789 #> 119  <NA>  119      118 0.1994944362  internal  0.82540175  2.94643376 #> 120  <NA>  120      118 0.1329600215  internal  0.18250929  1.87312200 #> 121  <NA>  121      117 0.1461010464  internal  0.71125182  2.11498215 #> 122  <NA>  122      115 0.3183401648  internal  1.88123312  2.52235493 #> 123  <NA>  123      122 0.5162956527  internal  1.62540354  1.75259450 #> 124  <NA>  124      102 1.5076279270  internal  1.07467482  2.69406705 #> 125  <NA>  125      124 0.5663931071  internal  0.81605854  3.06517183 #> 126  <NA>  126      124 0.9323497240  internal  1.44328773  2.84469772 #> 127  <NA>  127      126 0.4326234610  internal  1.77783916  3.55452384 #> 128  <NA>  128      101 0.0206999989  internal  1.38852884  1.28879004 #> 129  <NA>  129      128 0.2000464880  internal  1.33869173  1.25256763 #> 130  <NA>  130      129 0.0028896898  internal  1.33645716  1.25093770 #> 131  <NA>  131      130 1.4458553430  internal  0.26389060 -0.03977885 #> 132  <NA>  132      131 0.7455209135  internal  0.33208018  0.02167613 #> 133  <NA>  133      132 0.1228081933  internal  0.37751187 -0.02380741 #> 134  <NA>  134      129 0.6949407786  internal  1.70295554  1.51871663 #> 135  <NA>  135      134 0.9138552433  internal  1.13478525  2.30724483 #> 136  <NA>  136      135 0.6098818644  internal  1.98297090  2.97989486 #> 137  <NA>  137      136 0.0220324358  internal  2.04532689  3.03020353 #> 138  <NA>  138      135 1.0206777830  internal -0.91929472  2.06222134 #> 139  <NA>  139      138 0.2855883190  internal -0.61213304  2.18786984 #> 140  <NA>  140      134 0.0802496379  internal  1.79491314  1.48020658 #> 141  <NA>  141      140 0.2228818440  internal  1.93611785  1.40251215 #> 142  <NA>  142      141 0.2076500851  internal  1.83517586  1.14979654 #> 143  <NA>  143      142 1.8085337700  internal  1.34127779 -0.53915958 #> 144  <NA>  144      142 0.9458604351  internal  1.63368609  0.88198103 #> 145  <NA>  145      144 0.8489180060  internal  2.85678218  1.22689695 #> 146  <NA>  146      140 0.1770607381  internal  1.88563084  1.45696065 #> 147  <NA>  147      146 0.4159884892  internal  2.40357460  2.04245093 #> 148  <NA>  148      147 0.1695261804  internal  2.34525741  2.06207604 #> 149  <NA>  149      148 0.3666560998  internal  2.21751655  1.88955477 #> 150  <NA>  150      148 0.5255879506  internal  2.34756636  2.37022333 #> 151  <NA>  151      150 0.2079515725  internal  2.25494138  2.31503928 #> 152  <NA>  152      151 0.0978270115  internal  2.18389259  2.42967093 #> 153  <NA>  153      151 0.4560382411  internal  2.38302136  1.65964448 #> 154  <NA>  154      146 1.5427023170  internal  0.75523426 -0.91688085 #> 155  <NA>  155      154 0.2934517599  internal  0.68171630 -1.51387805 #> 156  <NA>  156      128 0.0400159638  internal  1.42392811  1.27607295 #> 157  <NA>  157      156 0.4026925133  internal  1.59094851  0.80617095 #> 158  <NA>  158      157 0.7951233038  internal  1.94014906  0.57576258 #> 159  <NA>  159      158 0.3736798197  internal  2.09528413  0.38387613 #> 160  <NA>  160      159 1.1492712710  internal  2.14639670  0.34532781 #> 161  <NA>  161      160 0.1063971509  internal  2.10365653  0.38456695 #> 162  <NA>  162      160 0.4580459438  internal  2.35076674  0.16103746 #> 163  <NA>  163      159 0.2335971502  internal  2.18187420  0.27175804 #> 164  <NA>  164      163 0.5346033834  internal  1.43309091 -0.13103237 #> 165  <NA>  165      164 0.1852396028  internal  1.22940201 -0.32658223 #> 166  <NA>  166      165 0.1474062575  internal  1.19702794 -0.34342541 #> 167  <NA>  167      166 0.2373231876  internal  0.75543298 -0.47728109 #> 168  <NA>  168      166 0.2494002564  internal  1.60632063 -0.23125539 #> 169  <NA>  169      163 0.4262080943  internal  2.93682275  0.38831503 #> 170  <NA>  170      169 0.5357838400  internal  3.31558918  0.40274303 #> 171  <NA>  171      170 0.4456870879  internal  1.82442522 -1.23884620 #> 172  <NA>  172      169 0.3680846598  internal  3.32860306  0.47906468 #> 173  <NA>  173      172 0.0080005555  internal  3.31402225  0.48288912 #> 174  <NA>  174      173 0.3273524485  internal  2.90843309  0.94379679 #> 175  <NA>  175      174 0.2194478311  internal  2.84691345  1.26996664 #> 176  <NA>  176      175 0.0938711603  internal  2.65733422  1.42071746 #> 177  <NA>  177      172 0.6133471602  internal  5.09924499  0.33708989 #> 178  <NA>  178      158 0.3661103260  internal  1.94894404  0.65767175 #> 179  <NA>  179      178 0.1412829703  internal  1.78053559  0.59541556 #> 180  <NA>  180      179 0.6766768859  internal  1.29098355  0.58146426 #> 181  <NA>  181      180 0.2686769929  internal  1.00489189  0.28918765 #> 182  <NA>  182      181 0.5253558386  internal  1.24584098 -0.38427402 #> 183  <NA>  183      178 0.8768792154  internal  3.01524389  1.24025010 #> 184  <NA>  184      183 0.3417308840  internal  2.71906704  1.85162298 #> 185  <NA>  185      184 0.2761477952  internal  2.00389796  2.43773069 #> 186  <NA>  186      157 0.4967710625  internal  1.57881801  0.37044145 #> 187  <NA>  187      186 0.8026320886  internal  2.63989652  0.47536690 #> 188  <NA>  188      187 1.3087289040  internal  3.73176237 -0.25942644 #> 189  <NA>  189      188 0.2083441725  internal  3.71974615  0.52049204 #> 190  <NA>  190      189 0.0255101041  internal  3.37587615  0.28880652 #> 191  <NA>  191      187 0.3703056422  internal  2.82049596  0.73168597 #> 192  <NA>  192      191 0.1968950188  internal  2.73597270  0.72052113 #> 193  <NA>  193      192 0.1534750686  internal  2.96263400  0.63791542 #> 194  <NA>  194      193 0.0152340122  internal  2.96727375  0.62302314 #> 195  <NA>  195      194 0.4604481907  internal  3.10148300  0.65510394 #> 196  <NA>  196      195 0.1642751276  internal  3.45213971  0.73212244 #> 197  <NA>  197      192 0.5324154713  internal  1.72111346  0.97689560 #> 198  <NA>  198      191 0.9118959007  internal  3.65669043  1.41459293 #> 199  <NA>  199      186 2.2775234810  internal -1.48767902 -1.92496075 #>               DD           RS           LS #> 1   -0.792261887 -3.392696532 -0.094767133 #> 2    