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<!DOCTYPE html>
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<title>Mutivariate analysis for spatio-temporal data</title>
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<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Mutivariate analysis for spatio-temporal data</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<p>Here is the link of the gith repos: <code>https://github.com/balglave/spatio-temp_tuto.git</code></p>
<section id="bering-sea-case-study" class="level1">
<h1>Bering Sea case study</h1>
<section id="load-toy-example-for-ordination" class="level2">
<h2 class="anchored" data-anchor-id="load-toy-example-for-ordination">Load toy example for ordination</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># load data set</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>example <span class="ot">=</span> <span class="fu">load_example</span>( <span class="at">data_set=</span><span class="st">"ordination"</span> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="configure-models-with-the-function-make_settings" class="level2">
<h2 class="anchored" data-anchor-id="configure-models-with-the-function-make_settings">Configure models with the function <code>make_settings</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Make settings:</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="co"># including modifications from default settings to match </span></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="co"># analysis in original paper</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>settings <span class="ot">=</span> <span class="fu">make_settings</span>( <span class="at">n_x=</span><span class="dv">50</span>,</span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a> <span class="at">Region=</span>example<span class="sc">$</span>Region,</span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="at">purpose=</span><span class="st">"EOF3"</span>,</span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> <span class="at">n_categories=</span><span class="dv">2</span>,</span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a> <span class="at">ObsModel=</span><span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">1</span>),</span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a> <span class="at">RhoConfig=</span><span class="fu">c</span>(<span class="st">"Beta1"</span><span class="ot">=</span><span class="dv">0</span>,<span class="st">"Beta2"</span><span class="ot">=</span><span class="dv">0</span>,<span class="st">"Epsilon1"</span><span class="ot">=</span><span class="dv">0</span>,<span class="st">"Epsilon2"</span><span class="ot">=</span><span class="dv">0</span>) )</span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a><span class="fu">help</span>(make_settings)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="fit-the-model" class="level2">
<h2 class="anchored" data-anchor-id="fit-the-model">Fit the model</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Run model (including settings to speed up run)</span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>fit <span class="ot">=</span> <span class="fu">fit_model</span>( <span class="at">settings=</span>settings,</span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a> <span class="at">Lat_i=</span>example<span class="sc">$</span>sampling_data[,<span class="st">'Lat'</span>],</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a> <span class="at">Lon_i=</span>example<span class="sc">$</span>sampling_data[,<span class="st">'Lon'</span>],</span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a> <span class="at">t_i=</span>example<span class="sc">$</span>sampling_data[,<span class="st">'Year'</span>],</span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a> <span class="at">c_i=</span>example<span class="sc">$</span>sampling_data[,<span class="st">'species_number'</span>]<span class="sc">-</span><span class="dv">1</span>,</span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a> <span class="at">b_i=</span>example<span class="sc">$</span>sampling_data[,<span class="st">'Catch_KG'</span>],</span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a> <span class="at">a_i=</span>example<span class="sc">$</span>sampling_data[,<span class="st">'AreaSwept_km2'</span>],</span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a> <span class="at">newtonsteps=</span><span class="dv">0</span>,</span>
<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a> <span class="at">Use_REML=</span><span class="cn">TRUE</span> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="plot-the-results" class="level2">
