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<!DOCTYPE html>
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<title>Section 4 Model comparisons | Malaria vaccine antigen identification for Plasmodium vivax</title>
<meta name="description" content="Section 4 Model comparisons | Malaria vaccine antigen identification for Plasmodium vivax" />
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<meta property="og:title" content="Section 4 Model comparisons | Malaria vaccine antigen identification for Plasmodium vivax" />
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<meta name="twitter:title" content="Section 4 Model comparisons | Malaria vaccine antigen identification for Plasmodium vivax" />
<meta name="author" content="Renee Ti Chou" />
<meta name="date" content="2023-06-06" />
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<ul class="summary">
<li><a href="./"><i>Positive-unlabeled learning for Pv RV</i></a></li>
<li class="divider"></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Preface</a></li>
<li class="chapter" data-level="1" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html"><i class="fa fa-check"></i><b>1</b> Data engineering</a>
<ul>
<li class="chapter" data-level="1.1" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#purf-package-installization"><i class="fa fa-check"></i><b>1.1</b> <code>purf</code> package installization</a></li>
<li class="chapter" data-level="1.2" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#retrieving-p.-vivax-protein-variables"><i class="fa fa-check"></i><b>1.2</b> Retrieving <em>P. vivax</em> protein variables</a>
<ul>
<li class="chapter" data-level="1.2.1" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#immunological-data-sets"><i class="fa fa-check"></i><b>1.2.1</b> Immunological data sets</a></li>
<li class="chapter" data-level="1.2.2" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#proteomic-data-sets"><i class="fa fa-check"></i><b>1.2.2</b> Proteomic data sets</a></li>
<li class="chapter" data-level="1.2.3" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#structural-data-sets"><i class="fa fa-check"></i><b>1.2.3</b> Structural data sets</a></li>
<li class="chapter" data-level="1.2.4" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#genomic-data-sets"><i class="fa fa-check"></i><b>1.2.4</b> Genomic data sets</a></li>
<li class="chapter" data-level="1.2.5" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#final-assembly"><i class="fa fa-check"></i><b>1.2.5</b> Final assembly</a></li>
</ul></li>
<li class="chapter" data-level="1.3" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#generating-ml-input"><i class="fa fa-check"></i><b>1.3</b> Generating ML input</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="id_02_model_training.html"><a href="id_02_model_training.html"><i class="fa fa-check"></i><b>2</b> Model training</a>
<ul>
<li class="chapter" data-level="2.1" data-path="id_02_model_training.html"><a href="id_02_model_training.html#hyper-parameter-tuning-for-purf"><i class="fa fa-check"></i><b>2.1</b> Hyper-parameter tuning for PURF</a>
<ul>
<li class="chapter" data-level="2.1.1" data-path="id_02_model_training.html"><a href="id_02_model_training.html#analysis"><i class="fa fa-check"></i><b>2.1.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="2.1.1.1" data-path="id_02_model_training.html"><a href="id_02_model_training.html#pv-data-set"><i class="fa fa-check"></i><b>2.1.1.1</b> Pv data set</a></li>
<li class="chapter" data-level="2.1.1.2" data-path="id_02_model_training.html"><a href="id_02_model_training.html#pv-pf-combined-data-set"><i class="fa fa-check"></i><b>2.1.1.2</b> Pv + Pf combined data set</a></li>
</ul></li>
<li class="chapter" data-level="2.1.2" data-path="id_02_model_training.html"><a href="id_02_model_training.html#plotting"><i class="fa fa-check"></i><b>2.1.2</b> Plotting</a>
<ul>
<li class="chapter" data-level="2.1.2.1" data-path="id_02_model_training.html"><a href="id_02_model_training.html#pv-data-set-1"><i class="fa fa-check"></i><b>2.1.2.1</b> Pv data set</a></li>
<li class="chapter" data-level="2.1.2.2" data-path="id_02_model_training.html"><a href="id_02_model_training.html#bimodal-distribution-plot"><i class="fa fa-check"></i><b>2.1.2.2</b> Bimodal distribution plot</a></li>
<li class="chapter" data-level="2.1.2.3" data-path="id_02_model_training.html"><a href="id_02_model_training.html#known-antigen-ranking"><i class="fa fa-check"></i><b>2.1.2.3</b> Known antigen ranking</a></li>
<li class="chapter" data-level="2.1.2.4" data-path="id_02_model_training.html"><a href="id_02_model_training.html#pv-pf-combined-data-set-1"><i class="fa fa-check"></i><b>2.1.2.4</b> Pv + Pf combined data set</a></li>
<li class="chapter" data-level="2.1.2.5" data-path="id_02_model_training.html"><a href="id_02_model_training.html#bimodal-distribution-plot-1"><i class="fa fa-check"></i><b>2.1.2.5</b> Bimodal distribution plot</a></li>
<li class="chapter" data-level="2.1.2.6" data-path="id_02_model_training.html"><a href="id_02_model_training.html#known-antigen-ranking-1"><i class="fa fa-check"></i><b>2.1.2.6</b> Known antigen ranking</a></li>
</ul></li>
<li class="chapter" data-level="2.1.3" data-path="id_02_model_training.html"><a href="id_02_model_training.html#results-for-positive-level-0.5"><i class="fa fa-check"></i><b>2.1.3</b> Results for positive level = 0.5</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html"><i class="fa fa-check"></i><b>3</b> Model evaluation</a>
<ul>
<li class="chapter" data-level="3.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#known-antigen-prediction-accuracy"><i class="fa fa-check"></i><b>3.1</b> Known antigen prediction accuracy</a>
<ul>
<li class="chapter" data-level="3.1.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#analysis-1"><i class="fa fa-check"></i><b>3.1.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="3.1.1.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#pv-model-cross-species-predictions"><i class="fa fa-check"></i><b>3.1.1.1</b> Pv model cross-species predictions</a></li>
<li class="chapter" data-level="3.1.1.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#pf-model-cross-species-predictions"><i class="fa fa-check"></i><b>3.1.1.2</b> Pf model cross-species predictions</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#adversarial-controls"><i class="fa fa-check"></i><b>3.2</b> Adversarial controls</a>
<ul>
<li class="chapter" data-level="3.2.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#analysis-2"><i class="fa fa-check"></i><b>3.2.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="3.2.1.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#pv-data-set-2"><i class="fa fa-check"></i><b>3.2.1.1</b> Pv data set</a></li>
<li class="chapter" data-level="3.2.1.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#pv-pf-combined-data-set-2"><i class="fa fa-check"></i><b>3.2.1.2</b> Pv + Pf combined data set</a></li>
</ul></li>
<li class="chapter" data-level="3.2.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#plotting-1"><i class="fa fa-check"></i><b>3.2.2</b> Plotting</a>
<ul>
<li class="chapter" data-level="3.2.2.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#mean-differences-in-scores"><i class="fa fa-check"></i><b>3.2.2.1</b> Mean differences in scores</a></li>
<li class="chapter" data-level="3.2.2.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#investigation-of-known-antigen-groups"><i class="fa fa-check"></i><b>3.2.2.2</b> Investigation of known antigen groups</a></li>
<li class="chapter" data-level="3.2.2.3" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#labeled-known-antigen-accuracies"><i class="fa fa-check"></i><b>3.2.2.3</b> Labeled known antigen accuracies</a></li>
</ul></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html"><i class="fa fa-check"></i><b>4</b> Model comparisons</a>
<ul>
<li class="chapter" data-level="4.1" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#known-antigen-score-comparisons"><i class="fa fa-check"></i><b>4.1</b> Known antigen score comparisons</a></li>
<li class="chapter" data-level="4.2" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#known-antigen-prediction-summary"><i class="fa fa-check"></i><b>4.2</b> Known antigen prediction summary</a></li>
<li class="chapter" data-level="4.3" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#score-and-species-association"><i class="fa fa-check"></i><b>4.3</b> Score and species association</a></li>
<li class="chapter" data-level="4.4" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#tree-depth-analysis"><i class="fa fa-check"></i><b>4.4</b> Tree depth analysis</a>
<ul>
<li class="chapter" data-level="4.4.1" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#analysis-3"><i class="fa fa-check"></i><b>4.4.1</b> Analysis</a></li>
<li class="chapter" data-level="4.4.2" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#plotting-2"><i class="fa fa-check"></i><b>4.4.2</b> Plotting</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html"><i class="fa fa-check"></i><b>5</b> Model interpretation</a>
<ul>
<li class="chapter" data-level="5.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#proximity-matrix-calculation"><i class="fa fa-check"></i><b>5.1</b> Proximity matrix calculation</a>
<ul>
<li class="chapter" data-level="5.1.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#analysis-4"><i class="fa fa-check"></i><b>5.1.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="5.1.1.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-data-set-3"><i class="fa fa-check"></i><b>5.1.1.1</b> Pv data set</a></li>
<li class="chapter" data-level="5.1.1.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-pf-combined-data-set-3"><i class="fa fa-check"></i><b>5.1.1.2</b> Pv + Pf combined data set</a></li>
</ul></li>
<li class="chapter" data-level="5.1.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#plotting-3"><i class="fa fa-check"></i><b>5.1.2</b> Plotting</a>
<ul>
<li class="chapter" data-level="5.1.2.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-pf-combined-data-set-4"><i class="fa fa-check"></i><b>5.1.2.1</b> Pv + Pf combined data set</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#clustering-of-predicted-positives"><i class="fa fa-check"></i><b>5.2</b> Clustering of predicted positives</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#analysis-5"><i class="fa fa-check"></i><b>5.2.1</b> Analysis</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#comparison-of-amino-acid-frequencies-between-species"><i class="fa fa-check"></i><b>5.3</b> Comparison of amino acid frequencies between species</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#analysis-6"><i class="fa fa-check"></i><b>5.3.1</b> Analysis</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#variable-importance"><i class="fa fa-check"></i><b>5.4</b> Variable importance</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#analysis-7"><i class="fa fa-check"></i><b>5.4.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="5.4.1.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-data-set-4"><i class="fa fa-check"></i><b>5.4.1.1</b> Pv data set</a></li>
<li class="chapter" data-level="5.4.1.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-pf-combined-data-set-5"><i class="fa fa-check"></i><b>5.4.1.2</b> Pv + Pf combined data set</a></li>
</ul></li>
<li class="chapter" data-level="5.4.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#plotting-4"><i class="fa fa-check"></i><b>5.4.2</b> Plotting</a>
<ul>
<li class="chapter" data-level="5.4.2.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-data-set-5"><i class="fa fa-check"></i><b>5.4.2.1</b> Pv data set</a></li>
<li class="chapter" data-level="5.4.2.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-pf-combined-data-set-6"><i class="fa fa-check"></i><b>5.4.2.2</b> Pv + Pf combined data set</a></li>
</ul></li>
<li class="chapter" data-level="5.4.3" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#comparison-of-top-10-important-variables"><i class="fa fa-check"></i><b>5.4.3</b> Comparison of top 10 important variables</a>
<ul>
<li class="chapter" data-level="5.4.3.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#venn-diagram"><i class="fa fa-check"></i><b>5.4.3.1</b> Venn diagram</a></li>
<li class="chapter" data-level="5.4.3.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#top-10-variables-from-combined-model"><i class="fa fa-check"></i><b>5.4.3.2</b> Top 10 variables from combined model</a></li>