1.764320772 -1.046718911 -2.146334945 #> 3   -1.806155037 -2.859660611 -0.632068429 #> 4    0.948874128 -0.278689412 -0.134264890 #> 5    1.624151256  0.220814157  0.608236202 #> 6    2.252422051  2.426804694  3.085533985 #> 7    4.108146451  1.633655726  1.223147978 #> 8   -1.160995541  0.999431600  0.517537813 #> 9    1.341758025  1.304985166  1.521502859 #> 10   0.570073147  0.720705268  1.017846421 #> 11   2.828030732  2.001705516 -0.919563025 #> 12   2.980595831  1.521314671  0.131015359 #> 13   1.359162717  2.162885763  1.163026706 #> 14   1.848692884  1.583433981  0.927126010 #> 15   2.141254323  0.189198068  1.812639133 #> 16   1.560178083  2.781747914  3.347392203 #> 17  -0.073939690  0.027354662  0.900742360 #> 18   3.402771712 -0.457261541 -0.106852864 #> 19   2.876235296  0.463291813  1.744751921 #> 20   2.660581053  0.222790773 -0.532153665 #> 21   2.299374032  3.217700305 -1.138669460 #> 22   1.993843377  2.765155326 -0.621091021 #> 23   2.443433385  2.335835676  0.469978073 #> 24   3.979027350  3.226436578  2.780465714 #> 25   2.034137013  0.942969691  3.576663764 #> 26   3.027626293  1.238032443  3.065084710 #> 27   3.714825776  1.176979136  1.534261968 #> 28   0.675597786  2.317952086 -0.218626950 #> 29  -2.974709277 -1.760554760 -1.239583231 #> 30   0.867846728  2.592129904  0.021198341 #> 31  -1.320245499  0.237320570 -0.105135494 #> 32  -1.143376610  0.425657695  0.271740269 #> 33   3.123728954  1.116995185  3.162476646 #> 34   1.753272053  2.688262363  4.250866454 #> 35   1.210588042  1.223837757  2.943572655 #> 36   0.909660193  2.451038343  1.895478114 #> 37   1.859861867  0.828466484  2.481719676 #> 38   2.717730773  0.796806294  1.126178674 #> 39   4.477326061  2.610442179  1.465738306 #> 40   2.277574874  0.484494584  1.791592125 #> 41   1.593822132  1.454823177  0.729183055 #> 42   2.322463839  0.204364321 -0.885061737 #> 43   2.292615149 -1.418461690  3.138543805 #> 44   2.146223656 -0.184209303  3.099199564 #> 45   2.055324236  2.083887955  2.952789127 #> 46   2.486684424  1.457198741  4.701207454 #> 47   1.420995810  1.601339097  1.396442779 #> 48   3.405244971  1.876423665  4.818320993 #> 49   2.446367879  4.942733281  1.918220026 #> 50   0.373382213 -0.811619200  2.145960417 #> 51   0.858730865  2.844229971  2.215893641 #> 52   2.048278126  1.876438183  2.253066255 #> 53  -0.979401859  0.066992787  1.239294862 #> 54  -1.520667823 -0.517780882  0.002562199 #> 55   0.649664697  0.296776545  0.993825267 #> 56   4.379073801  2.422662868  0.795863984 #> 57  -0.328722937  1.480830939 -1.445882168 #> 58   0.646239216  0.424770897 -1.916304907 #> 59   0.835999391  0.217055270 -0.355409430 #> 60   0.142267982  2.659357457 -0.333557662 #> 61   1.587819101  2.699486648 -0.405668792 #> 62   1.082524348 -0.011507182  0.161447095 #> 63  -1.299067758  1.555475543 -0.651822690 #> 64   0.351846112  0.605027979  2.046577980 #> 65  -0.279595862  1.236295365 -0.684431280 #> 66   0.115635072 -0.342677375 -0.311295514 #> 67   2.599415169 -0.513369614  2.115479969 #> 68  -0.943343694 -0.906440767  0.753327404 #> 69  -0.891525122 -0.467958901  1.752160922 #> 70  -0.375173649  1.154414206  0.965969722 #> 71  -0.592328994 -0.336852088  1.329634282 #> 72   0.719152392  1.226426188  0.316414278 #> 73   1.599438191  0.789638349  0.899306546 #> 74  -0.332396124 -0.433700522  0.629458828 #> 75   0.175928921  0.707616811  2.808930860 #> 76  -0.311789389 -1.996944450  3.564422436 #> 77   2.868493105  0.326425814 -0.441878566 #> 78  -0.250515866  1.272618452  0.526962588 #> 79   0.398301132  0.929595781  2.317926260 #> 80   0.382728205 -0.729808449  2.075454233 #> 81   1.380853148 -0.655486117  1.238821897 #> 82   1.096240272  0.151342211  1.187553629 #> 83   0.794919057  3.466323051  1.677363592 #> 84   0.659773370  3.554223820 -1.116737022 #> 85   1.416964480  3.808228110 -0.272035393 #> 86   0.430344619 -0.918540236  3.601938769 #> 87  -1.503773245 -0.173989015  2.884114421 #> 88  -0.529029913  0.420256120  5.698224578 #> 89   1.230771112 -0.287094234  2.761662804 #> 90   0.560078571  2.048855290  1.138288790 #> 91   1.959411459  0.763497433  1.756392549 #> 92   0.698357920  0.787654206  1.640998942 #> 93   0.678480280 -0.093837593  1.648291943 #> 94   0.840604819  0.001959162  3.568538018 #> 95   0.992731804  2.524498697  2.340271301 #> 96   1.033125330  3.258153919  2.484460337 #> 97   0.270032796  3.015785994  2.745792037 #> 98   0.144785071  4.052392486  1.909532374 #> 99  -1.029371553 -1.760670551 -1.074155886 #> 100 -0.954367914  1.702235497 -0.555582075 #> 101  1.308843827  1.116983364  0.941671321 #> 102  1.500843440  1.095518802  0.946854714 #> 103  1.494577889  1.072951763  0.919909252 #> 104  0.798558133 -0.636985822  0.003413918 #> 105  0.285513704 -1.433753796 -0.481099535 #> 106  0.126453352 -1.694516361 -0.600543380 #> 107  0.199419762 -1.801089988 -0.706065112 #> 108  1.633109628  1.327025910  0.877534736 #> 109  3.168548867  2.024896376  2.144656353 #> 110  1.560837730  1.359395853  0.764417737 #> 111  1.135439910  1.220869473  0.851058307 #> 112  0.261217479  1.163432444  0.991981768 #> 113  1.843241992  1.593584710  0.381671289 #> 114  2.293090839  1.445486375  0.169633396 #> 115  2.296740634  1.429809245  0.178562730 #> 116  2.068841007  1.518722645  0.489558785 #> 117  1.712187338  1.434417686  1.083257103 #> 118  1.940872105  1.366000045  1.054468126 #> 119  2.145414094  1.791237720  0.690549218 #> 120  1.978714109  1.030478751  1.275088906 #> 121  1.213570447  1.419050458  1.618787592 #> 122  2.719952322  0.630368111  0.220090980 #> 123  2.766821179  0.352451641  0.593650281 #> 124  2.594464616  1.756013836  1.877177529 #> 125  2.936896160  2.325167049  1.737290454 #> 126  2.707100980  1.227585072  2.682779876 #> 127  3.296961835  1.209751107  2.342513313 #> 128  1.296722306  1.118338487  0.941344078 #> 129  1.164383097  1.118495599  0.943855518 #> 130  1.160313003  1.118077898  0.940846150 #> 131 -0.649041547  0.346875063 -0.021614045 #> 132 -0.524727502  0.907274878  0.035813489 #> 133 -0.695460246  0.768245367  0.047280182 #> 134  1.683466167  1.219494219  