<h2 class="anchored" data-anchor-id="plot-the-results">Plot the results</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Plot results, including spatial term Omega1</span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>results <span class="ot">=</span> <span class="fu">plot</span>( fit,</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="at">check_residuals=</span><span class="cn">FALSE</span>,</span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> <span class="at">plot_set=</span><span class="fu">c</span>(<span class="dv">3</span>,<span class="dv">16</span>),</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> <span class="at">category_names =</span> <span class="fu">c</span>(<span class="st">"pollock"</span>, <span class="st">"cod"</span>, <span class="st">"arrowtooth"</span>, <span class="st">"snow_crab"</span>, <span class="st">"yellowfin"</span>) )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="plot-maps" class="level2">
<h2 class="anchored" data-anchor-id="plot-maps">Plot maps</h2>
<p>Spatial Factor maps are in <code>results$Factors$Rotated_projected_factors</code>.</p>
<div class="cell" data-layout-align="center" data-fig.asp="1">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="spatio-temp-tuto_files/figure-html/unnamed-chunk-8-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="plot-time-loadings" class="level2">
<h2 class="anchored" data-anchor-id="plot-time-loadings">Plot time loadings</h2>
<div class="cell" data-layout-align="center" data-fig.asp="0.5">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="spatio-temp-tuto_files/figure-html/unnamed-chunk-9-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="comparing-loadings-to-environmental-variables" class="level2">
<h2 class="anchored" data-anchor-id="comparing-loadings-to-environmental-variables">Comparing loadings to environmental variables</h2>
<div class="cell" data-layout-align="center" data-fig.asp="0.5">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="spatio-temp-tuto_files/figure-html/unnamed-chunk-10-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
</section>
<section id="bay-of-biscay-case-study" class="level1">
<h1>Bay of Biscay case study</h1>
<section id="load-evhoe-data" class="level2">
<h2 class="anchored" data-anchor-id="load-evhoe-data">Load EVHOE data</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co"># EVHOE data</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="fu">load</span>(<span class="st">"data/EVHOE_2008_2019.RData"</span>)</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="co"># Grid data</span></span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a><span class="fu">load</span>(<span class="st">"data/gridpolygon_sf.RData"</span>)</span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>gridpolygon_sp <span class="ot"><-</span> sf<span class="sc">::</span><span class="fu">as_Spatial</span>(gridpolygon_sf)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="spatio-temp-tuto_files/figure-html/unnamed-chunk-13-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="filter-some-species-of-interest" class="level2">
<h2 class="anchored" data-anchor-id="filter-some-species-of-interest">Filter some species of interest</h2>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="spatio-temp-tuto_files/figure-html/unnamed-chunk-15-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="prepare-data-with-make_settings" class="level2">
<h2 class="anchored" data-anchor-id="prepare-data-with-make_settings">Prepare data with <code>make_settings</code></h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>Catch_df_4 <span class="ot"><-</span> Catch_df_3 <span class="sc">%>%</span> </span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">pivot_wider</span>(<span class="at">names_from =</span> scientificname,<span class="at">values_from =</span> CatchWgt,<span class="at">values_fn =</span> mean) <span class="sc">%>%</span> </span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">as.data.frame</span>()</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a>Catch_df_6 <span class="ot"><-</span> Catch_df_5 <span class="ot"><-</span> Catch_df_4</span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a>Catch_df_5<span class="sc">$</span>spp <span class="ot"><-</span> <span class="cn">NA</span></span>
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a>Catch_df_5<span class="sc">$</span>catch <span class="ot"><-</span> <span class="cn">NA</span></span>
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span>(spp_i <span class="cf">in</span> species_to_select){</span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">print</span>(spp_i)</span>
