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ensemble.html

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evaluate.html

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+        <nav id="TOC" role="doc-toc" class="toc-active">
+    <h2 id="toc-title">Table of contents</h2>
+
+  <ul>
+  <li><a href="#more-resources" id="toc-more-resources" class="nav-link active" data-scroll-target="#more-resources"><span class="header-section-number">11.1</span> More Resources</a></li>
+  </ul>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/marinebon/sdm-book/edit/main/evaluate.qmd" class="toc-action">Edit this page</a></p></div></div></nav>
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 <figcaption class="figure-caption">Figure&nbsp;11.1: ROC curve generated by showing rates of false positive vs false negative as function of changing the threshold value (rainbow colors). Source: <a href="https://cran.rstudio.com/web/packages/ROCR/vignettes/ROCR.html">ROCR: visualizing classifier performance in R</a></figcaption>
 </figure>
 </div>
+<p>From the ROC curve, the area under the curve (<strong>AUC</strong>) is calculated, which is a measure of the model’s ability to distinguish between presence and absence. AUC values range from 0 to 1, with 0.5 being no better than random, and 1 being perfect.</p>
+<section id="more-resources" class="level2" data-number="11.1">
+<h2 data-number="11.1" class="anchored" data-anchor-id="more-resources"><span class="header-section-number">11.1</span> More Resources</h2>
+<ul>
+<li><a href="https://developers.google.com/machine-learning/crash-course/classification/roc-and-auc">Classification: ROC Curve and AUC | Machine Learning | Google for Developers</a></li>
+</ul>
 
 
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+</section>
 
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@@ -890,19 +903,25 @@
 <span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a>: Confusion matrix to understand predicted versus observed. {#tbl-confusion-matrix}</span>
 <span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a>!<span class="co">[</span><span class="ot">ROC curve generated by showing rates of false positive vs false negative as function of changing the threshold value (rainbow colors). Source: [ROCR: visualizing classifier performance in R](https://cran.rstudio.com/web/packages/ROCR/vignettes/ROCR.html)</span><span class="co">](figures/rocr.png)</span>{#fig-rocr}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a>!<span class="co">[</span><span class="ot">ROC curve generated by showing rates of false positive vs false negative as function of changing the threshold value (rainbow colors). Source: [ROCR: visualizing classifier performance in R](https://cran.rstudio.com/web/packages/ROCR/vignettes/ROCR.html)</span><span class="co">](figures/rocr.png)</span>{#fig-rocr}</span>
+<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a>From the ROC curve, the area under the curve (**AUC**) is calculated, which is a measure of the model's ability to distinguish between presence and absence. AUC values range from 0 to 1, with 0.5 being no better than random, and 1 being perfect.</span>
+<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="fu">## More Resources</span></span>
+<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="ss">* </span><span class="co">[</span><span class="ot">Classification: ROC Curve and AUC | Machine Learning | Google for Developers</span><span class="co">](https://developers.google.com/machine-learning/crash-course/classification/roc-and-auc)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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explorations/obis-top-spp-by-class.html

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explorations/sdm-1_predicts.html

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occ.html

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search.json

@@ -147,11 +147,11 @@
     "text": "The prediction step applies the environmental relationships from the fitted model to a new set of data, typically the seascape of interest, and perhaps with some sort of temporal snapshot (e.g., climatic annual or monthly average)."
   },
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-    "objectID": "evaluate.html",
-    "href": "evaluate.html",
+    "objectID": "evaluate.html#more-resources",
+    "href": "evaluate.html#more-resources",
     "title": "11  Evaluate",
-    "section": "",
-    "text": "Model evaluation uses the set aside test data from the earlier splitting to evaluate how well the model predicts the response of presence or absence. Since the test response data is binary [0,1] and the prediction from the model is continuous [0-1], a threshold needs to be applied to assign to convert the continuous response to binary. This is often performed through a Receiver Operator Characteristic (ROC) curve (Figure 11.1), which evaluates at each threshold the confusion matrix (Table 11.1).\n\n\nTable 11.1: Confusion matrix to understand predicted versus observed.\n\n\n\n\nPredicted\n\n\n\n\n\n0 (absence)\n1 (presence)\n\n\nObserved\n0 (absence)\nTrue absence\nFalse presence\n\n\n\n1 (presence)\nFalse absence\nTrue presence\n\n\n\n\n\n\n\nFigure 11.1: ROC curve generated by showing rates of false positive vs false negative as function of changing the threshold value (rainbow colors). Source: ROCR: visualizing classifier performance in R"
+    "section": "11.1 More Resources",
+    "text": "11.1 More Resources\n\nClassification: ROC Curve and AUC | Machine Learning | Google for Developers"
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software.html

@@ -432,12 +432,12 @@ <h2 data-number="17.1" class="anchored" data-anchor-id="r"><span class="header-s
 <ul>
 <li><p><a href="https://biomodhub.github.io/biomod2/"><code>biomod2</code></a><br>
 <em>Species distribution modeling, calibration and evaluation, ensemble modeling<br>
-</em><a href="https://biomodhub.github.io/biomod2/articles/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.png" class="lightbox" title="Graphical overview of `biomod2` functions for data formatting, single SDMs, ensemble methods and visualization. Source: [`biomod2`](https://biomodhub.github.io/biomod2/)" data-gallery="quarto-lightbox-gallery-1"><img src="https://biomodhub.github.io/biomod2/articles/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.png" class="img-fluid" alt="Graphical overview of `biomod2` functions for data formatting, single SDMs, ensemble methods and visualization. Source: [`biomod2`](https://biomodhub.github.io/biomod2/)"></a></p></li>
+</em><a href="https://biomodhub.github.io/biomod2/articles/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="Graphical overview of `biomod2` functions for data formatting, single SDMs, ensemble methods and visualization. Source: [`biomod2`](https://biomodhub.github.io/biomod2/)"><img src="https://biomodhub.github.io/biomod2/articles/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.png" class="img-fluid" alt="Graphical overview of `biomod2` functions for data formatting, single SDMs, ensemble methods and visualization. Source: [`biomod2`](https://biomodhub.github.io/biomod2/)"></a></p></li>
 <li><p><a href="https://cran.r-project.org/web/packages/eks/vignettes/tidysf_kde.html"><code>eks</code></a><br>
 <em>Tidy and Geospatial Kernel Smoothing for spatially filtering outlier observations</em></p>
 <div id="fig-eks" class="quarto-figure quarto-figure-center anchored">
 <figure class="figure">
-<p><a href="figures/software/eks.png" class="lightbox" title="Source: Kernel density estimates for tidy and geospatial data in the eks package" data-gallery="quarto-lightbox-gallery-2"><img src="figures/software/eks.png" class="img-fluid figure-img"></a></p>
+<p><a href="figures/software/eks.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" title="Source: Kernel density estimates for tidy and geospatial data in the eks package"><img src="figures/software/eks.png" class="img-fluid figure-img"></a></p>
 <figcaption class="figure-caption">Figure&nbsp;17.1: Source: <a href="https://cran.r-project.org/web/packages/eks/vignettes/tidysf_kde.html">Kernel density estimates for tidy and geospatial data in the eks package</a></figcaption>
 </figure>
 </div></li>
@@ -914,7 +914,7 @@ <h2 data-number="17.3" class="anchored" data-anchor-id="google-earth-engine"><sp
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