1.676302177 #> 135  1.810253231  1.473661832  2.372100281 #> 136  1.964019245  1.607147790  3.098631717 #> 137  1.940204635  1.624383130  3.123261340 #> 138  1.694523083  1.534142041  1.933333163 #> 139  2.150272810  0.980817437  1.834108238 #> 140  1.732274565  1.208837658  1.699781795 #> 141  2.018227402  1.159933763  1.598592939 #> 142  2.040386417  0.970299146  1.517515220 #> 143  1.937808809  0.969671787  1.265570786 #> 144  2.194970191  0.106828516  1.279967184 #> 145  2.218212435 -0.756502792  3.028091758 #> 146  1.612798864  1.224175296  1.831972593 #> 147  1.806870188  1.544144043  2.386029080 #> 148  1.861477377  1.621354858  2.555974674 #> 149  1.896798692  1.586139397  2.744450307 #> 150  1.980146158  1.911214308  2.812690102 #> 151  1.738063572  2.032954829  2.507484513 #> 152  1.667901811  2.039924690  2.405852377 #> 153  1.534247640  2.267440783  2.311944520 #> 154 -0.147891799  0.171198695  0.928999717 #> 155 -0.877011852 -0.091166271  0.725195972 #> 156  1.299761980  1.120926701  0.940209099 #> 157  0.948655082  0.985615977  0.946679770 #> 158  0.826966290  0.854360177  0.652302687 #> 159  0.621612795  0.779146856  0.439322451 #> 160  0.336050797  1.090538403 -0.928180900 #> 161  0.276575654  1.044332560 -1.180755300 #> 162  0.478283058  1.413563401 -0.385856446 #> 163  0.551283293  0.668836582  0.584137161 #> 164  0.594216305  1.017376552  0.175590443 #> 165  0.406613061  0.795359672  0.152480195 #> 166  0.119665632  0.783019034  0.132263730 #> 167 -0.226411699  0.956404490  0.461912941 #> 168 -0.002138993  0.579930789 -0.248365631 #> 169  0.388736091  0.189700133  1.174068323 #> 170  0.679411860 -0.359701226  1.522352945 #> 171 -0.855565241 -0.674511032  1.263190047 #> 172  0.048661117  0.153345062  1.444276295 #> 173  0.042746877  0.162667651  1.428068822 #> 174  0.014082113  0.037885115  1.000794444 #> 175  0.237042152  0.283856183  0.973912293 #> 176  1.156151241  1.005563482  0.609108318 #> 177 -0.064609116 -0.621932444  3.137044171 #> 178  0.972129054  0.867613889  0.725424288 #> 179  1.025171086  0.716639048  0.757475405 #> 180  1.123283232  0.595091884  0.699959101 #> 181  0.621294968  0.630106695  1.031045258 #> 182  0.405464837  0.134241374  2.121178648 #> 183  0.990603910  1.836390418  0.701632784 #> 184  0.953120717  2.926692616  0.486821499 #> 185  1.016547218  3.488081666 -0.392022456 #> 186  0.591549056  0.900698445  1.138580809 #> 187  0.563944049  1.086133686  2.126388552 #> 188  0.268872389 -0.355935806  3.459696990 #> 189  0.080471955 -0.092747344  3.547370950 #> 190 -0.936271794  0.107362828  4.236832864 #> 191  0.634698796  1.579721293  2.204867160 #> 192  0.752897750  1.473613342  2.223438386 #> 193  0.792236063  1.103061208  2.199555594 #> 194  0.795248656  1.086589529  2.171934487 #> 195  0.952624971  1.259177316  1.634498265 #> 196  1.192887579  0.950371055  1.675491901 #> 197  0.936047239  2.472161931  2.356507086 #> 198  0.261511431  3.286631493  2.312114168 #> 199 -0.967327452 -0.014804246 -0.784591384 (traits_SE = as_phylo4d(psem, what=\"Std. Error\")) #>     label node ancestor  edge.length node.type         BM         NL         DD #> 1      s1    1      107 0.5640308162       tip         NA         NA         NA #> 2      s2    2      107 0.5640308162       tip         NA         NA         NA #> 3      s3    3      106 0.6358275951       tip         NA         NA         NA #> 4      s4    4      105 0.7144448083       tip         NA         NA         NA #> 5      s5    5      104 1.1830950600       tip         NA         NA         NA #> 6      s6    6      109 0.0361022107       tip         NA         NA         NA #> 7      s7    7      109 0.0361022107       tip         NA         NA         NA #> 8      s8    8      112 0.5022074646       tip         NA         NA         NA #> 9      s9    9      112 0.5022074646       tip         NA         NA         NA #> 10    s10   10      111 1.7871837580       tip         NA         NA         NA #> 11    s11   11      116 0.5913975424       tip         NA         NA         NA #> 12    s12   12      119 0.0477228892       tip         NA         NA         NA #> 13    s13   13      119 0.0477228892       tip         NA         NA         NA #> 14    s14   14      120 0.1142573039       tip         NA         NA         NA #> 15    s15   15      120 0.1142573039       tip         NA         NA         NA #> 16    s16   16      121 0.2756963162       tip         NA         NA         NA #> 17    s17   17      121 0.2756963162       tip         NA         NA         NA #> 18    s18   18      122 0.5512595516       tip         NA         NA         NA #> 19    s19   19      123 0.0349638989       tip         NA         NA         NA #> 20    s20   20      123 0.0349638989       tip         NA         NA         NA #> 21    s21   21      114 0.8767527377       tip         NA         NA         NA #> 22    s22   22      113 1.7461743450       tip         NA         NA         NA #> 23    s23   23      125 0.9075157185       tip         NA         NA         NA #> 24    s24   24      125 0.9075157185       tip         NA         NA         NA #> 25    s25   25      126 0.5415591015       tip         NA         NA         NA #> 26    s26   26      127 0.1089356405       tip         NA         NA         NA #> 27    s27   27      127 0.1089356405       tip         NA         NA         NA #> 28    s28   28      130 3.0857795440       tip         NA         NA         NA #> 29    s29   29      131 1.6399242000       tip         NA         NA         NA #> 30    s30   30      132 0.8944032869       tip         NA         NA         NA #> 31    s31   31      133 0.7715950937       tip         NA         NA         NA #> 32    s32   32      133 0.7715950937       tip         NA         NA         NA #> 33    s33   33      136 0.8699913472       tip         NA         NA         NA #> 34    s34   34      137 0.8479589114       tip         NA         NA         NA #> 35    s35   35      137 0.8479589114       tip         NA         NA         NA #> 36    s36   36      138 0.4591954289       tip         