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a> test <span class="ot"><-</span> Catch_df_4[,spp_i]</span>
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a> Catch_df_5<span class="sc">$</span>spp <span class="ot"><-</span> <span class="fu">rep</span>(spp_i,<span class="fu">length</span>(test))</span>
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a> Catch_df_5<span class="sc">$</span>catch <span class="ot"><-</span> test</span>
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-15"><a href="#cb6-15" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span>(spp_i <span class="sc">==</span> species_to_select[<span class="dv">1</span>]){</span>
<span id="cb6-16"><a href="#cb6-16" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-17"><a href="#cb6-17" aria-hidden="true" tabindex="-1"></a> Catch_df_6 <span class="ot"><-</span> Catch_df_5</span>
<span id="cb6-18"><a href="#cb6-18" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-19"><a href="#cb6-19" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb6-20"><a href="#cb6-20" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-21"><a href="#cb6-21" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span>(spp_i <span class="sc">!=</span> species_to_select[<span class="dv">1</span>]){</span>
<span id="cb6-22"><a href="#cb6-22" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-23"><a href="#cb6-23" aria-hidden="true" tabindex="-1"></a> Catch_df_6 <span class="ot"><-</span> <span class="fu">rbind</span>(Catch_df_5,Catch_df_6)</span>
<span id="cb6-24"><a href="#cb6-24" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-25"><a href="#cb6-25" aria-hidden="true" tabindex="-1"></a> } </span>
<span id="cb6-26"><a href="#cb6-26" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb6-27"><a href="#cb6-27" aria-hidden="true" tabindex="-1"></a>}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] "Merluccius_merluccius"
[1] "Lepidorhombus_whiffiagonis"
[1] "Micromesistius_poutassou"
[1] "Trachurus_trachurus"
[1] "Lophius_piscatorius"
[1] "Lophius_budegassa"</code></pre>
</div>
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Make settings:</span></span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="co"># including modifications from default settings to match </span></span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="co"># analysis in original paper</span></span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a>settings <span class="ot">=</span> <span class="fu">make_settings</span>( <span class="at">n_x=</span><span class="dv">100</span>,</span>
<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a> <span class="at">Region=</span><span class="st">"user"</span>,</span>
<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a> <span class="co"># Region="EVHOE",</span></span>
<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a> <span class="at">purpose=</span><span class="st">"EOF3"</span>,</span>
<span id="cb8-8"><a href="#cb8-8" aria-hidden="true" tabindex="-1"></a> <span class="at">n_categories=</span><span class="dv">2</span>,</span>
<span id="cb8-9"><a href="#cb8-9" aria-hidden="true" tabindex="-1"></a> <span class="at">ObsModel=</span><span class="fu">c</span>(<span class="dv">2</span>,<span class="dv">1</span>),</span>
<span id="cb8-10"><a href="#cb8-10" aria-hidden="true" tabindex="-1"></a> <span class="at">RhoConfig=</span><span class="fu">c</span>(<span class="st">"Beta1"</span><span class="ot">=</span><span class="dv">3</span>,<span class="st">"Beta2"</span><span class="ot">=</span><span class="dv">3</span>,<span class="st">"Epsilon1"</span><span class="ot">=</span><span class="dv">0</span>,<span class="st">"Epsilon2"</span><span class="ot">=</span><span class="dv">0</span>),</span>
<span id="cb8-11"><a href="#cb8-11" aria-hidden="true" tabindex="-1"></a> <span class="at">use_anisotropy=</span><span class="cn">FALSE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="fit-the-model-1" class="level2">
<h2 class="anchored" data-anchor-id="fit-the-model-1">Fit the model</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>c_i_vec <span class="ot"><-</span> <span class="fu">as.numeric</span>(<span class="fu">as.factor</span>(Catch_df_6<span class="sc">$</span>spp))</span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(Catch_df_6)[<span class="dv">2</span>] <span class="ot"><-</span> <span class="st">"Lon"</span></span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(Catch_df_6)[<span class="dv">3</span>] <span class="ot"><-</span> <span class="st">"Lat"</span></span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a>Catch_df_6<span class="sc">$</span>catch[<span class="fu">which</span>(<span class="fu">is.na</span>(Catch_df_6<span class="sc">$</span>catch))] <span class="ot"><-</span> <span class="dv">0</span></span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a>gridpolygon_sp<span class="sc">@</span>data<span class="sc">$</span>Lon <span class="ot"><-</span> <span class="fu">coordinates</span>(gridpolygon_sp)[,<span class="dv">1</span>]</span>