</ul></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html"><i class="fa fa-check"></i><b>6</b> Top candidate comparisons</a>
<ul>
<li class="chapter" data-level="6.1" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#clustering-analysis"><i class="fa fa-check"></i><b>6.1</b> Clustering analysis</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#analysis-8"><i class="fa fa-check"></i><b>6.1.1</b> Analysis</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#gene-ontology-analysis"><i class="fa fa-check"></i><b>6.2</b> Gene ontology analysis</a>
<ul>
<li class="chapter" data-level="6.2.1" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#analysis-9"><i class="fa fa-check"></i><b>6.2.1</b> Analysis</a></li>
<li class="chapter" data-level="6.2.2" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#plotting-5"><i class="fa fa-check"></i><b>6.2.2</b> Plotting</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#candidate-antigen-characterization"><i class="fa fa-check"></i><b>6.3</b> Candidate antigen characterization</a>
<ul>
<li class="chapter" data-level="6.3.1" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#processing-table"><i class="fa fa-check"></i><b>6.3.1</b> Processing table</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="7" data-path="id_07_summary_of_candidates.html"><a href="id_07_summary_of_candidates.html"><i class="fa fa-check"></i><b>7</b> Summary of candidates</a></li>
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<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Malaria vaccine antigen identification for <em>Plasmodium vivax</em></a>
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<div id="id_04_model_comparisons" class="section level1 hasAnchor" number="4">
<h1><span class="header-section-number">Section 4</span> Model comparisons<a href="id_04_model_comparisons.html#id_04_model_comparisons" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="known-antigen-score-comparisons" class="section level2 hasAnchor" number="4.1">
<h2><span class="header-section-number">4.1</span> Known antigen score comparisons<a href="id_04_model_comparisons.html#known-antigen-score-comparisons" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><strong>In R: </strong></p>
<div class="sourceCode" id="cb74"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb74-1"><a href="id_04_model_comparisons.html#cb74-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb74-2"><a href="id_04_model_comparisons.html#cb74-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(reshape2)</span>
<span id="cb74-3"><a href="id_04_model_comparisons.html#cb74-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggdist)</span>
<span id="cb74-4"><a href="id_04_model_comparisons.html#cb74-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(gghalves)</span>
<span id="cb74-5"><a href="id_04_model_comparisons.html#cb74-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(cowplot)</span></code></pre></div>
<div class="sourceCode" id="cb75"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb75-1"><a href="id_04_model_comparisons.html#cb75-1" aria-hidden="true" tabindex="-1"></a>pv_scores <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pv_known_antigen_scores.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb75-2"><a href="id_04_model_comparisons.html#cb75-2" aria-hidden="true" tabindex="-1"></a>pv_unl_scores <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pv_unlabeled_protein_scores.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb75-3"><a href="id_04_model_comparisons.html#cb75-3" aria-hidden="true" tabindex="-1"></a>pv_scores<span class="sc">$</span>label <span class="ot"><-</span> <span class="dv">2</span></span>
<span id="cb75-4"><a href="id_04_model_comparisons.html#cb75-4" aria-hidden="true" tabindex="-1"></a>pv_unl_scores<span class="sc">$</span>label <span class="ot"><-</span> <span class="dv">1</span></span>
<span id="cb75-5"><a href="id_04_model_comparisons.html#cb75-5" aria-hidden="true" tabindex="-1"></a>data_ <span class="ot"><-</span> <span class="fu">melt</span>(<span class="fu">rbind</span>(pv_scores, pv_unl_scores), <span class="at">id.vars =</span> <span class="st">"label"</span>)</span>
<span id="cb75-6"><a href="id_04_model_comparisons.html#cb75-6" aria-hidden="true" tabindex="-1"></a>data_<span class="sc">$</span>variable <span class="ot"><-</span> <span class="fu">factor</span>(data_<span class="sc">$</span>variable, <span class="at">levels =</span> <span class="fu">c</span>(</span>
<span id="cb75-7"><a href="id_04_model_comparisons.html#cb75-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"pf_single_model"</span>,</span>
<span id="cb75-8"><a href="id_04_model_comparisons.html#cb75-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"pv_single_model"</span>, <span class="st">"pv_pf_pos"</span>,</span>
<span id="cb75-9"><a href="id_04_model_comparisons.html#cb75-9" aria-hidden="true" tabindex="-1"></a> <span class="st">"pfpv_combined_model"</span>,</span>
<span id="cb75-10"><a href="id_04_model_comparisons.html#cb75-10" aria-hidden="true" tabindex="-1"></a> <span class="st">"pv_pf_unl"</span></span>
<span id="cb75-11"><a href="id_04_model_comparisons.html#cb75-11" aria-hidden="true" tabindex="-1"></a>))</span>
<span id="cb75-12"><a href="id_04_model_comparisons.html#cb75-12" aria-hidden="true" tabindex="-1"></a>data_<span class="sc">$</span>label[data_<span class="sc">$</span>value <span class="sc"><</span> <span class="fl">0.5</span> <span class="sc">&</span> data_<span class="sc">$</span>label <span class="sc">==</span> <span class="dv">1</span>] <span class="ot"><-</span> <span class="dv">0</span></span>
<span id="cb75-13"><a href="id_04_model_comparisons.html#cb75-13" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">12</span>)</span>
<span id="cb75-14"><a href="id_04_model_comparisons.html#cb75-14" aria-hidden="true" tabindex="-1"></a>p1 <span class="ot"><-</span> <span class="fu">ggplot</span>(data_, <span class="fu">aes</span>(<span class="at">x =</span> variable, <span class="at">y =</span> value)) <span class="sc">+</span></span>
<span id="cb75-15"><a href="id_04_model_comparisons.html#cb75-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="fl">0.5</span>, <span class="at">color =</span> <span class="st">"grey70"</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>) <span class="sc">+</span></span>
<span id="cb75-16"><a href="id_04_model_comparisons.html#cb75-16" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_halfeye</span>(<span class="fu">aes</span>(<span class="at">fill =</span> <span class="fu">factor</span>(label, <span class="at">levels =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">1</span>, <span class="dv">0</span>))),</span>
<span id="cb75-17"><a href="id_04_model_comparisons.html#cb75-17" aria-hidden="true" tabindex="-1"></a> <span class="at">slab_color =</span> <span class="st">"black"</span>,</span>
<span id="cb75-18"><a href="id_04_model_comparisons.html#cb75-18" aria-hidden="true" tabindex="-1"></a> <span class="at">slab_linewidth =</span> <span class="fl">0.2</span>, <span class="at">adjust =</span> <span class="fl">0.5</span>, <span class="at">width =</span> <span class="fl">0.5</span>, <span class="at">.width =</span> <span class="dv">0</span>,</span>
<span id="cb75-19"><a href="id_04_model_comparisons.html#cb75-19" aria-hidden="true" tabindex="-1"></a> <span class="at">justification =</span> <span class="sc">-</span><span class="fl">0.2</span>, <span class="at">point_colour =</span> <span class="cn">NA</span>, <span class="at">alpha =</span> <span class="fl">0.6</span>, <span class="at">normalize =</span> <span class="st">"all"</span></span>
<span id="cb75-20"><a href="id_04_model_comparisons.html#cb75-20" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb75-21"><a href="id_04_model_comparisons.html#cb75-21" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="fu">aes</span>(<span class="at">fill =</span> <span class="fu">factor</span>(label, <span class="at">levels =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">1</span>, <span class="dv">0</span>))),</span>
<span id="cb75-22"><a href="id_04_model_comparisons.html#cb75-22" aria-hidden="true" tabindex="-1"></a> <span class="at">width =</span> <span class="fl">0.2</span>, <span class="at">outlier.color =</span> <span class="cn">NA</span>,</span>
<span id="cb75-23"><a href="id_04_model_comparisons.html#cb75-23" aria-hidden="true" tabindex="-1"></a> <span class="at">lwd =</span> <span class="fl">0.3</span>, <span class="at">show.legend =</span> <span class="cn">FALSE</span>, <span class="at">alpha =</span> <span class="fl">0.6</span>, <span class="at">color =</span> <span class="st">"black"</span></span>
<span id="cb75-24"><a href="id_04_model_comparisons.html#cb75-24" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb75-25"><a href="id_04_model_comparisons.html#cb75-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_half_point</span>(</span>
<span id="cb75-26"><a href="id_04_model_comparisons.html#cb75-26" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> data_[data_<span class="sc">$</span>label <span class="sc">==</span> <span class="dv">2</span>, ], <span class="at">fill =</span> <span class="st">"#FCB40A"</span>, <span class="at">side =</span> <span class="st">"l"</span>,</span>
<span id="cb75-27"><a href="id_04_model_comparisons.html#cb75-27" aria-hidden="true" tabindex="-1"></a> <span class="at">range_scale =</span> <span class="fl">0.3</span>, <span class="at">alpha =</span> <span class="fl">0.8</span>, <span class="at">shape =</span> <span class="dv">21</span>, <span class="at">color =</span> <span class="st">"black"</span>, <span class="at">stroke =</span> <span class="fl">0.1</span>, <span class="at">size =</span> <span class="dv">2</span></span>
<span id="cb75-28"><a href="id_04_model_comparisons.html#cb75-28" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb75-29"><a href="id_04_model_comparisons.html#cb75-29" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(</span>
<span id="cb75-30"><a href="id_04_model_comparisons.html#cb75-30" aria-hidden="true" tabindex="-1"></a> <span class="at">name =</span> <span class="st">""</span>, <span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#FCB40A"</span>, <span class="st">"#FF007F"</span>, <span class="st">"#0080FF"</span>), <span class="at">breaks =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">1</span>, <span class="dv">0</span>),</span>
<span id="cb75-31"><a href="id_04_model_comparisons.html#cb75-31" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Known antigen"</span>, <span class="st">"Predicted antigen"</span>, <span class="st">"Predicted non-antigen"</span>)</span>
<span id="cb75-32"><a href="id_04_model_comparisons.html#cb75-32" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb75-33"><a href="id_04_model_comparisons.html#cb75-33" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(</span>
<span id="cb75-34"><a href="id_04_model_comparisons.html#cb75-34" aria-hidden="true" tabindex="-1"></a> <span class="at">name =</span> <span class="st">""</span>, <span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#FCB40A"</span>, <span class="st">"#FF007F"</span>, <span class="st">"#0080FF"</span>), <span class="at">breaks =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">1</span>, <span class="dv">0</span>),</span>
<span id="cb75-35"><a href="id_04_model_comparisons.html#cb75-35" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Known antigen"</span>, <span class="st">"Predicted antigen"</span>, <span class="st">"Predicted non-antigen"</span>)</span>
<span id="cb75-36"><a href="id_04_model_comparisons.html#cb75-36" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb75-37"><a href="id_04_model_comparisons.html#cb75-37" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span></span>
<span id="cb75-38"><a href="id_04_model_comparisons.html#cb75-38" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(</span>
<span id="cb75-39"><a href="id_04_model_comparisons.html#cb75-39" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">c</span>(</span>
<span id="cb75-40"><a href="id_04_model_comparisons.html#cb75-40" aria-hidden="true" tabindex="-1"></a> <span class="st">"pf_single_model"</span>, <span class="st">"pv_single_model"</span>, <span class="st">"pv_pf_pos"</span>,</span>
