rendering bookdown

docs/404.html

@@ -23,7 +23,7 @@
 
 
 
-<meta name="date" content="2022-04-26" />
+<meta name="date" content="2022-04-28" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -134,8 +134,7 @@
 
 <ul class="summary">
 <li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
-<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-access"><i class="fa fa-check"></i><b>1.1</b> Data access</a></li>
-<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.2</b> Data processing</a></li>
+<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.1</b> Data processing</a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html"><i class="fa fa-check"></i><b>2</b> Selecting species of interest</a><ul>
 <li class="chapter" data-level="2.1" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html#prepare-libraries"><i class="fa fa-check"></i><b>2.1</b> Prepare libraries</a></li>

docs/adding-covariates-to-checklist-data.html

@@ -23,7 +23,7 @@
 
 
 
-<meta name="date" content="2022-04-26" />
+<meta name="date" content="2022-04-28" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -134,8 +134,7 @@
 
 <ul class="summary">
 <li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
-<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-access"><i class="fa fa-check"></i><b>1.1</b> Data access</a></li>
-<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.2</b> Data processing</a></li>
+<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.1</b> Data processing</a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html"><i class="fa fa-check"></i><b>2</b> Selecting species of interest</a><ul>
 <li class="chapter" data-level="2.1" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html#prepare-libraries"><i class="fa fa-check"></i><b>2.1</b> Prepare libraries</a></li>
@@ -321,7 +320,7 @@ <h2><span class="header-section-number">8.1</span> Prepare libraries and data</h
 <span id="cb69-19"><a href="adding-covariates-to-checklist-data.html#cb69-19"></a><span class="kw">library</span>(sf)</span>
 <span id="cb69-20"><a href="adding-covariates-to-checklist-data.html#cb69-20"></a></span>
 <span id="cb69-21"><a href="adding-covariates-to-checklist-data.html#cb69-21"></a><span class="co"># load saved data object</span></span>
-<span id="cb69-22"><a href="adding-covariates-to-checklist-data.html#cb69-22"></a><span class="kw">load</span>(<span class="st">&quot;data/01_data_prelim_processing.rdata&quot;</span>)</span></code></pre></div>
+<span id="cb69-22"><a href="adding-covariates-to-checklist-data.html#cb69-22"></a><span class="kw">load</span>(<span class="st">&quot;results/02_data_prelim_processing.rdata&quot;</span>)</span></code></pre></div>
 </div>
 <div id="spatial-subsampling" class="section level2">
 <h2><span class="header-section-number">8.2</span> Spatial subsampling</h2>
@@ -465,7 +464,7 @@ <h3><span class="header-section-number">8.3.1</span> Count absences after tempor
 <span id="cb75-5"><a href="adding-covariates-to-checklist-data.html#cb75-5"></a>  )</span>
 <span id="cb75-6"><a href="adding-covariates-to-checklist-data.html#cb75-6"></a></span>
 <span id="cb75-7"><a href="adding-covariates-to-checklist-data.html#cb75-7"></a><span class="co"># save data</span></span>
-<span id="cb75-8"><a href="adding-covariates-to-checklist-data.html#cb75-8"></a><span class="kw">write_csv</span>(data_presence_prop, <span class="st">&quot;data/results/data_class_balance.csv&quot;</span>)</span></code></pre></div>
+<span id="cb75-8"><a href="adding-covariates-to-checklist-data.html#cb75-8"></a><span class="kw">write_csv</span>(data_presence_prop, <span class="st">&quot;results/08_data-class-balance.csv&quot;</span>)</span></code></pre></div>
 <div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb76-1"><a href="adding-covariates-to-checklist-data.html#cb76-1"></a><span class="co"># bind all spatially and temporally thinned absences rows for data frame</span></span>
 <span id="cb76-2"><a href="adding-covariates-to-checklist-data.html#cb76-2"></a>dataSubsample &lt;-<span class="st"> </span><span class="kw">bind_rows</span>(dataSubsample)</span>
 <span id="cb76-3"><a href="adding-covariates-to-checklist-data.html#cb76-3"></a></span>
@@ -503,7 +502,7 @@ <h3><span class="header-section-number">8.3.1</span> Count absences after tempor
 <h2><span class="header-section-number">8.4</span> Add checklist calibration index</h2>
 <p>Load the CCI computed in the previous section. The CCI was the lone observer’s expertise score for single-observer checklists, and the highest expertise score among observers for group checklists.</p>
 <div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb77-1"><a href="adding-covariates-to-checklist-data.html#cb77-1"></a><span class="co"># read in obs score and extract numbers</span></span>
-<span id="cb77-2"><a href="adding-covariates-to-checklist-data.html#cb77-2"></a>expertiseScore &lt;-<span class="st"> </span><span class="kw">read_csv</span>(<span class="st">&quot;data/03_data-obsExpertise-score.csv&quot;</span>) <span class="op">%&gt;%</span></span>
+<span id="cb77-2"><a href="adding-covariates-to-checklist-data.html#cb77-2"></a>expertiseScore &lt;-<span class="st"> </span><span class="kw">read_csv</span>(<span class="st">&quot;results/04_data-obsExpertise-score.csv&quot;</span>) <span class="op">%&gt;%</span></span>
 <span id="cb77-3"><a href="adding-covariates-to-checklist-data.html#cb77-3"></a><span class="st">  </span><span class="kw">mutate</span>(<span class="dt">numObserver =</span> <span class="kw">str_extract</span>(observer, <span class="st">&quot;</span><span class="ch">\\</span><span class="st">d+&quot;</span>)) <span class="op">%&gt;%</span></span>
 <span id="cb77-4"><a href="adding-covariates-to-checklist-data.html#cb77-4"></a><span class="st">  </span>dplyr<span class="op">::</span><span class="kw">select</span>(<span class="op">-</span>observer)</span>
 <span id="cb77-5"><a href="adding-covariates-to-checklist-data.html#cb77-5"></a></span>
@@ -641,7 +640,7 @@ <h3><span class="header-section-number">8.7.3</span> Link environmental covariat
 <span id="cb82-7"><a href="adding-covariates-to-checklist-data.html#cb82-7"></a>)</span></code></pre></div>
 <p>Save data to file.</p>
 <div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb83-1"><a href="adding-covariates-to-checklist-data.html#cb83-1"></a><span class="co"># write to file</span></span>
-<span id="cb83-2"><a href="adding-covariates-to-checklist-data.html#cb83-2"></a><span class="kw">write_csv</span>(dataSubsample, <span class="dt">path =</span> <span class="kw">glue</span>(<span class="st">&quot;data/04_data-covars-2.5km.csv&quot;</span>))</span></code></pre></div>
+<span id="cb83-2"><a href="adding-covariates-to-checklist-data.html#cb83-2"></a><span class="kw">write_csv</span>(dataSubsample, <span class="dt">path =</span> <span class="kw">glue</span>(<span class="st">&quot;results/08_data-covars-2.5km.csv&quot;</span>))</span></code></pre></div>
 