<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a>gridpolygon_sp<span class="sc">@</span>data<span class="sc">$</span>Lat <span class="ot"><-</span> <span class="fu">coordinates</span>(gridpolygon_sp)[,<span class="dv">2</span>]</span>
<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a>gridpolygon_sp<span class="sc">@</span>data<span class="sc">$</span>Area_km2 <span class="ot"><-</span> <span class="fu">rep</span>(<span class="dv">1</span>,<span class="fu">length</span>(gridpolygon_sp<span class="sc">@</span>data<span class="sc">$</span>Lat))</span>
<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a><span class="co"># Run model (including settings to speed up run)</span></span>
<span id="cb9-13"><a href="#cb9-13" aria-hidden="true" tabindex="-1"></a>fit <span class="ot">=</span> <span class="fu">fit_model</span>( <span class="at">settings=</span>settings,</span>
<span id="cb9-14"><a href="#cb9-14" aria-hidden="true" tabindex="-1"></a> <span class="at">Lat_i=</span>Catch_df_6[,<span class="st">"Lat"</span>],</span>
<span id="cb9-15"><a href="#cb9-15" aria-hidden="true" tabindex="-1"></a> <span class="at">Lon_i=</span>Catch_df_6[,<span class="st">"Lon"</span>],</span>
<span id="cb9-16"><a href="#cb9-16" aria-hidden="true" tabindex="-1"></a> <span class="at">observations_LL =</span> Catch_df_6[,<span class="fu">c</span>(<span class="st">"Lat"</span>,<span class="st">"Lon"</span>)],</span>
<span id="cb9-17"><a href="#cb9-17" aria-hidden="true" tabindex="-1"></a> <span class="at">t_i=</span>Catch_df_6<span class="sc">$</span>Year,</span>
<span id="cb9-18"><a href="#cb9-18" aria-hidden="true" tabindex="-1"></a> <span class="at">c_i=</span>c_i_vec<span class="dv">-1</span>,</span>
<span id="cb9-19"><a href="#cb9-19" aria-hidden="true" tabindex="-1"></a> <span class="at">b_i=</span>Catch_df_6<span class="sc">$</span>catch,</span>
<span id="cb9-20"><a href="#cb9-20" aria-hidden="true" tabindex="-1"></a> <span class="at">a_i=</span> <span class="fu">rep</span>(<span class="fu">as_units</span>(<span class="dv">1</span>, <span class="st">"kg"</span>),<span class="fu">nrow</span>(Catch_df_6)),</span>
<span id="cb9-21"><a href="#cb9-21" aria-hidden="true" tabindex="-1"></a> <span class="at">newtonsteps=</span><span class="dv">0</span>,<span class="at">REML=</span>T,</span>
<span id="cb9-22"><a href="#cb9-22" aria-hidden="true" tabindex="-1"></a> <span class="at">input_grid =</span> gridpolygon_sp<span class="sc">@</span>data)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>results <span class="ot">=</span> <span class="fu">plot</span>( fit,</span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a> <span class="at">check_residuals=</span><span class="cn">FALSE</span>,</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a> <span class="at">plot_set=</span><span class="fu">c</span>(<span class="dv">3</span>,<span class="dv">16</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p><strong>Exercice:</strong></p>
<ul>
<li><p>Plot spatial factors and temporal loadings forthe Bay of Biscay case study.</p></li>
<li><p>Modify the species to make something ecologically relevant.</p></li>
<li><p>Change the type of rotation between the spatial factors using the function <code>plot_factors</code> (below is a reference to understand how the rotations work)</p></li>
</ul>
<p>Hannachi, A., Jolliffe, I. T., & Stephenson, D. B. (2007). Empirical orthogonal functions and related techniques in atmospheric science: A review. International Journal of Climatology: A Journal of the Royal Meteorological Society, 27(9), 1119-1152.</p>
<ul>
<li><p>Modify the observation model (type <code>?make_data</code>)).</p></li>
<li><p>Dig in the codes of VAST and explain the overall structure of the model (<code>https://github.com/James-Thorson-NOAA/VAST/tree/main/inst/executables</code>) - if anyone want to recode it from scratch ;)</p></li>
</ul>
<p>Another toy example is available in <code>https://github.com/James-Thorson-NOAA/VAST/wiki/Ordination</code> for computing correlation among species.</p>
</section>
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