Update docs

docs/_sources/ug-graphem.rst

@@ -4,7 +4,5 @@ GraphEM
 .. toctree::
     :maxdepth: 1
 
-    notebooks/graphem-cli
-    .. notebooks/graphem-real-pages2k
-    .. notebooks/graphem-ppe-pages2k
-    .. notebooks/graphem-quickstart
+    notebooks/graphem-real-pages2k
+    notebooks/graphem-cli

docs/genindex.html

@@ -172,6 +172,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/index.html

@@ -174,6 +174,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/climate-io.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/climate-ops.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/compare.html

@@ -176,6 +176,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/graphem-cli.html

@@ -55,7 +55,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="API Reference" href="../ug-api.html" />
-    <link rel="prev" title="GraphEM" href="../ug-graphem.html" />
+    <link rel="prev" title="Reconstructing the tropical Pacific SST with PAGES2k and GraphEM" href="graphem-real-pages2k.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2 current active"><a class="current reference internal" href="#">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>
@@ -782,12 +783,12 @@ <h2>Leveraging the CLI<a class="headerlink" href="#Leveraging-the-CLI" title="Pe
                   <!-- Previous / next buttons -->
 <div class="prev-next-area">
     <a class="left-prev"
-       href="../ug-graphem.html"
+       href="graphem-real-pages2k.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">GraphEM</p>
+        <p class="prev-next-title">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</p>
       </div>
     </a>
     <a class="right-next"

docs/notebooks/graphem-real-pages2k.html

@@ -54,6 +54,8 @@
     <script>DOCUMENTATION_OPTIONS.pagename = 'notebooks/graphem-real-pages2k';</script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="Running GraphEM with the Command Line Interface (CLI)" href="graphem-cli.html" />
+    <link rel="prev" title="GraphEM" href="../ug-graphem.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -137,7 +139,7 @@
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
     <div class="bd-toc-item navbar-nav active">
         <p aria-level="2" class="caption" role="heading"><span class="caption-text">User Guide</span></p>
-<ul class="nav bd-sidenav">
+<ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../ug-installation.html">Installation</a></li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-pp2k.html">pseudoPAGES2k</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
 <li class="toctree-l2"><a class="reference internal" href="pp2k-pdb-load-viz.html">Loading and Visualization</a></li>
@@ -175,7 +177,8 @@
 <li class="toctree-l2"><a class="reference internal" href="lmr-cli.html">Running DA with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l1 current active has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
+<li class="toctree-l2 current active"><a class="current reference internal" href="#">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>
@@ -1248,6 +1251,24 @@ <h2>Comparison to the LMR/PDA based reconstruction<a class="headerlink" href="#C
                 <footer class="bd-footer-article">
                   <!-- Previous / next buttons -->
 <div class="prev-next-area">
+    <a class="left-prev"
+       href="../ug-graphem.html"
+       title="previous page">
+      <i class="fa-solid fa-angle-left"></i>
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">previous</p>
+        <p class="prev-next-title">GraphEM</p>
+      </div>
+    </a>
+    <a class="right-next"
+       href="graphem-cli.html"
+       title="next page">
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">next</p>
+        <p class="prev-next-title">Running GraphEM with the Command Line Interface (CLI)</p>
+      </div>
+      <i class="fa-solid fa-angle-right"></i>
+    </a>
 </div>
                 </footer>
 

docs/notebooks/lmr-assim-no-calib.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/lmr-cli.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/lmr-pages2k-iCESM-dOTC-BC.html

@@ -176,6 +176,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/lmr-pages2k-iCESM-dOTC.html

@@ -176,6 +176,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/lmr-pages2k-iCESM.html

@@ -176,6 +176,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/lmr-pages2k.html

@@ -176,6 +176,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/lmr-real-pages2k.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/pp2k-dashboards.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/pp2k-pdb-filter.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/pp2k-pdb-load-viz.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/pp2k-ppe-graphem.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/pp2k-ppe-pda.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/proxy-analysis.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/proxy-composites.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/proxy-dups.html

@@ -176,6 +176,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/proxy-io.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>

docs/notebooks/proxy-ops.html

@@ -178,6 +178,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
 </li>