 </div>
 </div>

docs/checking-temporal-sampling-frequency.html

@@ -23,7 +23,7 @@
 
 
 
-<meta name="date" content="2022-04-26" />
+<meta name="date" content="2022-04-28" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -134,8 +134,7 @@
 
 <ul class="summary">
 <li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
-<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-access"><i class="fa fa-check"></i><b>1.1</b> Data access</a></li>
-<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.2</b> Data processing</a></li>
+<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.1</b> Data processing</a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html"><i class="fa fa-check"></i><b>2</b> Selecting species of interest</a><ul>
 <li class="chapter" data-level="2.1" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html#prepare-libraries"><i class="fa fa-check"></i><b>2.1</b> Prepare libraries</a></li>
@@ -316,7 +315,7 @@ <h2><span class="header-section-number">7.1</span> Load libraries</h2>
 <h2><span class="header-section-number">7.2</span> Load checklist data</h2>
 <p>Here we load filtered checklist data and convert to UTM 43N coordinates.</p>
 <div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb62-1"><a href="checking-temporal-sampling-frequency.html#cb62-1"></a><span class="co"># load checklist data</span></span>
-<span id="cb62-2"><a href="checking-temporal-sampling-frequency.html#cb62-2"></a><span class="kw">load</span>(<span class="st">&quot;data/01_data_prelim_processing.rdata&quot;</span>)</span>
+<span id="cb62-2"><a href="checking-temporal-sampling-frequency.html#cb62-2"></a><span class="kw">load</span>(<span class="st">&quot;results/02_data_prelim_processing.rdata&quot;</span>)</span>
 <span id="cb62-3"><a href="checking-temporal-sampling-frequency.html#cb62-3"></a></span>
 <span id="cb62-4"><a href="checking-temporal-sampling-frequency.html#cb62-4"></a><span class="co"># get checklists</span></span>
 <span id="cb62-5"><a href="checking-temporal-sampling-frequency.html#cb62-5"></a>data &lt;-<span class="st"> </span><span class="kw">distinct</span>(</span>

docs/examining-spatial-sampling-bias.html

@@ -23,7 +23,7 @@
 
 
 
-<meta name="date" content="2022-04-26" />
+<meta name="date" content="2022-04-28" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -134,8 +134,7 @@
 