<span id="cb75-41"><a href="id_04_model_comparisons.html#cb75-41" aria-hidden="true" tabindex="-1"></a> <span class="st">"pfpv_combined_model"</span>, <span class="st">"pv_pf_unl"</span></span>
<span id="cb75-42"><a href="id_04_model_comparisons.html#cb75-42" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb75-43"><a href="id_04_model_comparisons.html#cb75-43" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(</span>
<span id="cb75-44"><a href="id_04_model_comparisons.html#cb75-44" aria-hidden="true" tabindex="-1"></a> <span class="st">"Heterologous model"</span>, <span class="st">"Autologous model"</span>,</span>
<span id="cb75-45"><a href="id_04_model_comparisons.html#cb75-45" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous with</span><span class="sc">\n</span><span class="st"> heterologous positives model"</span>,</span>
<span id="cb75-46"><a href="id_04_model_comparisons.html#cb75-46" aria-hidden="true" tabindex="-1"></a> <span class="st">"Combined model"</span>,</span>
<span id="cb75-47"><a href="id_04_model_comparisons.html#cb75-47" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous with</span><span class="sc">\n</span><span class="st"> heterologous unlabeled model"</span></span>
<span id="cb75-48"><a href="id_04_model_comparisons.html#cb75-48" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb75-49"><a href="id_04_model_comparisons.html#cb75-49" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> rev</span>
<span id="cb75-50"><a href="id_04_model_comparisons.html#cb75-50" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb75-51"><a href="id_04_model_comparisons.html#cb75-51" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb75-52"><a href="id_04_model_comparisons.html#cb75-52" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb75-53"><a href="id_04_model_comparisons.html#cb75-53" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb75-54"><a href="id_04_model_comparisons.html#cb75-54" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb75-55"><a href="id_04_model_comparisons.html#cb75-55" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb75-56"><a href="id_04_model_comparisons.html#cb75-56" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb75-57"><a href="id_04_model_comparisons.html#cb75-57" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb75-58"><a href="id_04_model_comparisons.html#cb75-58" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.5</span>, <span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb75-59"><a href="id_04_model_comparisons.html#cb75-59" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> ggplot2<span class="sc">::</span><span class="fu">margin</span>(<span class="dv">5</span>, <span class="dv">5</span>, <span class="dv">5</span>, <span class="dv">5</span>, <span class="st">"pt"</span>),</span>
<span id="cb75-60"><a href="id_04_model_comparisons.html#cb75-60" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="st">"none"</span></span>
<span id="cb75-61"><a href="id_04_model_comparisons.html#cb75-61" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb75-62"><a href="id_04_model_comparisons.html#cb75-62" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylim</span>(<span class="dv">0</span>, <span class="dv">1</span>) <span class="sc">+</span></span>
<span id="cb75-63"><a href="id_04_model_comparisons.html#cb75-63" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"Score (proportion of votes)"</span>)</span>
<span id="cb75-64"><a href="id_04_model_comparisons.html#cb75-64" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb75-65"><a href="id_04_model_comparisons.html#cb75-65" aria-hidden="true" tabindex="-1"></a>legend <span class="ot"><-</span> <span class="fu">get_legend</span>(p2 <span class="sc">+</span></span>
<span id="cb75-66"><a href="id_04_model_comparisons.html#cb75-66" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb75-67"><a href="id_04_model_comparisons.html#cb75-67" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.direction =</span> <span class="st">"horizontal"</span>,</span>
<span id="cb75-68"><a href="id_04_model_comparisons.html#cb75-68" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="st">"bottom"</span>,</span>
<span id="cb75-69"><a href="id_04_model_comparisons.html#cb75-69" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.title =</span> <span class="fu">element_blank</span>()</span>
<span id="cb75-70"><a href="id_04_model_comparisons.html#cb75-70" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb75-71"><a href="id_04_model_comparisons.html#cb75-71" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="fu">guide_legend</span>(<span class="at">title =</span> <span class="st">""</span>)))</span></code></pre></div>
<div class="sourceCode" id="cb76"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb76-1"><a href="id_04_model_comparisons.html#cb76-1" aria-hidden="true" tabindex="-1"></a>pf_scores <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pf_known_antigen_scores.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb76-2"><a href="id_04_model_comparisons.html#cb76-2" aria-hidden="true" tabindex="-1"></a>pf_unl_scores <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pf_unlabeled_protein_scores.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb76-3"><a href="id_04_model_comparisons.html#cb76-3" aria-hidden="true" tabindex="-1"></a>pf_scores<span class="sc">$</span>label <span class="ot"><-</span> <span class="dv">2</span></span>
<span id="cb76-4"><a href="id_04_model_comparisons.html#cb76-4" aria-hidden="true" tabindex="-1"></a>pf_unl_scores<span class="sc">$</span>label <span class="ot"><-</span> <span class="dv">1</span></span>
<span id="cb76-5"><a href="id_04_model_comparisons.html#cb76-5" aria-hidden="true" tabindex="-1"></a>data_ <span class="ot"><-</span> <span class="fu">melt</span>(<span class="fu">rbind</span>(pf_scores, pf_unl_scores), <span class="at">id.vars =</span> <span class="st">"label"</span>)</span>
<span id="cb76-6"><a href="id_04_model_comparisons.html#cb76-6" aria-hidden="true" tabindex="-1"></a>data_<span class="sc">$</span>variable <span class="ot"><-</span> <span class="fu">factor</span>(data_<span class="sc">$</span>variable, <span class="at">levels =</span> <span class="fu">c</span>(</span>
<span id="cb76-7"><a href="id_04_model_comparisons.html#cb76-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"pv_single_model"</span>,</span>
<span id="cb76-8"><a href="id_04_model_comparisons.html#cb76-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"pf_single_model"</span>, <span class="st">"pf_pv_pos"</span>,</span>
<span id="cb76-9"><a href="id_04_model_comparisons.html#cb76-9" aria-hidden="true" tabindex="-1"></a> <span class="st">"pfpv_combined_model"</span>,</span>
<span id="cb76-10"><a href="id_04_model_comparisons.html#cb76-10" aria-hidden="true" tabindex="-1"></a> <span class="st">"pf_pv_unl"</span></span>
<span id="cb76-11"><a href="id_04_model_comparisons.html#cb76-11" aria-hidden="true" tabindex="-1"></a>))</span>
<span id="cb76-12"><a href="id_04_model_comparisons.html#cb76-12" aria-hidden="true" tabindex="-1"></a>data_<span class="sc">$</span>label[data_<span class="sc">$</span>value <span class="sc"><</span> <span class="fl">0.5</span> <span class="sc">&</span> data_<span class="sc">$</span>label <span class="sc">==</span> <span class="dv">1</span>] <span class="ot"><-</span> <span class="dv">0</span></span>
<span id="cb76-13"><a href="id_04_model_comparisons.html#cb76-13" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">12</span>)</span>
<span id="cb76-14"><a href="id_04_model_comparisons.html#cb76-14" aria-hidden="true" tabindex="-1"></a>p2 <span class="ot"><-</span> <span class="fu">ggplot</span>(data_, <span class="fu">aes</span>(<span class="at">x =</span> variable, <span class="at">y =</span> value)) <span class="sc">+</span></span>
<span id="cb76-15"><a href="id_04_model_comparisons.html#cb76-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="fl">0.5</span>, <span class="at">color =</span> <span class="st">"grey70"</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>) <span class="sc">+</span></span>
<span id="cb76-16"><a href="id_04_model_comparisons.html#cb76-16" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_halfeye</span>(<span class="fu">aes</span>(<span class="at">fill =</span> <span class="fu">factor</span>(label, <span class="at">levels =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">1</span>, <span class="dv">0</span>))),</span>
<span id="cb76-17"><a href="id_04_model_comparisons.html#cb76-17" aria-hidden="true" tabindex="-1"></a> <span class="at">slab_color =</span> <span class="st">"black"</span>,</span>
<span id="cb76-18"><a href="id_04_model_comparisons.html#cb76-18" aria-hidden="true" tabindex="-1"></a> <span class="at">slab_linewidth =</span> <span class="fl">0.2</span>, <span class="at">adjust =</span> <span class="fl">0.5</span>, <span class="at">width =</span> <span class="fl">0.5</span>, <span class="at">.width =</span> <span class="dv">0</span>,</span>
<span id="cb76-19"><a href="id_04_model_comparisons.html#cb76-19" aria-hidden="true" tabindex="-1"></a> <span class="at">justification =</span> <span class="sc">-</span><span class="fl">0.2</span>, <span class="at">point_colour =</span> <span class="cn">NA</span>, <span class="at">alpha =</span> <span class="fl">0.6</span>, <span class="at">normalize =</span> <span class="st">"all"</span></span>
<span id="cb76-20"><a href="id_04_model_comparisons.html#cb76-20" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb76-21"><a href="id_04_model_comparisons.html#cb76-21" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="fu">aes</span>(<span class="at">fill =</span> <span class="fu">factor</span>(label, <span class="at">levels =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">1</span>, <span class="dv">0</span>))),</span>
<span id="cb76-22"><a href="id_04_model_comparisons.html#cb76-22" aria-hidden="true" tabindex="-1"></a> <span class="at">width =</span> <span class="fl">0.2</span>, <span class="at">outlier.color =</span> <span class="cn">NA</span>,</span>
<span id="cb76-23"><a href="id_04_model_comparisons.html#cb76-23" aria-hidden="true" tabindex="-1"></a> <span class="at">lwd =</span> <span class="fl">0.3</span>, <span class="at">show.legend =</span> <span class="cn">FALSE</span>, <span class="at">alpha =</span> <span class="fl">0.6</span>, <span class="at">color =</span> <span class="st">"black"</span></span>
<span id="cb76-24"><a href="id_04_model_comparisons.html#cb76-24" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb76-25"><a href="id_04_model_comparisons.html#cb76-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_half_point</span>(</span>
<span id="cb76-26"><a href="id_04_model_comparisons.html#cb76-26" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> data_[data_<span class="sc">$</span>label <span class="sc">==</span> <span class="dv">2</span>, ], <span class="at">fill =</span> <span class="st">"#FCB40A"</span>, <span class="at">side =</span> <span class="st">"l"</span>,</span>
<span id="cb76-27"><a href="id_04_model_comparisons.html#cb76-27" aria-hidden="true" tabindex="-1"></a> <span class="at">range_scale =</span> <span class="fl">0.3</span>, <span class="at">alpha =</span> <span class="fl">0.8</span>, <span class="at">shape =</span> <span class="dv">21</span>, <span class="at">color =</span> <span class="st">"black"</span>, <span class="at">stroke =</span> <span class="fl">0.1</span>, <span class="at">size =</span> <span class="dv">2</span></span>
<span id="cb76-28"><a href="id_04_model_comparisons.html#cb76-28" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb76-29"><a href="id_04_model_comparisons.html#cb76-29" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(</span>
<span id="cb76-30"><a href="id_04_model_comparisons.html#cb76-30" aria-hidden="true" tabindex="-1"></a> <span class="at">name =</span> <span class="st">""</span>, <span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#FCB40A"</span>, <span class="st">"#FF007F"</span>, <span class="st">"#0080FF"</span>), <span class="at">breaks =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">1</span>, <span class="dv">0</span>),</span>
<span id="cb76-31"><a href="id_04_model_comparisons.html#cb76-31" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Known antigen"</span>, <span class="st">"Predicted antigen"</span>, <span class="st">"Predicted non-antigen"</span>)</span>