NA         NA         NA #> 37    s37   37      139 0.1736071099       tip         NA         NA         NA #> 38    s38   38      139 0.1736071099       tip         NA         NA         NA #> 39    s39   39      141 2.0905969730       tip         NA         NA         NA #> 40    s40   40      143 0.0744131178       tip         NA         NA         NA #> 41    s41   41      143 0.0744131178       tip         NA         NA         NA #> 42    s42   42      144 0.9370864528       tip         NA         NA         NA #> 43    s43   43      145 0.0881684468       tip         NA         NA         NA #> 44    s44   44      145 0.0881684468       tip         NA         NA         NA #> 45    s45   45      147 1.7204295900       tip         NA         NA         NA #> 46    s46   46      149 1.1842473100       tip         NA         NA         NA #> 47    s47   47      149 1.1842473100       tip         NA         NA         NA #> 48    s48   48      150 1.0253154590       tip         NA         NA         NA #> 49    s49   49      152 0.7195368746       tip         NA         NA         NA #> 50    s50   50      152 0.7195368746       tip         NA         NA         NA #> 51    s51   51      153 0.3613256451       tip         NA         NA         NA #> 52    s52   52      153 0.3613256451       tip         NA         NA         NA #> 53    s53   53      155 0.3002640020       tip         NA         NA         NA #> 54    s54   54      155 0.3002640020       tip         NA         NA         NA #> 55    s55   55      154 0.5937157619       tip         NA         NA         NA #> 56    s56   56      156 3.2486997580       tip         NA         NA         NA #> 57    s57   57      161 0.4215356986       tip         NA         NA         NA #> 58    s58   58      161 0.4215356986       tip         NA         NA         NA #> 59    s59   59      162 0.0698869058       tip         NA         NA         NA #> 60    s60   60      162 0.0698869058       tip         NA         NA         NA #> 61    s61   61      164 0.9090035873       tip         NA         NA         NA #> 62    s62   62      165 0.7237639845       tip         NA         NA         NA #> 63    s63   63      167 0.3390345394       tip         NA         NA         NA #> 64    s64   64      167 0.3390345394       tip         NA         NA         NA #> 65    s65   65      168 0.3269574705       tip         NA         NA         NA #> 66    s66   66      168 0.3269574705       tip         NA         NA         NA #> 67    s67   67      170 0.4816150364       tip         NA         NA         NA #> 68    s68   68      171 0.0359279485       tip         NA         NA         NA #> 69    s69   69      171 0.0359279485       tip         NA         NA         NA #> 70    s70   70      173 0.6413136611       tip         NA         NA         NA #> 71    s71   71      175 0.0945133814       tip         NA         NA         NA #> 72    s72   72      176 0.0006422211       tip         NA         NA         NA #> 73    s73   73      176 0.0006422211       tip         NA         NA         NA #> 74    s74   74      174 0.3139612126       tip         NA         NA         NA #> 75    s75   75      177 0.0359670563       tip         NA         NA         NA #> 76    s76   76      177 0.0359670563       tip         NA         NA         NA #> 77    s77   77      180 0.8668137583       tip         NA         NA         NA #> 78    s78   78      181 0.5981367654       tip         NA         NA         NA #> 79    s79   79      182 0.0727809267       tip         NA         NA         NA #> 80    s80   80      182 0.0727809267       tip         NA         NA         NA #> 81    s81   81      179 1.5434906440       tip         NA         NA         NA #> 82    s82   82      183 0.8078943991       tip         NA         NA         NA #> 83    s83   83      184 0.4661635151       tip         NA         NA         NA #> 84    s84   84      185 0.1900157199       tip         NA         NA         NA #> 85    s85   85      185 0.1900157199       tip         NA         NA         NA #> 86    s86   86      188 0.2378751898       tip         NA         NA         NA #> 87    s87   87      190 0.0040209131       tip         NA         NA         NA #> 88    s88   88      190 0.0040209131       tip         NA         NA         NA #> 89    s89   89      189 0.0295310172       tip         NA         NA         NA #> 90    s90   90      195 0.3502461608       tip         NA         NA         NA #> 91    s91   91      196 0.1859710332       tip         NA         NA         NA #> 92    s92   92      196 0.1859710332       tip         NA         NA         NA #> 93    s93   93      194 0.8106943515       tip         NA         NA         NA #> 94    s94   94      193 0.8259283637       tip         NA         NA         NA #> 95    s95   95      197 0.4469879611       tip         NA         NA         NA #> 96    s96   96      197 0.4469879611       tip         NA         NA         NA #> 97    s97   97      198 0.2644025504       tip         NA         NA         NA #> 98    s98   98      198 0.2644025504       tip         NA         NA         NA #> 99    s99   99      199 0.0717127012       tip         NA         NA         NA #> 100  s100  100      199 0.0717127012       tip         NA         NA         NA #> 101  <NA>  101        0           NA      root 1.22322635 1.61418789 1.72525631 #> 102  <NA>  102      101 0.3278789676  internal 1.30071498 1.71644304 1.83454740 #> 103  <NA>  103      102 0.0448143702  internal 1.31380257 1.73371363 1.85300633 #> 104  <NA>  104      103 1.7536273230  internal 1.37288352 1.81167774 1.93633497 #> 105  <NA>  105      104 0.4686502517  internal 0.97714845 1.28945978 1.37818444 #> 106  <NA>  106      105 0.0786172132  internal 0.91260141 1.20428254 1.28714636 #> 107  <NA>  107      106 0.0717967789  internal 0.91028188 1.20122166 1.28387486 #> 108  <NA>  108      103 0.5388417629  internal 1.39262282 1.83772602 1.96417557 #> 109  <NA>  109      108 2.3617784090  internal 0.30636597 0.40428514 0.43210304 #> 110  <NA>  110      108 0.1838847379  internal 1.36644386 1.80317986 1.92725237 #> 111  <NA>  111      110 0.4268121240  internal 1.51142111 1.99449403 2.13173041 #> 112  <NA>  112      111 1.2849762930  internal 1.07717612 1.42145781 1.51926493 #> 113  <NA>  113      110 0.4678215366  internal 1.44312706 1.90437217 2.03540748 #> 114  <NA>  114      113 0.8694216075  internal 0.97715330 1.28946619 1.37819129 #> 115  <NA>  115      114 0.0071530214  internal 0.97044019 1.28060746 1.36872301 #> 116  <NA>  116      115 0.2782021739  internal 0.88470104 1.16746480 1.24779527 #> 117  <NA>  117      116 0.1696001798  internal 0.74979954 0.98944675 1.05752823 #> 118  <NA>  118      117 0.1745800373  internal 0.64458322 0.85060171 0.90912959 #> 119  <NA>  119      118 0.1994944362  internal 0.34098890 0.44997408 0.48093573 #> 120  <NA>  120      118 0.1329600215  internal 0.49663196 0.65536300 0.70045697 #> 121  <NA>  121      117 0.1461010464  internal 0.70970095 0.93653205 1.00097259 #> 122  <NA>  122      115 0.3183401648  internal 0.98266488 1.29673935 1.38596490 #> 123  <NA>  123      122 0.5162956527  internal 0.29920899 0.39484068 0.42200872 #> 124  <NA>  124      102 1.5076279270  internal 1.49221553 1.96915006 2.10464258 #> 125  <NA>  125      124 0.5663931071  internal 1.32624680 1.75013522 1.87055785 #> 126  <NA>  126      124 0.9323497240  internal 1.07523634 1.41889804 1.51652903 #> 127  <NA>  127      126 0.4326234610  internal 0.51732351 0.68266788 0.72964063 #> 128  <NA>  128      101 0.0206999989  internal 1.20634454 1.59191040 1.70144596 #> 129  <NA>  129      128 0.2000464880  internal 1.25574263 1.65709685 1.77111774 #> 130  <NA>  130      129 0.0028896898  internal 1.25884677 1.66119313 1.77549587 #> 131  <NA>  131      130 1.4458553430  internal 1.57854250 2.08306843 2.22639940 #> 132  <NA>  132      131 0.7455209135  internal 1.18802246 1.56773230 1.67560422 #> 133  <NA>  133      132 0.1228081933  internal 1.13999603 1.50435591 1.60786705 #> 134  <NA>  134      129 0.6949407786  internal 1.20257065 1.58693032 1.69612321 #> 135  <NA>  135      134 0.9138552433  internal 1.38787894 1.83146592 1.95748473 #> 136  <NA>  136      135 0.6098818644  internal 1.11567674 1.47226380 1.57356677 #> 137  <NA>  137      136 0.0220324358  internal 1.11103546 1.46613910 1.56702064 #> 138  <NA>  138      135 1.0206777830  internal 0.97459019 1.28608387 1.37457624 #> 139  <NA>  139      138 0.2855883190  internal 0.63244106 0.83457873 0.89200411 #> 140  <NA>  140      134 0.0802496379  internal 1.16877200 1.54232911 1.64845310 #> 141  <NA>  141      140 0.2228818440  internal 1.28533627 1.69614907 1.81285704 #> 142  <NA>  142      141 0.2076500851  internal 1.37909625 1.81987615 1.94509749 #> 143  <NA>  143      142 1.8085337700  internal 0.43767253 0.57755925 0.61729973 #> 144  <NA>  144      142 0.9458604351  internal 1.34725029 1.77785174 1.90018148 #> 145  <NA>  145      144 0.8489180060  internal 0.47300751 0.62418782 0.66713669 #> 146  <NA>  146      140 0.1770607381  internal 1.23211080 1.62591193 1.73778706 #> 147  <NA>  147      146 0.4159884892  internal 1.24623965 1.64455658 1.75771460 #> 148  <NA>  148      147 0.1695261804  internal 1.21017992 1.59697162 1.70685543 #> 149  <NA>  149      148 0.3666560998  internal 1.32044920 1.74248462 1.86238084 #> 150  <NA>  150      148 0.5255879506  internal 1.12365874 1.48279697 1.58482469 #> 151  <NA>  151      150 0.2079515725  internal 1.00451302 1.32557048 1.41677983 #> 152  <NA>  152      151 0.0978270115  internal 1.01302888 1.33680815 1.42879073 #> 153  <NA>  153      151 0.4560382411  internal 0.87087189 1.14921565 1.22829044 #> 154  <NA>  154      146 1.5427023170  internal 1.08223037 1.42812747 1.52639352 #> 155  <NA>  155      154 0.2934517599  internal 0.80865458 1.06711274 1.14053822 #> 156  <NA>  156      128 0.0400159638  internal 1.23140386 1.62497905 1.73678999 #> 157  <NA>  157      156 0.4026925133  internal 1.35918408 1.79359975 1.91701308 #> 158  <NA>  158      157 0.7951233038  internal 1.27358140 1.68063717 1.79627781 #> 159  <NA>  159      158 0.3736798197  internal 1.22652022 1.61853452 1.72990203 #> 160  <NA>  160      159 1.1492712710  internal 0.94650940 1.24902804 1.33497069 #> 161  <NA>  161      160 0.1063971509  internal 0.87500944 1.15467562 1.23412609 #> 162  <NA>  162      160 0.4580459438  internal 0.41761870 0.55109591 0.58901551 #> 163  <NA>  163      159 0.2335971502  internal 1.16536491 1.53783306 1.64364769 #> 164  <NA>  164      163 0.5346033834  internal 1.07091058 1.41318971 1.51042792 #> 165  <NA>  165      164 0.1852396028  internal 0.95150270 1.25561727 1.34201330 #> 166  <NA>  166      165 0.1474062575  internal 0.86886630 1.14656904 1.22546172 #> 167  <NA>  167      166 0.2373231876  internal 0.80532548 1.06271962 1.13584282 #> 168  <NA>  168      166 0.2494002564  internal 0.79695072 1.05166816 1.12403094 #> 169  <NA>  169      163 0.4262080943  internal 1.10440718 1.45739233 1.55767202 #> 170  <NA>  170      169 0.5357838400  internal 0.98598517 1.30112086 1.39064788 #> 171  <NA>  171      170 0.4456870879  internal 0.30302820 0.39988057 0.42739540 #> 172  <NA>  172      169 0.3680846598  internal 0.89979805 1.18738704 1.26908831 #> 173  <NA>  173      172 0.0080005555  internal 0.89702741 1.18373086 1.26518056 #> 174  <NA>  174      173 0.3273524485  internal 0.77398260 1.02135908 1.09163636 #> 175  <NA>  175      174 0.2194478311  internal 0.47112032 0.62169745 0.66447497 #> 176  <NA>  176      175 0.0938711603  internal 0.04095469 0.05404443 0.05776309 #> 177  <NA>  177      172 0.6133471602  internal 0.30345934 0.40044951 0.42800348 #> 178  <NA>  178      158 0.3661103260  internal 1.25575706 1.65711591 1.77113810 #> 179  <NA>  179      178 0.1412829703  internal 1.28149047 1.69107409 1.80743287 #> 180  <NA>  180      179 0.6766768859  internal 1.16906592 1.54271697 1.64886765 #> 181  <NA>  181      180 0.2686769929  internal 1.04754240 1.38235271 1.47746911 #> 182  <NA>  182      181 0.5253558386  internal 0.42744225 0.56405922 0.60287079 #> 183  <NA>  183      178 0.8768792154  