 <ul class="summary">
 <li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
-<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-access"><i class="fa fa-check"></i><b>1.1</b> Data access</a></li>
-<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.2</b> Data processing</a></li>
+<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.1</b> Data processing</a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html"><i class="fa fa-check"></i><b>2</b> Selecting species of interest</a><ul>
 <li class="chapter" data-level="2.1" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html#prepare-libraries"><i class="fa fa-check"></i><b>2.1</b> Prepare libraries</a></li>
@@ -327,7 +326,7 @@ <h2><span class="header-section-number">6.1</span> Prepare libraries</h2>
 <h2><span class="header-section-number">6.2</span> Read checklist data</h2>
 <p>Read in checklist data with distance to nearest neighbouring site, and the distance to the nearest road.</p>
 <div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb54-1"><a href="examining-spatial-sampling-bias.html#cb54-1"></a><span class="co"># read from local file</span></span>
-<span id="cb54-2"><a href="examining-spatial-sampling-bias.html#cb54-2"></a>chkCovars &lt;-<span class="st"> </span><span class="kw">read_csv</span>(<span class="st">&quot;data/03_data-covars-perChklist.csv&quot;</span>)</span></code></pre></div>
+<span id="cb54-2"><a href="examining-spatial-sampling-bias.html#cb54-2"></a>chkCovars &lt;-<span class="st"> </span><span class="kw">read_csv</span>(<span class="st">&quot;results/04_data-covars-perChklist.csv&quot;</span>)</span></code></pre></div>
 <div id="spatially-explicit-filter-on-checklists-1" class="section level3">
 <h3><span class="header-section-number">6.2.1</span> Spatially explicit filter on checklists</h3>
 <p>We filter the checklists by the boundary of the study area. This is <em>not</em> the extent.</p>
@@ -383,7 +382,7 @@ <h3><span class="header-section-number">6.3.2</span> Table: Distance to roads</h
 <span id="cb57-11"><a href="examining-spatial-sampling-bias.html#cb57-11"></a>    <span class="kw">vars</span>(value),</span>
 <span id="cb57-12"><a href="examining-spatial-sampling-bias.html#cb57-12"></a>    <span class="kw">list</span>(<span class="op">~</span><span class="st"> </span><span class="kw">mean</span>(.), <span class="op">~</span><span class="st"> </span><span class="kw">sd</span>(.), <span class="op">~</span><span class="st"> </span><span class="kw">min</span>(.), <span class="op">~</span><span class="st"> </span><span class="kw">max</span>(.))</span>
 <span id="cb57-13"><a href="examining-spatial-sampling-bias.html#cb57-13"></a>  ) <span class="op">%&gt;%</span></span>
-<span id="cb57-14"><a href="examining-spatial-sampling-bias.html#cb57-14"></a><span class="st">  </span><span class="kw">write_csv</span>(<span class="st">&quot;data/results/distance_roads_sites.csv&quot;</span>)</span></code></pre></div>
+<span id="cb57-14"><a href="examining-spatial-sampling-bias.html#cb57-14"></a><span class="st">  </span><span class="kw">write_csv</span>(<span class="st">&quot;results/06_distance-roads-sites.csv&quot;</span>)</span></code></pre></div>
 </div>
 <div id="distance-to-nearest-neighbouring-site" class="section level3">
 <h3><span class="header-section-number">6.3.3</span> Distance to nearest neighbouring site</h3>

docs/index.html

@@ -23,7 +23,7 @@
 
 
 
-<meta name="date" content="2022-04-26" />
+<meta name="date" content="2022-04-28" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -134,8 +134,7 @@
 
 <ul class="summary">
 <li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
-<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-access"><i class="fa fa-check"></i><b>1.1</b> Data access</a></li>
-<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.2</b> Data processing</a></li>
+<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#data-processing"><i class="fa fa-check"></i><b>1.1</b> Data processing</a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html"><i class="fa fa-check"></i><b>2</b> Selecting species of interest</a><ul>
 <li class="chapter" data-level="2.1" data-path="selecting-species-of-interest.html"><a href="selecting-species-of-interest.html#prepare-libraries"><i class="fa fa-check"></i><b>2.1</b> Prepare libraries</a></li>
@@ -297,18 +296,14 @@ <h1>
             <section class="normal" id="section-">
 <div id="header">
 <h1 class="title">Source code and supplementary material for <em>Using citizen science to parse climatic and landcover influences on bird occupancy within a tropical biodiversity hotspot</em></h1>
-<p class="date"><em>2022-04-26</em></p>
+<p class="date"><em>2022-04-28</em></p>
 </div>
 <div id="introduction" class="section level1">
 <h1><span class="header-section-number">Section 1</span> Introduction</h1>
-<p>This is the readable version containing analysis that models associations between environmental predictors (climate and landcover) and citizen science observations of birds across the Nilgiri and Anamalai Hills of the Western Ghats Biodiversity Hotspot.</p>
+<p>This is the readable version containing analysis that models associations between environmental predictors (climate and landcover) and citizen science observations of birds across the Nilgiri and Anamalai Hills of the Western Ghats Biodiversity hotspot.</p>
 <p>Methods and format are derived from <a href="https://cornelllabofornithology.github.io/ebird-best-practices/" class="uri">https://cornelllabofornithology.github.io/ebird-best-practices/</a>.</p>
-<div id="data-access" class="section level2">
-<h2><span class="header-section-number">1.1</span> Data access</h2>
-<p>The data used in this work are available from <a href="http://ebird.org/data/download">eBird</a>.</p>
-</div>
 <div id="data-processing" class="section level2">
-<h2><span class="header-section-number">1.2</span> Data processing</h2>
+<h2><span class="header-section-number">1.1</span> Data processing</h2>
 <p>The data processing for this project is described in the following sections. Navigate through them using the links in the sidebar.</p>
 <hr />
 <div class="figure">