<span id="cb76-32"><a href="id_04_model_comparisons.html#cb76-32" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb76-33"><a href="id_04_model_comparisons.html#cb76-33" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(</span>
<span id="cb76-34"><a href="id_04_model_comparisons.html#cb76-34" aria-hidden="true" tabindex="-1"></a> <span class="at">name =</span> <span class="st">""</span>, <span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#FCB40A"</span>, <span class="st">"#FF007F"</span>, <span class="st">"#0080FF"</span>), <span class="at">breaks =</span> <span class="fu">c</span>(<span class="dv">2</span>, <span class="dv">1</span>, <span class="dv">0</span>),</span>
<span id="cb76-35"><a href="id_04_model_comparisons.html#cb76-35" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Known antigen"</span>, <span class="st">"Predicted antigen"</span>, <span class="st">"Predicted non-antigen"</span>)</span>
<span id="cb76-36"><a href="id_04_model_comparisons.html#cb76-36" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb76-37"><a href="id_04_model_comparisons.html#cb76-37" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>() <span class="sc">+</span></span>
<span id="cb76-38"><a href="id_04_model_comparisons.html#cb76-38" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(</span>
<span id="cb76-39"><a href="id_04_model_comparisons.html#cb76-39" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">c</span>(</span>
<span id="cb76-40"><a href="id_04_model_comparisons.html#cb76-40" aria-hidden="true" tabindex="-1"></a> <span class="st">"pv_single_model"</span>, <span class="st">"pf_single_model"</span>, <span class="st">"pf_pv_pos"</span>,</span>
<span id="cb76-41"><a href="id_04_model_comparisons.html#cb76-41" aria-hidden="true" tabindex="-1"></a> <span class="st">"pfpv_combined_model"</span>, <span class="st">"pf_pv_unl"</span></span>
<span id="cb76-42"><a href="id_04_model_comparisons.html#cb76-42" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb76-43"><a href="id_04_model_comparisons.html#cb76-43" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(</span>
<span id="cb76-44"><a href="id_04_model_comparisons.html#cb76-44" aria-hidden="true" tabindex="-1"></a> <span class="st">"Heterologous model"</span>, <span class="st">"Autologous model"</span>,</span>
<span id="cb76-45"><a href="id_04_model_comparisons.html#cb76-45" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous with</span><span class="sc">\n</span><span class="st"> heterologous positives model"</span>,</span>
<span id="cb76-46"><a href="id_04_model_comparisons.html#cb76-46" aria-hidden="true" tabindex="-1"></a> <span class="st">"Combined model"</span>,</span>
<span id="cb76-47"><a href="id_04_model_comparisons.html#cb76-47" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous with</span><span class="sc">\n</span><span class="st"> heterologous unlabeled model"</span></span>
<span id="cb76-48"><a href="id_04_model_comparisons.html#cb76-48" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb76-49"><a href="id_04_model_comparisons.html#cb76-49" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> rev</span>
<span id="cb76-50"><a href="id_04_model_comparisons.html#cb76-50" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb76-51"><a href="id_04_model_comparisons.html#cb76-51" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb76-52"><a href="id_04_model_comparisons.html#cb76-52" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb76-53"><a href="id_04_model_comparisons.html#cb76-53" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb76-54"><a href="id_04_model_comparisons.html#cb76-54" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb76-55"><a href="id_04_model_comparisons.html#cb76-55" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb76-56"><a href="id_04_model_comparisons.html#cb76-56" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb76-57"><a href="id_04_model_comparisons.html#cb76-57" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb76-58"><a href="id_04_model_comparisons.html#cb76-58" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.5</span>, <span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb76-59"><a href="id_04_model_comparisons.html#cb76-59" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> ggplot2<span class="sc">::</span><span class="fu">margin</span>(<span class="dv">5</span>, <span class="dv">5</span>, <span class="dv">5</span>, <span class="dv">5</span>, <span class="st">"pt"</span>),</span>
<span id="cb76-60"><a href="id_04_model_comparisons.html#cb76-60" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.title =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb76-61"><a href="id_04_model_comparisons.html#cb76-61" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb76-62"><a href="id_04_model_comparisons.html#cb76-62" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="st">"none"</span></span>
<span id="cb76-63"><a href="id_04_model_comparisons.html#cb76-63" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb76-64"><a href="id_04_model_comparisons.html#cb76-64" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylim</span>(<span class="dv">0</span>, <span class="dv">1</span>) <span class="sc">+</span></span>
<span id="cb76-65"><a href="id_04_model_comparisons.html#cb76-65" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"Score (proportion of votes)"</span>)</span></code></pre></div>
<div class="sourceCode" id="cb77"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb77-1"><a href="id_04_model_comparisons.html#cb77-1" aria-hidden="true" tabindex="-1"></a>p_combined <span class="ot"><-</span> <span class="fu">plot_grid</span>(p1, p2, <span class="fu">plot_grid</span>(<span class="cn">NULL</span>, legend, <span class="at">rel_widths =</span> <span class="fu">c</span>(<span class="fl">0.2</span>, <span class="fl">0.8</span>)),</span>
<span id="cb77-2"><a href="id_04_model_comparisons.html#cb77-2" aria-hidden="true" tabindex="-1"></a> <span class="at">ncol =</span> <span class="dv">2</span>,</span>
<span id="cb77-3"><a href="id_04_model_comparisons.html#cb77-3" aria-hidden="true" tabindex="-1"></a> <span class="at">rel_heights =</span> <span class="fu">c</span>(<span class="dv">1</span>, <span class="fl">0.1</span>), <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"a"</span>, <span class="st">"b"</span>, <span class="st">""</span>, <span class="st">""</span>)</span>
<span id="cb77-4"><a href="id_04_model_comparisons.html#cb77-4" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb77-5"><a href="id_04_model_comparisons.html#cb77-5" aria-hidden="true" tabindex="-1"></a>p_combined</span></code></pre></div>
<div class="sourceCode" id="cb78"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb78-1"><a href="id_04_model_comparisons.html#cb78-1" aria-hidden="true" tabindex="-1"></a><span class="fu">png</span>(<span class="at">file =</span> <span class="st">"./figures/Fig 2.png"</span>, <span class="at">width =</span> <span class="dv">7500</span>, <span class="at">height =</span> <span class="dv">4000</span>, <span class="at">res =</span> <span class="dv">600</span>)</span>
<span id="cb78-2"><a href="id_04_model_comparisons.html#cb78-2" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(p_combined)</span>
<span id="cb78-3"><a href="id_04_model_comparisons.html#cb78-3" aria-hidden="true" tabindex="-1"></a><span class="fu">dev.off</span>()</span>
<span id="cb78-4"><a href="id_04_model_comparisons.html#cb78-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb78-5"><a href="id_04_model_comparisons.html#cb78-5" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span>(<span class="at">file =</span> <span class="st">"../figures/Fig 2.pdf"</span>, <span class="at">width =</span> <span class="dv">13</span>, <span class="at">height =</span> <span class="dv">7</span>)</span>
<span id="cb78-6"><a href="id_04_model_comparisons.html#cb78-6" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(p_combined)</span>
<span id="cb78-7"><a href="id_04_model_comparisons.html#cb78-7" aria-hidden="true" tabindex="-1"></a><span class="fu">dev.off</span>()</span></code></pre></div>
<p><img src="figures/Fig%202.png" width="100%" style="display: block; margin: auto;" /></p>
</div>
<div id="known-antigen-prediction-summary" class="section level2 hasAnchor" number="4.2">
<h2><span class="header-section-number">4.2</span> Known antigen prediction summary<a href="id_04_model_comparisons.html#known-antigen-prediction-summary" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><strong>In R: </strong></p>
<div class="sourceCode" id="cb79"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb79-1"><a href="id_04_model_comparisons.html#cb79-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(pracma)</span>
<span id="cb79-2"><a href="id_04_model_comparisons.html#cb79-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggsci)</span></code></pre></div>
<div class="sourceCode" id="cb80"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb80-1"><a href="id_04_model_comparisons.html#cb80-1" aria-hidden="true" tabindex="-1"></a>pv_scores <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pv_known_antigen_scores.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb80-2"><a href="id_04_model_comparisons.html#cb80-2" aria-hidden="true" tabindex="-1"></a>pv_unl_scores <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pv_unlabeled_protein_scores.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb80-3"><a href="id_04_model_comparisons.html#cb80-3" aria-hidden="true" tabindex="-1"></a>pv_scores<span class="sc">$</span>label <span class="ot"><-</span> <span class="dv">1</span></span>
<span id="cb80-4"><a href="id_04_model_comparisons.html#cb80-4" aria-hidden="true" tabindex="-1"></a>pv_unl_scores<span class="sc">$</span>label <span class="ot"><-</span> <span class="dv">0</span></span>
<span id="cb80-5"><a href="id_04_model_comparisons.html#cb80-5" aria-hidden="true" tabindex="-1"></a>pv_all <span class="ot"><-</span> <span class="fu">rbind</span>(pv_scores, pv_unl_scores)</span>
<span id="cb80-6"><a href="id_04_model_comparisons.html#cb80-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb80-7"><a href="id_04_model_comparisons.html#cb80-7" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">data.frame</span>(</span>
<span id="cb80-8"><a href="id_04_model_comparisons.html#cb80-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"antigen_label"</span> <span class="ot">=</span> pv_all<span class="sc">$</span>label,</span>
<span id="cb80-9"><a href="id_04_model_comparisons.html#cb80-9" aria-hidden="true" tabindex="-1"></a> <span class="st">"Heterologous model"</span> <span class="ot">=</span> pv_all<span class="sc">$</span>pf_single_model,</span>
<span id="cb80-10"><a href="id_04_model_comparisons.html#cb80-10" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous model"</span> <span class="ot">=</span> pv_all<span class="sc">$</span>pv_single_model,</span>
<span id="cb80-11"><a href="id_04_model_comparisons.html#cb80-11" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous with heterologous positives model"</span> <span class="ot">=</span> pv_all<span class="sc">$</span>pv_pf_pos,</span>
<span id="cb80-12"><a href="id_04_model_comparisons.html#cb80-12" aria-hidden="true" tabindex="-1"></a> <span class="st">"Combined model"</span> <span class="ot">=</span> pv_all<span class="sc">$</span>pfpv_combined_model,</span>
<span id="cb80-13"><a href="id_04_model_comparisons.html#cb80-13" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous with heterologous unlabeled model"</span> <span class="ot">=</span> pv_all<span class="sc">$</span>pv_pf_unl,</span>
<span id="cb80-14"><a href="id_04_model_comparisons.html#cb80-14" aria-hidden="true" tabindex="-1"></a> <span class="at">check.names =</span> <span class="cn">FALSE</span></span>
<span id="cb80-15"><a href="id_04_model_comparisons.html#cb80-15" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb80-16"><a href="id_04_model_comparisons.html#cb80-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb80-17"><a href="id_04_model_comparisons.html#cb80-17" aria-hidden="true" tabindex="-1"></a><span class="co"># Calculate percent rank for labeled positives</span></span>