internal 1.16688879 1.53984400 1.64579700 #> 184  <NA>  184      183 0.3417308840  internal 0.93124907 1.22889027 1.31344729 #> 185  <NA>  185      184 0.2761477952  internal 0.65326012 0.86205188 0.92136761 #> 186  <NA>  186      157 0.4967710625  internal 1.52763597 2.01589140 2.15460008 #> 187  <NA>  187      186 0.8026320886  internal 1.36167014 1.79688039 1.92051945 #> 188  <NA>  188      187 1.3087289040  internal 0.75183416 0.99213166 1.06039788 #> 189  <NA>  189      188 0.2083441725  internal 0.26849975 0.35431631 0.37869597 #> 190  <NA>  190      189 0.0255101041  internal 0.10068396 0.13286406 0.14200612 #> 191  <NA>  191      187 0.3703056422  internal 1.13842365 1.50228097 1.60564934 #> 192  <NA>  192      191 0.1968950188  internal 1.00764393 1.32970209 1.42119572 #> 193  <NA>  193      192 0.1534750686  internal 0.94424288 1.24603711 1.33177395 #> 194  <NA>  194      193 0.0152340122  internal 0.94588044 1.24819805 1.33408359 #> 195  <NA>  195      194 0.4604481907  internal 0.80011381 1.05584222 1.12849221 #> 196  <NA>  196      195 0.1642751276  internal 0.62798360 0.82869660 0.88571724 #> 197  <NA>  197      192 0.5324154713  internal 0.95527123 1.26059028 1.34732849 #> 198  <NA>  198      191 0.9118959007  internal 0.79057873 1.04325957 1.11504378 #> 199  <NA>  199      186 2.2775234810  internal 0.43045988 0.56804132 0.60712690 #>             RS         LS #> 1           NA         NA #> 2           NA         NA #> 3           NA         NA #> 4           NA         NA #> 5           NA         NA #> 6           NA         NA #> 7           NA         NA #> 8           NA         NA #> 9           NA         NA #> 10          NA         NA #> 11          NA         NA #> 12          NA         NA #> 13          NA         NA #> 14          NA         NA #> 15          NA         NA #> 16          NA         NA #> 17          NA         NA #> 18          NA         NA #> 19          NA         NA #> 20          NA         NA #> 21          NA         NA #> 22          NA         NA #> 23          NA         NA #> 24          NA         NA #> 25          NA         NA #> 26          NA         NA #> 27          NA         NA #> 28          NA         NA #> 29          NA         NA #> 30          NA         NA #> 31          NA         NA #> 32          NA         NA #> 33          NA         NA #> 34          NA         NA #> 35          NA         NA #> 36          NA         NA #> 37          NA         NA #> 38          NA         NA #> 39          NA         NA #> 40          NA         NA #> 41          NA         NA #> 42          NA         NA #> 43          NA         NA #> 44          NA         NA #> 45          NA         NA #> 46          NA         NA #> 47          NA         NA #> 48          NA         NA #> 49          NA         NA #> 50          NA         NA #> 51          NA         NA #> 52          NA         NA #> 53          NA         NA #> 54          NA         NA #> 55          NA         NA #> 56          NA         NA #> 57          NA         NA #> 58          NA         NA #> 59          NA         NA #> 60          NA         NA #> 61          NA         NA #> 62          NA         NA #> 63          NA         NA #> 64          NA         NA #> 65          NA         NA #> 66          NA         NA #> 67          NA         NA #> 68          NA         NA #> 69          NA         NA #> 70          NA         NA #> 71          NA         NA #> 72          NA         NA #> 73          NA         NA #> 74          NA         NA #> 75          NA         NA #> 76          NA         NA #> 77          NA         NA #> 78          NA         NA #> 79          NA         NA #> 80          NA         NA #> 81          NA         NA #> 82          NA         NA #> 83          NA         NA #> 84          NA         NA #> 85          NA         NA #> 86          NA         NA #> 87          NA         NA #> 88          NA         NA #> 89          NA         NA #> 90          NA         NA #> 91          NA         NA #> 92          NA         NA #> 93          NA         NA #> 94          NA         NA #> 95          NA         NA #> 96          NA         NA #> 97          NA         NA #> 98          NA         NA #> 99          NA         NA #> 100         NA         NA #> 101 1.34657639 2.14730314 #> 102 1.43187897 2.28332994 #> 103 1.44628631 2.30630446 #> 104 1.51132499 2.41001765 #> 105 1.07568402 1.71532760 #> 106 1.00462806 1.60201901 #> 107 1.00207463 1.59794722 #> 108 1.53305479 2.44466885 #> 109 0.33725989 0.53780774 #> 110 1.50423594 2.39871319 #> 111 1.66383269 2.65321238 #> 112 1.18579847 1.89092040 #> 113 1.58865188 2.53332612 #> 114 1.07568936 1.71533613 #> 115 1.06829930 1.70355164 #> 116 0.97391422 1.55304153 #> 117 0.82540927 1.31622975 #> 118 0.70958294 1.13152858 #> 119 0.37537419 0.59858630 #> 120 0.54671228 0.87180869 #> 121 0.78126714 1.24583899 #> 122 1.08175673 1.72501138 #> 123 0.32938120 0.52524408 #> 124 1.64269043 2.61949810 #> 125 1.45998542 2.32814958 #> 126 1.18366308 1.88751522 #> 127 0.56949037 0.90813151 #> 128 1.32799223 2.11766810 #> 129 1.38237161 2.20438358 #> 130 1.38578878 2.20983273 #> 131 1.73772260 2.77104010 #> 132 1.30782254 2.08550473 #> 133 1.25495314 2.00119713 #> 134 1.32383778 2.11104325 #> 135 1.52783254 2.43634124 #> 136 1.22818149 1.95850601 #> 137 1.22307219 1.95035852 #> 138 1.07286779 1.71083674 #> 139 0.69621637 1.11021372 #> 140 1.28663087 2.05171168 #> 141 1.41494947 2.25633350 #> 142 1.51816420 2.42092373 #> 143 0.48180739 0.76830882 #> 144 1.48310690 2.36501999 #> 145 0.52070554 0.83033733 #> 146 1.35635675 2.16289927 #> 147 1.37191036 2.18770166 #> 148 1.33221436 2.12440088 #> 149 1.45360319 2.31797223 #> 150 1.23696839 1.97251795 #> 151 1.10580803 1.76336452 #> 152 1.11518263 1.77831364 #> 153 0.95869054 1.52876526 #> 154 1.19136239 1.89979285 #> 155 0.89019924 1.41954636 #> 156 1.35557853 2.16165828 #> 157 1.49624409 2.38596907 #> 158 1.40200925 2.23569852 #> 159 1.35020242 2.15308533 #> 160 1.04195534 1.66154254 #> 161 0.96324532 1.53602848 #> 162 0.45973133 0.73310547 #> 