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2 changes: 1 addition & 1 deletion 04-spatial-operations.md
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At this point, there are three identical (in all but row names) versions of `canterbury_height`, one created using the `[` operator, one created via an intermediary selection object, and another using **sf**'s convenience function `st_filter()`.
<!-- RL: commented out for now as old. Todo: if we ever update that vignette uncomment the next line. -->
<!-- To explore spatial subsetting in more detail, see the supplementary vignettes on `subsetting` and [`tidyverse-pitfalls`](https://geocompr.github.io/geocompkg/articles/) on the [geocompkg website](https://geocompr.github.io/geocompkg/articles/). -->
The next section explores different types of spatial relation, also known as binary predicates, that can be used to identify whether or not two features are spatially related or not.
The next section explores different types of spatial relation, also known as binary predicates, that can be used to identify whether two features are spatially related or not.

### Topological relations

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<p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-12-11.</p>
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<p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-12-11.</p>
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<p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-12-11.</p>
<p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-12-14.</p>
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<p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-12-11.</p>
<p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-12-14.</p>
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<p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-12-11.</p>
<p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-12-14.</p>
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<code class="sourceCode R"><span><span class="co"># presence-absence matrix</span></span>
<span><span class="va">pa</span> <span class="op">=</span> <span class="fu">vegan</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/vegan/man/decostand.html">decostand</a></span><span class="op">(</span><span class="va">comm</span>, <span class="st">"pa"</span><span class="op">)</span> <span class="co"># 100 rows (sites), 69 columns (species)</span></span>
<span><span class="co"># keep only sites in which at least one species was found</span></span>
<span><span class="va">pa</span> <span class="op">=</span> <span class="va">pa</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/colSums.html">rowSums</a></span><span class="op">(</span><span class="va">pa</span><span class="op">)</span> <span class="op">!=</span> <span class="fl">0</span>, <span class="op">]</span> <span class="co"># 84 rows, 69 columns</span></span></code></pre></div>
<span><span class="va">pa</span> <span class="op">=</span> <span class="va">pa</span><span class="op">[</span><span class="fu"><a href="https://rspatial.github.io/terra/reference/rowSums.html">rowSums</a></span><span class="op">(</span><span class="va">pa</span><span class="op">)</span> <span class="op">!=</span> <span class="fl">0</span>, <span class="op">]</span> <span class="co"># 84 rows, 69 columns</span></span></code></pre></div>
<p>The resulting matrix serves as input for the NMDS.
<code>k</code> specifies the number of output axes, here, set to 4.<a class="footnote-ref" tabindex="0" data-toggle="popover" data-content='&lt;p&gt;
One way of choosing &lt;code&gt;k&lt;/code&gt; is to try &lt;code&gt;k&lt;/code&gt; values between 1 and 6 and then using the result which yields the best stress value &lt;span class="citation"&gt;(&lt;a href="references.html#ref-mccune_analysis_2002"&gt;McCune, Grace, and Urban 2002&lt;/a&gt;)&lt;/span&gt;.&lt;/p&gt;'><sup>103</sup></a>
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<p>In case, <code><a href="https://rspatial.github.io/terra/reference/predict.html">terra::predict()</a></code> does not support a model algorithm, you can still make the predictions manually.</p>
<div class="sourceCode" id="cb510"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">newdata</span> <span class="op">=</span> <span class="fu"><a href="https://rspatial.github.io/terra/reference/as.data.frame.html">as.data.frame</a></span><span class="op">(</span><span class="fu"><a href="https://rspatial.github.io/terra/reference/coerce.html">as.matrix</a></span><span class="op">(</span><span class="va">ep</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/colSums.html">colSums</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">newdata</span><span class="op">)</span><span class="op">)</span> <span class="co"># 0 NAs</span></span>
<span><span class="fu"><a href="https://rspatial.github.io/terra/reference/rowSums.html">colSums</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">newdata</span><span class="op">)</span><span class="op">)</span> <span class="co"># 0 NAs</span></span>
<span><span class="co"># but assuming there were 0s results in a more generic approach</span></span>
<span><span class="va">ind</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/colSums.html">rowSums</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">newdata</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="fl">0</span></span>
<span><span class="va">ind</span> <span class="op">=</span> <span class="fu"><a href="https://rspatial.github.io/terra/reference/rowSums.html">rowSums</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">newdata</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="fl">0</span></span>
<span><span class="va">tmp</span> <span class="op">=</span> <span class="va">autotuner_rf</span><span class="op">$</span><span class="fu">predict_newdata</span><span class="op">(</span>newdata <span class="op">=</span> <span class="va">newdata</span><span class="op">[</span><span class="va">ind</span>, <span class="op">]</span>, task <span class="op">=</span> <span class="va">task</span><span class="op">)</span></span>
<span><span class="va">newdata</span><span class="op">[</span><span class="va">ind</span>, <span class="st">"pred"</span><span class="op">]</span> <span class="op">=</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/data.table/man/as.data.table.html">as.data.table</a></span><span class="op">(</span><span class="va">tmp</span><span class="op">)</span><span class="op">[[</span><span class="st">"response"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">pred_2</span> <span class="op">=</span> <span class="va">ep</span><span class="op">$</span><span class="va">dem</span></span>
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Expand Up @@ -121,7 +121,7 @@ <h1>Welcome<a class="anchor" aria-label="anchor" href="#welcome"><i class="fas f
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---
title: 'Geocomputation with R'
author: 'Robin Lovelace, Jakub Nowosad, Jannes Muenchow'
date: '2024-12-11'
date: '2024-12-14'
site: bookdown::bookdown_site
output: bookdown::bs4_book
documentclass: krantz
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