<span id="cb80-18"><a href="id_04_model_comparisons.html#cb80-18" aria-hidden="true" tabindex="-1"></a>model_names <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb80-19"><a href="id_04_model_comparisons.html#cb80-19" aria-hidden="true" tabindex="-1"></a>x <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb80-20"><a href="id_04_model_comparisons.html#cb80-20" aria-hidden="true" tabindex="-1"></a>percent_rank <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb80-21"><a href="id_04_model_comparisons.html#cb80-21" aria-hidden="true" tabindex="-1"></a>auc <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb80-22"><a href="id_04_model_comparisons.html#cb80-22" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (model <span class="cf">in</span> <span class="fu">colnames</span>(data)[<span class="sc">-</span><span class="dv">1</span>]) {</span>
<span id="cb80-23"><a href="id_04_model_comparisons.html#cb80-23" aria-hidden="true" tabindex="-1"></a> data_ <span class="ot"><-</span> data[<span class="fu">c</span>(<span class="st">"antigen_label"</span>, model)]</span>
<span id="cb80-24"><a href="id_04_model_comparisons.html#cb80-24" aria-hidden="true" tabindex="-1"></a> percent_rank_ <span class="ot"><-</span> (<span class="fu">rank</span>(data_[[model]]) <span class="sc">/</span> <span class="fu">nrow</span>(data))[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">1</span>]</span>
<span id="cb80-25"><a href="id_04_model_comparisons.html#cb80-25" aria-hidden="true" tabindex="-1"></a> percent_rank <span class="ot"><-</span> <span class="fu">c</span>(percent_rank, percent_rank_[<span class="fu">order</span>(<span class="sc">-</span>percent_rank_)])</span>
<span id="cb80-26"><a href="id_04_model_comparisons.html#cb80-26" aria-hidden="true" tabindex="-1"></a> data_ <span class="ot"><-</span> data_[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">1</span>, ]</span>
<span id="cb80-27"><a href="id_04_model_comparisons.html#cb80-27" aria-hidden="true" tabindex="-1"></a> data_ <span class="ot"><-</span> data_[<span class="fu">order</span>(<span class="sc">-</span>percent_rank_), ]</span>
<span id="cb80-28"><a href="id_04_model_comparisons.html#cb80-28" aria-hidden="true" tabindex="-1"></a> x_ <span class="ot"><-</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">nrow</span>(data_) <span class="sc">/</span> <span class="fu">nrow</span>(data_)</span>
<span id="cb80-29"><a href="id_04_model_comparisons.html#cb80-29" aria-hidden="true" tabindex="-1"></a> x <span class="ot"><-</span> <span class="fu">c</span>(x, x_)</span>
<span id="cb80-30"><a href="id_04_model_comparisons.html#cb80-30" aria-hidden="true" tabindex="-1"></a> model_names <span class="ot"><-</span> <span class="fu">c</span>(model_names, <span class="fu">rep</span>(model, <span class="fu">nrow</span>(data_)))</span>
<span id="cb80-31"><a href="id_04_model_comparisons.html#cb80-31" aria-hidden="true" tabindex="-1"></a> auc <span class="ot"><-</span> <span class="fu">c</span>(auc, <span class="fu">round</span>(<span class="fu">trapz</span>(<span class="fu">c</span>(<span class="dv">0</span>, x_, <span class="dv">1</span>), <span class="fu">c</span>(<span class="dv">1</span>, percent_rank_, <span class="dv">0</span>)), <span class="dv">2</span>))</span>
<span id="cb80-32"><a href="id_04_model_comparisons.html#cb80-32" aria-hidden="true" tabindex="-1"></a> <span class="fu">cat</span>(<span class="fu">paste0</span>(<span class="st">"EPR: "</span>, <span class="fu">sum</span>(data_[[model]] <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="sc">/</span> <span class="fu">nrow</span>(data_), <span class="st">"</span><span class="sc">\n</span><span class="st">"</span>))</span>
<span id="cb80-33"><a href="id_04_model_comparisons.html#cb80-33" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb80-34"><a href="id_04_model_comparisons.html#cb80-34" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(auc) <span class="ot"><-</span> <span class="fu">colnames</span>(data)[<span class="sc">-</span><span class="dv">1</span>]</span>
<span id="cb80-35"><a href="id_04_model_comparisons.html#cb80-35" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb80-36"><a href="id_04_model_comparisons.html#cb80-36" aria-hidden="true" tabindex="-1"></a>res <span class="ot"><-</span> <span class="fu">data.frame</span>(<span class="at">model =</span> model_names, <span class="at">x =</span> x, <span class="at">percent_rank =</span> percent_rank)</span>
<span id="cb80-37"><a href="id_04_model_comparisons.html#cb80-37" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb80-38"><a href="id_04_model_comparisons.html#cb80-38" aria-hidden="true" tabindex="-1"></a>p1 <span class="ot"><-</span> <span class="fu">ggplot</span>(res, <span class="fu">aes</span>(<span class="at">x =</span> x, <span class="at">y =</span> <span class="st">`</span><span class="at">percent_rank</span><span class="st">`</span>, <span class="at">group =</span> model)) <span class="sc">+</span></span>
<span id="cb80-39"><a href="id_04_model_comparisons.html#cb80-39" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="fl">0.5</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>, <span class="at">color =</span> <span class="st">"grey50"</span>) <span class="sc">+</span></span>
<span id="cb80-40"><a href="id_04_model_comparisons.html#cb80-40" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_line</span>(<span class="at">linewidth =</span> <span class="fl">0.1</span>, <span class="at">color =</span> <span class="st">"grey30"</span>) <span class="sc">+</span></span>
<span id="cb80-41"><a href="id_04_model_comparisons.html#cb80-41" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>(<span class="fu">aes</span>(<span class="at">fill =</span> model),</span>
<span id="cb80-42"><a href="id_04_model_comparisons.html#cb80-42" aria-hidden="true" tabindex="-1"></a> <span class="at">size =</span> <span class="fl">2.2</span>, <span class="at">shape =</span> <span class="dv">21</span>, <span class="at">color =</span> <span class="st">"grey30"</span>, <span class="at">stroke =</span> <span class="fl">0.1</span>,</span>
<span id="cb80-43"><a href="id_04_model_comparisons.html#cb80-43" aria-hidden="true" tabindex="-1"></a> <span class="at">alpha =</span> <span class="fl">0.8</span></span>
<span id="cb80-44"><a href="id_04_model_comparisons.html#cb80-44" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb80-45"><a href="id_04_model_comparisons.html#cb80-45" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_jco</span>(</span>
<span id="cb80-46"><a href="id_04_model_comparisons.html#cb80-46" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">colnames</span>(data)[<span class="sc">-</span><span class="dv">1</span>][<span class="fu">order</span>(<span class="sc">-</span>auc)],</span>
<span id="cb80-47"><a href="id_04_model_comparisons.html#cb80-47" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">sapply</span>(<span class="fu">colnames</span>(data)[<span class="sc">-</span><span class="dv">1</span>][<span class="fu">order</span>(<span class="sc">-</span>auc)], <span class="cf">function</span>(x) {</span>
<span id="cb80-48"><a href="id_04_model_comparisons.html#cb80-48" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste0</span>(</span>
<span id="cb80-49"><a href="id_04_model_comparisons.html#cb80-49" aria-hidden="true" tabindex="-1"></a> x, <span class="st">" (AUC = "</span>,</span>
<span id="cb80-50"><a href="id_04_model_comparisons.html#cb80-50" aria-hidden="true" tabindex="-1"></a> auc[x], <span class="st">")"</span></span>
<span id="cb80-51"><a href="id_04_model_comparisons.html#cb80-51" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb80-52"><a href="id_04_model_comparisons.html#cb80-52" aria-hidden="true" tabindex="-1"></a> })</span>
<span id="cb80-53"><a href="id_04_model_comparisons.html#cb80-53" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb80-54"><a href="id_04_model_comparisons.html#cb80-54" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb80-55"><a href="id_04_model_comparisons.html#cb80-55" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb80-56"><a href="id_04_model_comparisons.html#cb80-56" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb80-57"><a href="id_04_model_comparisons.html#cb80-57" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb80-58"><a href="id_04_model_comparisons.html#cb80-58" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb80-59"><a href="id_04_model_comparisons.html#cb80-59" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb80-60"><a href="id_04_model_comparisons.html#cb80-60" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.5</span>, <span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb80-61"><a href="id_04_model_comparisons.html#cb80-61" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.5</span>, <span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">angle =</span> <span class="dv">0</span>),</span>
<span id="cb80-62"><a href="id_04_model_comparisons.html#cb80-62" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb80-63"><a href="id_04_model_comparisons.html#cb80-63" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="fu">c</span>(<span class="fl">0.34</span>, <span class="fl">0.16</span>),</span>
<span id="cb80-64"><a href="id_04_model_comparisons.html#cb80-64" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.background =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb80-65"><a href="id_04_model_comparisons.html#cb80-65" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.key =</span> <span class="fu">element_rect</span>(<span class="at">colour =</span> <span class="st">"transparent"</span>, <span class="at">fill =</span> <span class="st">"transparent"</span>)</span>
<span id="cb80-66"><a href="id_04_model_comparisons.html#cb80-66" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb80-67"><a href="id_04_model_comparisons.html#cb80-67" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">fill =</span> <span class="st">""</span>) <span class="sc">+</span></span>
<span id="cb80-68"><a href="id_04_model_comparisons.html#cb80-68" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylim</span>(<span class="dv">0</span>, <span class="dv">1</span>) <span class="sc">+</span></span>
<span id="cb80-69"><a href="id_04_model_comparisons.html#cb80-69" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">"Ranked known antigens (scaled)"</span>) <span class="sc">+</span></span>
<span id="cb80-70"><a href="id_04_model_comparisons.html#cb80-70" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"Percent rank"</span>)</span></code></pre></div>
<div class="sourceCode" id="cb81"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb81-1"><a href="id_04_model_comparisons.html#cb81-1" aria-hidden="true" tabindex="-1"></a>pf_scores <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pf_known_antigen_scores.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb81-2"><a href="id_04_model_comparisons.html#cb81-2" aria-hidden="true" tabindex="-1"></a>pf_unl_scores <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pf_unlabeled_protein_scores.csv"</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb81-3"><a href="id_04_model_comparisons.html#cb81-3" aria-hidden="true" tabindex="-1"></a>pf_scores<span class="sc">$</span>label <span class="ot"><-</span> <span class="dv">1</span></span>
<span id="cb81-4"><a href="id_04_model_comparisons.html#cb81-4" aria-hidden="true" tabindex="-1"></a>pf_unl_scores<span class="sc">$</span>label <span class="ot"><-</span> <span class="dv">0</span></span>
<span id="cb81-5"><a href="id_04_model_comparisons.html#cb81-5" aria-hidden="true" tabindex="-1"></a>pf_all <span class="ot"><-</span> <span class="fu">rbind</span>(pf_scores, pf_unl_scores)</span>
<span id="cb81-6"><a href="id_04_model_comparisons.html#cb81-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-7"><a href="id_04_model_comparisons.html#cb81-7" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">data.frame</span>(</span>
<span id="cb81-8"><a href="id_04_model_comparisons.html#cb81-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"antigen_label"</span> <span class="ot">=</span> pf_all<span class="sc">$</span>label,</span>
<span id="cb81-9"><a href="id_04_model_comparisons.html#cb81-9" aria-hidden="true" tabindex="-1"></a> <span class="st">"Heterologous model"</span> <span class="ot">=</span> pf_all<span class="sc">$</span>pv_single_model,</span>
<span id="cb81-10"><a href="id_04_model_comparisons.html#cb81-10" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous model"</span> <span class="ot">=</span> pf_all<span class="sc">$</span>pf_single_model,</span>