163 1.28288021 2.04573073 #> 164 1.17890112 1.87992161 #> 165 1.04745215 1.67030797 #> 166 0.95648271 1.52524456 #> 167 0.88653444 1.41370232 #> 168 0.87731517 1.39900092 #> 169 1.21577551 1.93872296 #> 170 1.08541183 1.73083996 #> 171 0.33358554 0.53194849 #> 172 0.99053361 1.57954346 #> 173 0.98748358 1.57467976 #> 174 0.85203094 1.35868171 #> 175 0.51862805 0.82702448 #> 176 0.04508456 0.07189359 #> 177 0.33406015 0.53270532 #> 178 1.38238750 2.20440892 #> 179 1.41071586 2.24958242 #> 180 1.28695443 2.05222763 #> 181 1.15317650 1.83890013 #> 182 0.47054549 0.75035015 #> 183 1.28455776 2.04840581 #> 184 1.02515615 1.63475390 #> 185 0.71913482 1.14676037 #> 186 1.68168266 2.68167663 #> 187 1.49898084 2.39033320 #> 188 0.82764906 1.31980140 #> 189 0.29557524 0.47133579 #> 190 0.11083692 0.17674487 #> 191 1.25322220 1.99843690 #> 192 1.10925466 1.76886067 #> 193 1.03946026 1.65756379 #> 194 1.04126295 1.66043843 #> 195 0.88079722 1.40455354 #> 196 0.69130942 1.10238891 #> 197 1.05160070 1.67692341 #> 198 0.87030062 1.38781525 #> 199 0.47386741 0.75564742  # Convert to sem and plot library(sem) my_sem = as_sem(psem) pathDiagram( model = my_sem,                   style = \"traditional\",                   edge.labels = \"values\" ) #> Loading required namespace: DiagrammeR effects( my_sem ) #>  #>  Total Effects (column on row) #>            BM         NL         DD #> DD  0.6296696  0.6750692  0.0000000 #> RS -0.1387108 -0.1487120 -0.2202914 #> LS  1.3366815  0.0000000  0.0000000 #> NL  0.9327482  0.0000000  0.0000000 #>  #>  Direct Effects #>           BM        NL         DD #> DD 0.0000000 0.6750692  0.0000000 #> RS 0.0000000 0.0000000 -0.2202914 #> LS 1.3366815 0.0000000  0.0000000 #> NL 0.9327482 0.0000000  0.0000000 #>  #>  Indirect Effects #>            BM        NL DD #> DD  0.6296696  0.000000  0 #> RS -0.1387108 -0.148712  0 #> LS  0.0000000  0.000000  0 #> NL  0.0000000  0.000000  0  # Plot using semPlot if( require(semPlot) ){   myplot = semPlotModel( my_sem )   semPaths( my_sem,                    nodeLabels = myplot@Vars$name ) } #> Loading required package: semPlot"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem_control.html","id":null,"dir":"Reference","previous_headings":"","what":"Detailed control for phylosem structure — phylosem_control","title":"Detailed control for phylosem structure — phylosem_control","text":"Define list control parameters.  Note format input likely change rapidly phylosem","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detailed control for phylosem structure — phylosem_control","text":"","code":"phylosem_control(   nlminb_loops = 1,   newton_loops = 1,   trace = 0,   eval.max = 1000,   iter.max = 1000,   getsd = TRUE,   quiet = FALSE,   run_model = TRUE,   getJointPrecision = FALSE )"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detailed control for phylosem structure — phylosem_control","text":"nlminb_loops Integer number times call nlminb. newton_loops Integer number Newton steps running nlminb. trace Parameter values printed every `trace` iteration outer optimizer. Passed `control` nlminb. eval.max Maximum number evaluations objective function allowed. Passed `control` nlminb. iter.max Maximum number iterations allowed. Passed `control` nlminb. getsd Boolean indicating whether call sdreport quiet Boolean indicating whether run model printing messages terminal ; run_model Boolean indicating whether estimate parameters (default), instead return model inputs compiled TMB object without running; getJointPrecision whether get joint precision matrix.  Passed sdreport.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/phylosem_control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detailed control for phylosem structure — phylosem_control","text":"S3 object class \"phylosem_control\" specifies detailed model settings, allowing user specification also specifying default values","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Print parameter estimates and standard errors. — print.phylosem","title":"Print parameter estimates and standard errors. — print.phylosem","text":"Print parameter estimates","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print parameter estimates and standard errors. — print.phylosem","text":"","code":"# S3 method for phylosem print(x, ...)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print parameter estimates and standard errors. — print.phylosem","text":"x Output phylosem ... used","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print parameter estimates and standard errors. — print.phylosem","text":"prints (invisibly returns) output nlminb","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/reinstalling.html","id":null,"dir":"Reference","previous_headings":"","what":"Reinstalling binary dependencies — reinstalling","title":"Reinstalling binary dependencies — reinstalling","text":"phylosem package depends several upstream packages, uses way depends heavily internal (binary) structure. Sometimes, therefore, installing update one packages require re-install binary-compatible version phylosem, .e. version compiled updated version upstream package. development tools (compilers etc.) installed, able re-install binary-compatible version package running install.packages(\"phylosem\", type=\"source\"). want install development version phylosem instead, can use remotes::install_github(\"James-Thorson-NOAA/phylosem\"). (Windows, can install development tools following instructions https://cran.r-project.org/bin/windows/Rtools/; MacOS, see https://mac.r-project.org/tools/.) development tools /want install (install packages compiled code source), can revert upstream package(s) previous binary version. example, using checkpoint package: similar recipe (substituting Matrix TMB TMB phylosem) can used get warnings incompatibility TMB Matrix.","code":"## load (installing if necessary) the checkpoint package while (!require(\"checkpoint\")) install.packages(\"checkpoint\") ## retrieve build date of installed version of phylosem bd <- as.character(asDateBuilt(       packageDescription(\"phylosem\",fields=\"Built\"))) oldrepo <- getOption(\"repos\") use_mran_snapshot(bd) ## was setSnapshot() pre-checkpoint v1.0.0 install.packages(\"TMB\") options(repos=oldrepo) ## restore original repo"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/reinstalling.