<span id="cb81-11"><a href="id_04_model_comparisons.html#cb81-11" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous with heterologous positives model"</span> <span class="ot">=</span> pf_all<span class="sc">$</span>pf_pv_pos,</span>
<span id="cb81-12"><a href="id_04_model_comparisons.html#cb81-12" aria-hidden="true" tabindex="-1"></a> <span class="st">"Combined model"</span> <span class="ot">=</span> pf_all<span class="sc">$</span>pfpv_combined_model,</span>
<span id="cb81-13"><a href="id_04_model_comparisons.html#cb81-13" aria-hidden="true" tabindex="-1"></a> <span class="st">"Autologous with heterologous unlabeled model"</span> <span class="ot">=</span> pf_all<span class="sc">$</span>pf_pv_unl,</span>
<span id="cb81-14"><a href="id_04_model_comparisons.html#cb81-14" aria-hidden="true" tabindex="-1"></a> <span class="at">check.names =</span> <span class="cn">FALSE</span></span>
<span id="cb81-15"><a href="id_04_model_comparisons.html#cb81-15" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-16"><a href="id_04_model_comparisons.html#cb81-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-17"><a href="id_04_model_comparisons.html#cb81-17" aria-hidden="true" tabindex="-1"></a><span class="co"># Calculate percent rank for labeled positives</span></span>
<span id="cb81-18"><a href="id_04_model_comparisons.html#cb81-18" aria-hidden="true" tabindex="-1"></a>model_names <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb81-19"><a href="id_04_model_comparisons.html#cb81-19" aria-hidden="true" tabindex="-1"></a>x <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb81-20"><a href="id_04_model_comparisons.html#cb81-20" aria-hidden="true" tabindex="-1"></a>percent_rank <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb81-21"><a href="id_04_model_comparisons.html#cb81-21" aria-hidden="true" tabindex="-1"></a>auc <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb81-22"><a href="id_04_model_comparisons.html#cb81-22" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (model <span class="cf">in</span> <span class="fu">colnames</span>(data)[<span class="sc">-</span><span class="dv">1</span>]) {</span>
<span id="cb81-23"><a href="id_04_model_comparisons.html#cb81-23" aria-hidden="true" tabindex="-1"></a> data_ <span class="ot"><-</span> data[<span class="fu">c</span>(<span class="st">"antigen_label"</span>, model)]</span>
<span id="cb81-24"><a href="id_04_model_comparisons.html#cb81-24" aria-hidden="true" tabindex="-1"></a> percent_rank_ <span class="ot"><-</span> (<span class="fu">rank</span>(data_[[model]]) <span class="sc">/</span> <span class="fu">nrow</span>(data))[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">1</span>]</span>
<span id="cb81-25"><a href="id_04_model_comparisons.html#cb81-25" aria-hidden="true" tabindex="-1"></a> percent_rank <span class="ot"><-</span> <span class="fu">c</span>(percent_rank, percent_rank_[<span class="fu">order</span>(<span class="sc">-</span>percent_rank_)])</span>
<span id="cb81-26"><a href="id_04_model_comparisons.html#cb81-26" aria-hidden="true" tabindex="-1"></a> data_ <span class="ot"><-</span> data_[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">1</span>, ]</span>
<span id="cb81-27"><a href="id_04_model_comparisons.html#cb81-27" aria-hidden="true" tabindex="-1"></a> data_ <span class="ot"><-</span> data_[<span class="fu">order</span>(<span class="sc">-</span>percent_rank_), ]</span>
<span id="cb81-28"><a href="id_04_model_comparisons.html#cb81-28" aria-hidden="true" tabindex="-1"></a> x_ <span class="ot"><-</span> <span class="dv">1</span><span class="sc">:</span><span class="fu">nrow</span>(data_) <span class="sc">/</span> <span class="fu">nrow</span>(data_)</span>
<span id="cb81-29"><a href="id_04_model_comparisons.html#cb81-29" aria-hidden="true" tabindex="-1"></a> x <span class="ot"><-</span> <span class="fu">c</span>(x, x_)</span>
<span id="cb81-30"><a href="id_04_model_comparisons.html#cb81-30" aria-hidden="true" tabindex="-1"></a> model_names <span class="ot"><-</span> <span class="fu">c</span>(model_names, <span class="fu">rep</span>(model, <span class="fu">nrow</span>(data_)))</span>
<span id="cb81-31"><a href="id_04_model_comparisons.html#cb81-31" aria-hidden="true" tabindex="-1"></a> auc <span class="ot"><-</span> <span class="fu">c</span>(auc, <span class="fu">round</span>(<span class="fu">trapz</span>(<span class="fu">c</span>(<span class="dv">0</span>, x_, <span class="dv">1</span>), <span class="fu">c</span>(<span class="dv">1</span>, percent_rank_, <span class="dv">0</span>)), <span class="dv">2</span>))</span>
<span id="cb81-32"><a href="id_04_model_comparisons.html#cb81-32" aria-hidden="true" tabindex="-1"></a> <span class="fu">cat</span>(<span class="fu">paste0</span>(<span class="st">"EPR: "</span>, <span class="fu">sum</span>(data_[[model]] <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="sc">/</span> <span class="fu">nrow</span>(data_), <span class="st">"</span><span class="sc">\n</span><span class="st">"</span>))</span>
<span id="cb81-33"><a href="id_04_model_comparisons.html#cb81-33" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb81-34"><a href="id_04_model_comparisons.html#cb81-34" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(auc) <span class="ot"><-</span> <span class="fu">colnames</span>(data)[<span class="sc">-</span><span class="dv">1</span>]</span>
<span id="cb81-35"><a href="id_04_model_comparisons.html#cb81-35" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-36"><a href="id_04_model_comparisons.html#cb81-36" aria-hidden="true" tabindex="-1"></a>res <span class="ot"><-</span> <span class="fu">data.frame</span>(<span class="at">model =</span> model_names, <span class="at">x =</span> x, <span class="at">percent_rank =</span> percent_rank)</span>
<span id="cb81-37"><a href="id_04_model_comparisons.html#cb81-37" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-38"><a href="id_04_model_comparisons.html#cb81-38" aria-hidden="true" tabindex="-1"></a>p2 <span class="ot"><-</span> <span class="fu">ggplot</span>(res, <span class="fu">aes</span>(<span class="at">x =</span> x, <span class="at">y =</span> <span class="st">`</span><span class="at">percent_rank</span><span class="st">`</span>, <span class="at">group =</span> model)) <span class="sc">+</span></span>
<span id="cb81-39"><a href="id_04_model_comparisons.html#cb81-39" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_hline</span>(<span class="at">yintercept =</span> <span class="fl">0.5</span>, <span class="at">linetype =</span> <span class="st">"dashed"</span>, <span class="at">color =</span> <span class="st">"grey50"</span>) <span class="sc">+</span></span>
<span id="cb81-40"><a href="id_04_model_comparisons.html#cb81-40" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_line</span>(<span class="at">linewidth =</span> <span class="fl">0.1</span>, <span class="at">color =</span> <span class="st">"grey30"</span>) <span class="sc">+</span></span>
<span id="cb81-41"><a href="id_04_model_comparisons.html#cb81-41" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>(<span class="fu">aes</span>(<span class="at">fill =</span> model),</span>
<span id="cb81-42"><a href="id_04_model_comparisons.html#cb81-42" aria-hidden="true" tabindex="-1"></a> <span class="at">size =</span> <span class="fl">2.2</span>, <span class="at">shape =</span> <span class="dv">21</span>, <span class="at">color =</span> <span class="st">"grey30"</span>, <span class="at">stroke =</span> <span class="fl">0.1</span>,</span>
<span id="cb81-43"><a href="id_04_model_comparisons.html#cb81-43" aria-hidden="true" tabindex="-1"></a> <span class="at">alpha =</span> <span class="fl">0.8</span></span>
<span id="cb81-44"><a href="id_04_model_comparisons.html#cb81-44" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb81-45"><a href="id_04_model_comparisons.html#cb81-45" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_jco</span>(</span>
<span id="cb81-46"><a href="id_04_model_comparisons.html#cb81-46" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">colnames</span>(data)[<span class="sc">-</span><span class="dv">1</span>][<span class="fu">order</span>(<span class="sc">-</span>auc)],</span>
<span id="cb81-47"><a href="id_04_model_comparisons.html#cb81-47" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">sapply</span>(<span class="fu">colnames</span>(data)[<span class="sc">-</span><span class="dv">1</span>][<span class="fu">order</span>(<span class="sc">-</span>auc)], <span class="cf">function</span>(x) {</span>
<span id="cb81-48"><a href="id_04_model_comparisons.html#cb81-48" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste0</span>(</span>
<span id="cb81-49"><a href="id_04_model_comparisons.html#cb81-49" aria-hidden="true" tabindex="-1"></a> x, <span class="st">" (AUC = "</span>,</span>
<span id="cb81-50"><a href="id_04_model_comparisons.html#cb81-50" aria-hidden="true" tabindex="-1"></a> auc[x], <span class="st">")"</span></span>
<span id="cb81-51"><a href="id_04_model_comparisons.html#cb81-51" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb81-52"><a href="id_04_model_comparisons.html#cb81-52" aria-hidden="true" tabindex="-1"></a> })</span>
<span id="cb81-53"><a href="id_04_model_comparisons.html#cb81-53" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb81-54"><a href="id_04_model_comparisons.html#cb81-54" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb81-55"><a href="id_04_model_comparisons.html#cb81-55" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb81-56"><a href="id_04_model_comparisons.html#cb81-56" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb81-57"><a href="id_04_model_comparisons.html#cb81-57" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb81-58"><a href="id_04_model_comparisons.html#cb81-58" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb81-59"><a href="id_04_model_comparisons.html#cb81-59" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb81-60"><a href="id_04_model_comparisons.html#cb81-60" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.5</span>, <span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb81-61"><a href="id_04_model_comparisons.html#cb81-61" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.title =</span> <span class="fu">element_text</span>(<span class="at">hjust =</span> <span class="fl">0.5</span>, <span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">angle =</span> <span class="dv">0</span>),</span>
<span id="cb81-62"><a href="id_04_model_comparisons.html#cb81-62" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb81-63"><a href="id_04_model_comparisons.html#cb81-63" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="fu">c</span>(<span class="fl">0.34</span>, <span class="fl">0.16</span>),</span>
<span id="cb81-64"><a href="id_04_model_comparisons.html#cb81-64" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.background =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb81-65"><a href="id_04_model_comparisons.html#cb81-65" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.key =</span> <span class="fu">element_rect</span>(<span class="at">colour =</span> <span class="st">"transparent"</span>, <span class="at">fill =</span> <span class="st">"transparent"</span>)</span>
<span id="cb81-66"><a href="id_04_model_comparisons.html#cb81-66" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb81-67"><a href="id_04_model_comparisons.html#cb81-67" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">fill =</span> <span class="st">""</span>) <span class="sc">+</span></span>
<span id="cb81-68"><a href="id_04_model_comparisons.html#cb81-68" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylim</span>(<span class="dv">0</span>, <span class="dv">1</span>) <span class="sc">+</span></span>
<span id="cb81-69"><a href="id_04_model_comparisons.html#cb81-69" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">"Ranked known antigens (scaled)"</span>) <span class="sc">+</span></span>
<span id="cb81-70"><a href="id_04_model_comparisons.html#cb81-70" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"Percent rank"</span>)</span></code></pre></div>
<div class="sourceCode" id="cb82"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb82-1"><a href="id_04_model_comparisons.html#cb82-1" aria-hidden="true" tabindex="-1"></a>p_combined <span class="ot"><-</span> <span class="fu">plot_grid</span>(p1, p2, <span class="at">nrow =</span> <span class="dv">1</span>, <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"a"</span>, <span class="st">"b"</span>))</span>
<span id="cb82-2"><a href="id_04_model_comparisons.html#cb82-2" aria-hidden="true" tabindex="-1"></a>p_combined</span></code></pre></div>
<div class="sourceCode" id="cb83"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb83-1"><a href="id_04_model_comparisons.html#cb83-1" aria-hidden="true" tabindex="-1"></a><span class="fu">png</span>(<span class="at">file =</span> <span class="st">"./figures/Supplementary Fig 6.png"</span>, <span class="at">width =</span> <span class="dv">7600</span>, <span class="at">height =</span> <span class="dv">3500</span>, <span class="at">res =</span> <span class="dv">600</span>)</span>
<span id="cb83-2"><a href="id_04_model_comparisons.html#cb83-2" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(p_combined)</span>
<span id="cb83-3"><a href="id_04_model_comparisons.html#cb83-3" aria-hidden="true" tabindex="-1"></a><span class="fu">dev.off</span>()</span>
<span id="cb83-4"><a href="id_04_model_comparisons.html#cb83-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb83-5"><a href="id_04_model_comparisons.html#cb83-5" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span>(<span class="at">file =</span> <span class="st">"../supplementary_figures/Supplementary Fig 6.pdf"</span>, <span class="at">width =</span> <span class="fl">15.2</span>, <span class="at">height =</span> <span class="dv">7</span>)</span>
<span id="cb83-6"><a href="id_04_model_comparisons.html#cb83-6" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(p_combined)</span>
<span id="cb83-7"><a href="id_04_model_comparisons.html#cb83-7" aria-hidden="true" tabindex="-1"></a><span class="fu">dev.off</span>()</span></code></pre></div>
<p><img src="figures/Supplementary%20Fig%206.png" width="100%" style="display: block; margin: auto;" /></p>
</div>
<div id="score-and-species-association" class="section level2 hasAnchor" number="4.3">
<h2><span class="header-section-number">4.3</span> Score and species association<a href="id_04_model_comparisons.html#score-and-species-association" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><strong>In R: </strong></p>
<div class="sourceCode" id="cb84"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb84-1"><a href="id_04_model_comparisons.html#cb84-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(scales)</span>
<span id="cb84-2"><a href="id_04_model_comparisons.html#cb84-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(rlist)</span>
<span id="cb84-3"><a href="id_04_model_comparisons.html#cb84-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(rcompanion)</span>
<span id="cb84-4"><a href="id_04_model_comparisons.html#cb84-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(DT)</span></code></pre></div>
<div class="sourceCode" id="cb85"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb85-1"><a href="id_04_model_comparisons.html#cb85-1" aria-hidden="true" tabindex="-1"></a>scientific <span class="ot"><-</span> <span class="cf">function</span>(x) {</span>
<span id="cb85-2"><a href="id_04_model_comparisons.html#cb85-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">ifelse</span>(x <span class="sc">==</span> <span class="dv">0</span>, <span class="st">"0"</span>, <span class="fu">gsub</span>(<span class="st">"e"</span>, <span class="st">" * 10^"</span>, <span class="fu">scientific_format</span>(<span class="at">digits =</span> <span class="dv">3</span>)(x)))</span>
<span id="cb85-3"><a href="id_04_model_comparisons.html#cb85-3" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb85-4"><a href="id_04_model_comparisons.html#cb85-4" aria-hidden="true" tabindex="-1"></a>contingency_table <span class="ot"><-</span> <span class="fu">list</span>()</span>
<span id="cb85-5"><a href="id_04_model_comparisons.html#cb85-5" aria-hidden="true" tabindex="-1"></a>chisq_pval <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb85-6"><a href="id_04_model_comparisons.html#cb85-6" aria-hidden="true" tabindex="-1"></a>cramer_res <span class="ot"><-</span> <span class="fu">list</span>()</span>
<span id="cb85-7"><a href="id_04_model_comparisons.html#cb85-7" aria-hidden="true" tabindex="-1"></a><span class="co"># Combined</span></span>
<span id="cb85-8"><a href="id_04_model_comparisons.html#cb85-8" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./data/supplementary_data_5_pfpv_purf_oob_predictions.csv"</span>, <span class="at">check.names =</span> <span class="cn">FALSE</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb85-9"><a href="id_04_model_comparisons.html#cb85-9" aria-hidden="true" tabindex="-1"></a>pred <span class="ot"><-</span> <span class="fu">sapply</span>(data<span class="sc">$</span><span class="st">`</span><span class="at">OOB score filtered</span><span class="st">`</span>[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>], <span class="cf">function</span>(x) <span class="cf">if</span> (x <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="st">"pos"</span> <span class="cf">else</span> <span class="st">"neg"</span>)</span>
<span id="cb85-10"><a href="id_04_model_comparisons.html#cb85-10" aria-hidden="true" tabindex="-1"></a>species <span class="ot"><-</span> data<span class="sc">$</span>species[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>]</span>
<span id="cb85-11"><a href="id_04_model_comparisons.html#cb85-11" aria-hidden="true" tabindex="-1"></a>M <span class="ot"><-</span> <span class="fu">table</span>(pred, species)</span>
<span id="cb85-12"><a href="id_04_model_comparisons.html#cb85-12" aria-hidden="true" tabindex="-1"></a>Xsq <span class="ot"><-</span> <span class="fu">chisq.test</span>(M, <span class="at">correct =</span> <span class="cn">FALSE</span>)</span>
<span id="cb85-13"><a href="id_04_model_comparisons.html#cb85-13" aria-hidden="true" tabindex="-1"></a>cramerV <span class="ot"><-</span> <span class="fu">cramerV</span>(M, <span class="at">ci =</span> <span class="cn">TRUE</span>)</span>
<span id="cb85-14"><a href="id_04_model_comparisons.html#cb85-14" aria-hidden="true" tabindex="-1"></a>contingency_table <span class="ot"><-</span> <span class="fu">list.append</span>(contingency_table, M)</span>
<span id="cb85-15"><a href="id_04_model_comparisons.html#cb85-15" aria-hidden="true" tabindex="-1"></a>chisq_pval <span class="ot"><-</span> <span class="fu">c</span>(chisq_pval, Xsq<span class="sc">$</span>p.value)</span>
<span id="cb85-16"><a href="id_04_model_comparisons.html#cb85-16" aria-hidden="true" tabindex="-1"></a>cramer_res <span class="ot"><-</span> <span class="fu">list.append</span>(cramer_res, <span class="fu">sprintf</span>(<span class="st">"%0.2f"</span>, cramerV))</span>
<span id="cb85-17"><a href="id_04_model_comparisons.html#cb85-17" aria-hidden="true" tabindex="-1"></a><span class="co"># P. vivax & P. falciparum single models</span></span>
<span id="cb85-18"><a href="id_04_model_comparisons.html#cb85-18" aria-hidden="true" tabindex="-1"></a>data_1 <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pf_single_pv_single_scores.csv"</span>, <span class="at">check.names =</span> <span class="cn">FALSE</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb85-19"><a href="id_04_model_comparisons.html#cb85-19" aria-hidden="true" tabindex="-1"></a>data_2 <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pf_single_pv_single_cross_predictions.csv"</span>, <span class="at">check.names =</span> <span class="cn">FALSE</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb85-20"><a href="id_04_model_comparisons.html#cb85-20" aria-hidden="true" tabindex="-1"></a>pred_1 <span class="ot"><-</span> <span class="fu">sapply</span>(data_1<span class="sc">$</span><span class="st">`</span><span class="at">OOB score filtered</span><span class="st">`</span>[data_1<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>], <span class="cf">function</span>(x) <span class="cf">if</span> (x <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="st">"pos"</span> <span class="cf">else</span> <span class="st">"neg"</span>)</span>
<span id="cb85-21"><a href="id_04_model_comparisons.html#cb85-21" aria-hidden="true" tabindex="-1"></a>species_1 <span class="ot"><-</span> data_1<span class="sc">$</span>species[data_1<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>]</span>
<span id="cb85-22"><a href="id_04_model_comparisons.html#cb85-22" aria-hidden="true" tabindex="-1"></a>pred_2 <span class="ot"><-</span> <span class="fu">sapply</span>(data_2<span class="sc">$</span><span class="st">`</span><span class="at">OOB score filtered</span><span class="st">`</span>[data_2<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>], <span class="cf">function</span>(x) <span class="cf">if</span> (x <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="st">"pos"</span> <span class="cf">else</span> <span class="st">"neg"</span>)</span>
<span id="cb85-23"><a href="id_04_model_comparisons.html#cb85-23" aria-hidden="true" tabindex="-1"></a>species_2 <span class="ot"><-</span> data_2<span class="sc">$</span>species[data_2<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>]</span>
<span id="cb85-24"><a href="id_04_model_comparisons.html#cb85-24" aria-hidden="true" tabindex="-1"></a><span class="do">## P. vivax</span></span>
<span id="cb85-25"><a href="id_04_model_comparisons.html#cb85-25" aria-hidden="true" tabindex="-1"></a>M <span class="ot"><-</span> <span class="fu">table</span>(</span>
<span id="cb85-26"><a href="id_04_model_comparisons.html#cb85-26" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(pred_1[species_1 <span class="sc">==</span> <span class="st">"pv"</span>], pred_2[species_2 <span class="sc">==</span> <span class="st">"pf"</span>]),</span>
<span id="cb85-27"><a href="id_04_model_comparisons.html#cb85-27" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="fu">rep</span>(<span class="st">"pv"</span>, <span class="fu">length</span>(pred_1[species_1 <span class="sc">==</span> <span class="st">"pv"</span>])), <span class="fu">rep</span>(<span class="st">"pf"</span>, <span class="fu">length</span>(pred_2[species_2 <span class="sc">==</span> <span class="st">"pf"</span>])))</span>
<span id="cb85-28"><a href="id_04_model_comparisons.html#cb85-28" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb85-29"><a href="id_04_model_comparisons.html#cb85-29" aria-hidden="true" tabindex="-1"></a>Xsq <span class="ot"><-</span> <span class="fu">chisq.test</span>(M, <span class="at">correct =</span> <span class="cn">FALSE</span>)</span>
<span id="cb85-30"><a href="id_04_model_comparisons.html#cb85-30" aria-hidden="true" tabindex="-1"></a>cramerV <span class="ot"><-</span> <span class="fu">cramerV</span>(M, <span class="at">ci =</span> <span class="cn">TRUE</span>)</span>
<span id="cb85-31"><a href="id_04_model_comparisons.html#cb85-31" aria-hidden="true" tabindex="-1"></a>contingency_table <span class="ot"><-</span> <span class="fu">list.append</span>(contingency_table, M)</span>
<span id="cb85-32"><a href="id_04_model_comparisons.html#cb85-32" aria-hidden="true" tabindex="-1"></a>chisq_pval <span class="ot"><-</span> <span class="fu">c</span>(chisq_pval, Xsq<span class="sc">$</span>p.value)</span>
<span id="cb85-33"><a href="id_04_model_comparisons.html#cb85-33" aria-hidden="true" tabindex="-1"></a>cramer_res <span class="ot"><-</span> <span class="fu">list.append</span>(cramer_res, <span class="fu">sprintf</span>(<span class="st">"%0.2f"</span>, cramerV))</span>
<span id="cb85-34"><a href="id_04_model_comparisons.html#cb85-34" aria-hidden="true" tabindex="-1"></a><span class="do">## P. falciparum</span></span>
<span id="cb85-35"><a href="id_04_model_comparisons.html#cb85-35" aria-hidden="true" tabindex="-1"></a>M <span class="ot"><-</span> <span class="fu">table</span>(</span>
<span id="cb85-36"><a href="id_04_model_comparisons.html#cb85-36" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(pred_1[species_1 <span class="sc">==</span> <span class="st">"pf"</span>], pred_2[species_2 <span class="sc">==</span> <span class="st">"pv"</span>]),</span>
<span id="cb85-37"><a href="id_04_model_comparisons.html#cb85-37" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="fu">rep</span>(<span class="st">"pf"</span>, <span class="fu">length</span>(pred_1[species_1 <span class="sc">==</span> <span class="st">"pf"</span>])), <span class="fu">rep</span>(<span class="st">"pv"</span>, <span class="fu">length</span>(pred_2[species_2 <span class="sc">==</span> <span class="st">"pv"</span>])))</span>