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reinstalling binary dependencies — reinstalling","text":"Copied glmmTMB permission","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/summary.phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"summarize phylosem — summary.phylosem","title":"summarize phylosem — summary.phylosem","text":"Summarize phylosem output phylosem, including calculating intercepts tree root","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/summary.phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarize phylosem — summary.phylosem","text":"","code":"# S3 method for phylosem summary(object, ...)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/summary.phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarize phylosem — summary.phylosem","text":"object Output phylosem ... used","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/summary.phylosem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"summarize phylosem — summary.phylosem","text":"Data-frame containing estimated intercepts, path coefficients, variance-covariance parameters         well standard errors","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/vcov.phylosem.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract Variance-Covariance Matrix — vcov.phylosem","title":"Extract Variance-Covariance Matrix — vcov.phylosem","text":"extract covariance fixed effects, fixed random effects.","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/vcov.phylosem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract Variance-Covariance Matrix — vcov.phylosem","text":"","code":"# S3 method for phylosem vcov(object, which = c(\"fixed\", \"random\", \"both\"), ...)"},{"path":"https://james-thorson-noaa.github.io/phylosem/reference/vcov.phylosem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract Variance-Covariance Matrix — vcov.phylosem","text":"object output phylosem whether extract covariance among fixed effects, random effects, ... ignored, method compatibility","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-113","dir":"Changelog","previous_headings":"","what":"phylosem 1.1.3","title":"phylosem 1.1.3","text":"CRAN release: 2024-02-01 Removing fit_tmb simplify code remove unnecessary warnings Adding codecov extra tests Fixing R-CMD-check force build Matrix/TMB source","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-112","dir":"Changelog","previous_headings":"","what":"phylosem 1.1.2","title":"phylosem 1.1.2","text":"CRAN release: 2023-12-20 Adding new functions provide warning Matrix version doesn’t match ’s expected TMB","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-111","dir":"Changelog","previous_headings":"","what":"phylosem 1.1.1","title":"phylosem 1.1.1","text":"CRAN release: 2023-11-26 Re-adding phylosignal SUGGESTS Re-adding phylosignal Fisheries vignette adding arguemnt as_phylo4d allow easy extraction standard errors","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-110","dir":"Changelog","previous_headings":"","what":"phylosem 1.1.0","title":"phylosem 1.1.0","text":"CRAN release: 2023-10-06 Adding new S3 generic functions: logLik vcov Adding vignette “fisheries” associated paper “Trees fishes: neglected role phylogenetic comparative methods fisheries science” accepted Fish Fisheries","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-102","dir":"Changelog","previous_headings":"","what":"phylosem 1.0.2","title":"phylosem 1.0.2","text":"CRAN release: 2023-09-22 Fixed bug arising data missing observations earliest tips first inputted variable Updating vignette show confidence intervals alpha/kappa/lambda well lnalppha/lnkappa/logitlambda","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-101","dir":"Changelog","previous_headings":"","what":"phylosem 1.0.1","title":"phylosem 1.0.1","text":"CRAN release: 2023-09-19 Address request CRAN use Suggests packages conditionally examples Continuing use Suggests packages unconditionally vignettes based Wickham guidance online","code":""},{"path":"https://james-thorson-noaa.github.io/phylosem/news/index.html","id":"phylosem-100","dir":"Changelog","previous_headings":"","what":"phylosem 1.0.0","title":"phylosem 1.0.0","text":"CRAN release: 2023-08-25 Attempting fix warnings","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index 2da2ab9..0e01d84 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -27,12 +27,6 @@
   <url>
     <loc>https://james-thorson-noaa.github.io/phylosem/news/index.html</loc>
   </url>
-  <url>
-    <loc>https://james-thorson-noaa.github.io/phylosem/reference/Mlifehist_ver1_0.html</loc>
-  </url>
-  <url>
-    <loc>https://james-thorson-noaa.github.io/phylosem/reference/TMBAIC.html</loc>
-  </url>
   <url>
     <loc>https://james-thorson-noaa.github.io/phylosem/reference/as_fitted_DAG.html</loc>
   </url>
@@ -69,21 +63,24 @@
   <url>
     <loc>https://james-thorson-noaa.github.io/phylosem/reference/compare_phylosem.html</loc>
   </url>
-  <url>
-    <loc>https://james-thorson-noaa.github.io/phylosem/reference/fit_tmb.html</loc>
-  </url>
   <url>
     <loc>https://james-thorson-noaa.github.io/phylosem/reference/index.html</loc>
   </url>
   <url>
     <loc>https://james-thorson-noaa.github.io/phylosem/reference/list_parameters.html</loc>
   </url>
+  <url>
+    <loc>https://james-thorson-noaa.github.io/phylosem/reference/Mlifehist_ver1_0.html</loc>
+  </url>
   <url>
     <loc>https://james-thorson-noaa.github.io/phylosem/reference/parse_path.html</loc>
   </url>
   <url>
     <loc>https://james-thorson-noaa.github.io/phylosem/reference/phylosem.html</loc>
   </url>
+  <url>
+    <loc>https://james-thorson-noaa.github.io/phylosem/reference/phylosem_control.html</loc>
+  </url>
   <url>
     <loc>https://james-thorson-noaa.github.io/phylosem/reference/print.phylosem.html</loc>
   </url>