<span id="cb85-38"><a href="id_04_model_comparisons.html#cb85-38" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb85-39"><a href="id_04_model_comparisons.html#cb85-39" aria-hidden="true" tabindex="-1"></a>Xsq <span class="ot"><-</span> <span class="fu">chisq.test</span>(M, <span class="at">correct =</span> <span class="cn">FALSE</span>)</span>
<span id="cb85-40"><a href="id_04_model_comparisons.html#cb85-40" aria-hidden="true" tabindex="-1"></a>cramerV <span class="ot"><-</span> <span class="fu">cramerV</span>(M, <span class="at">ci =</span> <span class="cn">TRUE</span>)</span>
<span id="cb85-41"><a href="id_04_model_comparisons.html#cb85-41" aria-hidden="true" tabindex="-1"></a>contingency_table <span class="ot"><-</span> <span class="fu">list.append</span>(contingency_table, M)</span>
<span id="cb85-42"><a href="id_04_model_comparisons.html#cb85-42" aria-hidden="true" tabindex="-1"></a>chisq_pval <span class="ot"><-</span> <span class="fu">c</span>(chisq_pval, Xsq<span class="sc">$</span>p.value)</span>
<span id="cb85-43"><a href="id_04_model_comparisons.html#cb85-43" aria-hidden="true" tabindex="-1"></a>cramer_res <span class="ot"><-</span> <span class="fu">list.append</span>(cramer_res, <span class="fu">sprintf</span>(<span class="st">"%0.2f"</span>, cramerV))</span>
<span id="cb85-44"><a href="id_04_model_comparisons.html#cb85-44" aria-hidden="true" tabindex="-1"></a><span class="co"># P. vivax with heterologous positives</span></span>
<span id="cb85-45"><a href="id_04_model_comparisons.html#cb85-45" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pv_pf_pos_scores.csv"</span>, <span class="at">check.names =</span> <span class="cn">FALSE</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb85-46"><a href="id_04_model_comparisons.html#cb85-46" aria-hidden="true" tabindex="-1"></a>pred <span class="ot"><-</span> <span class="fu">sapply</span>(data<span class="sc">$</span><span class="st">`</span><span class="at">OOB scores</span><span class="st">`</span>[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>], <span class="cf">function</span>(x) <span class="cf">if</span> (x <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="st">"pos"</span> <span class="cf">else</span> <span class="st">"neg"</span>)</span>
<span id="cb85-47"><a href="id_04_model_comparisons.html#cb85-47" aria-hidden="true" tabindex="-1"></a>species <span class="ot"><-</span> data<span class="sc">$</span>species[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>]</span>
<span id="cb85-48"><a href="id_04_model_comparisons.html#cb85-48" aria-hidden="true" tabindex="-1"></a>M <span class="ot"><-</span> <span class="fu">table</span>(pred, species)</span>
<span id="cb85-49"><a href="id_04_model_comparisons.html#cb85-49" aria-hidden="true" tabindex="-1"></a>Xsq <span class="ot"><-</span> <span class="fu">chisq.test</span>(M, <span class="at">correct =</span> <span class="cn">FALSE</span>)</span>
<span id="cb85-50"><a href="id_04_model_comparisons.html#cb85-50" aria-hidden="true" tabindex="-1"></a>cramerV <span class="ot"><-</span> <span class="fu">cramerV</span>(M, <span class="at">ci =</span> <span class="cn">TRUE</span>)</span>
<span id="cb85-51"><a href="id_04_model_comparisons.html#cb85-51" aria-hidden="true" tabindex="-1"></a>contingency_table <span class="ot"><-</span> <span class="fu">list.append</span>(contingency_table, M)</span>
<span id="cb85-52"><a href="id_04_model_comparisons.html#cb85-52" aria-hidden="true" tabindex="-1"></a>chisq_pval <span class="ot"><-</span> <span class="fu">c</span>(chisq_pval, Xsq<span class="sc">$</span>p.value)</span>
<span id="cb85-53"><a href="id_04_model_comparisons.html#cb85-53" aria-hidden="true" tabindex="-1"></a>cramer_res <span class="ot"><-</span> <span class="fu">list.append</span>(cramer_res, <span class="fu">sprintf</span>(<span class="st">"%0.2f"</span>, cramerV))</span>
<span id="cb85-54"><a href="id_04_model_comparisons.html#cb85-54" aria-hidden="true" tabindex="-1"></a><span class="co"># P. falciparum with heterologous positives</span></span>
<span id="cb85-55"><a href="id_04_model_comparisons.html#cb85-55" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pf_pv_pos_scores.csv"</span>, <span class="at">check.names =</span> <span class="cn">FALSE</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb85-56"><a href="id_04_model_comparisons.html#cb85-56" aria-hidden="true" tabindex="-1"></a>pred <span class="ot"><-</span> <span class="fu">sapply</span>(data<span class="sc">$</span><span class="st">`</span><span class="at">OOB scores</span><span class="st">`</span>[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>], <span class="cf">function</span>(x) <span class="cf">if</span> (x <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="st">"pos"</span> <span class="cf">else</span> <span class="st">"neg"</span>)</span>
<span id="cb85-57"><a href="id_04_model_comparisons.html#cb85-57" aria-hidden="true" tabindex="-1"></a>species <span class="ot"><-</span> data<span class="sc">$</span>species[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>]</span>
<span id="cb85-58"><a href="id_04_model_comparisons.html#cb85-58" aria-hidden="true" tabindex="-1"></a>M <span class="ot"><-</span> <span class="fu">table</span>(pred, species)</span>
<span id="cb85-59"><a href="id_04_model_comparisons.html#cb85-59" aria-hidden="true" tabindex="-1"></a>Xsq <span class="ot"><-</span> <span class="fu">chisq.test</span>(M, <span class="at">correct =</span> <span class="cn">FALSE</span>)</span>
<span id="cb85-60"><a href="id_04_model_comparisons.html#cb85-60" aria-hidden="true" tabindex="-1"></a>cramerV <span class="ot"><-</span> <span class="fu">cramerV</span>(M, <span class="at">ci =</span> <span class="cn">TRUE</span>)</span>
<span id="cb85-61"><a href="id_04_model_comparisons.html#cb85-61" aria-hidden="true" tabindex="-1"></a>contingency_table <span class="ot"><-</span> <span class="fu">list.append</span>(contingency_table, M)</span>
<span id="cb85-62"><a href="id_04_model_comparisons.html#cb85-62" aria-hidden="true" tabindex="-1"></a>chisq_pval <span class="ot"><-</span> <span class="fu">c</span>(chisq_pval, Xsq<span class="sc">$</span>p.value)</span>
<span id="cb85-63"><a href="id_04_model_comparisons.html#cb85-63" aria-hidden="true" tabindex="-1"></a>cramer_res <span class="ot"><-</span> <span class="fu">list.append</span>(cramer_res, <span class="fu">sprintf</span>(<span class="st">"%0.2f"</span>, cramerV))</span>
<span id="cb85-64"><a href="id_04_model_comparisons.html#cb85-64" aria-hidden="true" tabindex="-1"></a><span class="co"># P. vivax with heterologous unlabeled</span></span>
<span id="cb85-65"><a href="id_04_model_comparisons.html#cb85-65" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pv_pf_unl_scores.csv"</span>, <span class="at">check.names =</span> <span class="cn">FALSE</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb85-66"><a href="id_04_model_comparisons.html#cb85-66" aria-hidden="true" tabindex="-1"></a>pred <span class="ot"><-</span> <span class="fu">sapply</span>(data<span class="sc">$</span><span class="st">`</span><span class="at">OOB scores</span><span class="st">`</span>[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>], <span class="cf">function</span>(x) <span class="cf">if</span> (x <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="st">"pos"</span> <span class="cf">else</span> <span class="st">"neg"</span>)</span>
<span id="cb85-67"><a href="id_04_model_comparisons.html#cb85-67" aria-hidden="true" tabindex="-1"></a>species <span class="ot"><-</span> data<span class="sc">$</span>species[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>]</span>
<span id="cb85-68"><a href="id_04_model_comparisons.html#cb85-68" aria-hidden="true" tabindex="-1"></a>M <span class="ot"><-</span> <span class="fu">table</span>(pred, species)</span>
<span id="cb85-69"><a href="id_04_model_comparisons.html#cb85-69" aria-hidden="true" tabindex="-1"></a>Xsq <span class="ot"><-</span> <span class="fu">chisq.test</span>(M, <span class="at">correct =</span> <span class="cn">FALSE</span>)</span>
<span id="cb85-70"><a href="id_04_model_comparisons.html#cb85-70" aria-hidden="true" tabindex="-1"></a>cramerV <span class="ot"><-</span> <span class="fu">cramerV</span>(M, <span class="at">ci =</span> <span class="cn">TRUE</span>)</span>
<span id="cb85-71"><a href="id_04_model_comparisons.html#cb85-71" aria-hidden="true" tabindex="-1"></a>contingency_table <span class="ot"><-</span> <span class="fu">list.append</span>(contingency_table, M)</span>
<span id="cb85-72"><a href="id_04_model_comparisons.html#cb85-72" aria-hidden="true" tabindex="-1"></a>chisq_pval <span class="ot"><-</span> <span class="fu">c</span>(chisq_pval, Xsq<span class="sc">$</span>p.value)</span>
<span id="cb85-73"><a href="id_04_model_comparisons.html#cb85-73" aria-hidden="true" tabindex="-1"></a>cramer_res <span class="ot"><-</span> <span class="fu">list.append</span>(cramer_res, <span class="fu">sprintf</span>(<span class="st">"%0.2f"</span>, cramerV))</span>
<span id="cb85-74"><a href="id_04_model_comparisons.html#cb85-74" aria-hidden="true" tabindex="-1"></a><span class="co"># P. falciparum with heterologous unlabeled</span></span>
<span id="cb85-75"><a href="id_04_model_comparisons.html#cb85-75" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/pf_pv_unl_scores.csv"</span>, <span class="at">check.names =</span> <span class="cn">FALSE</span>, <span class="at">row.names =</span> <span class="dv">1</span>)</span>
<span id="cb85-76"><a href="id_04_model_comparisons.html#cb85-76" aria-hidden="true" tabindex="-1"></a>pred <span class="ot"><-</span> <span class="fu">sapply</span>(data<span class="sc">$</span><span class="st">`</span><span class="at">OOB scores</span><span class="st">`</span>[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>], <span class="cf">function</span>(x) <span class="cf">if</span> (x <span class="sc">>=</span> <span class="fl">0.5</span>) <span class="st">"pos"</span> <span class="cf">else</span> <span class="st">"neg"</span>)</span>
<span id="cb85-77"><a href="id_04_model_comparisons.html#cb85-77" aria-hidden="true" tabindex="-1"></a>species <span class="ot"><-</span> data<span class="sc">$</span>species[data<span class="sc">$</span>antigen_label <span class="sc">==</span> <span class="dv">0</span>]</span>
<span id="cb85-78"><a href="id_04_model_comparisons.html#cb85-78" aria-hidden="true" tabindex="-1"></a>M <span class="ot"><-</span> <span class="fu">table</span>(pred, species)</span>
<span id="cb85-79"><a href="id_04_model_comparisons.html#cb85-79" aria-hidden="true" tabindex="-1"></a>Xsq <span class="ot"><-</span> <span class="fu">chisq.test</span>(M, <span class="at">correct =</span> <span class="cn">FALSE</span>)</span>
<span id="cb85-80"><a href="id_04_model_comparisons.html#cb85-80" aria-hidden="true" tabindex="-1"></a>cramerV <span class="ot"><-</span> <span class="fu">cramerV</span>(M, <span class="at">ci =</span> <span class="cn">TRUE</span>)</span>
<span id="cb85-81"><a href="id_04_model_comparisons.html#cb85-81" aria-hidden="true" tabindex="-1"></a>contingency_table <span class="ot"><-</span> <span class="fu">list.append</span>(contingency_table, M)</span>
<span id="cb85-82"><a href="id_04_model_comparisons.html#cb85-82" aria-hidden="true" tabindex="-1"></a>chisq_pval <span class="ot"><-</span> <span class="fu">c</span>(chisq_pval, Xsq<span class="sc">$</span>p.value)</span>
<span id="cb85-83"><a href="id_04_model_comparisons.html#cb85-83" aria-hidden="true" tabindex="-1"></a>cramer_res <span class="ot"><-</span> <span class="fu">list.append</span>(cramer_res, <span class="fu">sprintf</span>(<span class="st">"%0.2f"</span>, cramerV))</span>
<span id="cb85-84"><a href="id_04_model_comparisons.html#cb85-84" aria-hidden="true" tabindex="-1"></a><span class="co"># Save results</span></span>
<span id="cb85-85"><a href="id_04_model_comparisons.html#cb85-85" aria-hidden="true" tabindex="-1"></a>df <span class="ot"><-</span> <span class="fu">as.data.frame</span>(<span class="fu">cbind</span>(</span>
<span id="cb85-86"><a href="id_04_model_comparisons.html#cb85-86" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb85-87"><a href="id_04_model_comparisons.html#cb85-87" aria-hidden="true" tabindex="-1"></a> <span class="st">"Combined"</span>, <span class="st">"P. vivax"</span>, <span class="st">"P. falciparum"</span>,</span>
<span id="cb85-88"><a href="id_04_model_comparisons.html#cb85-88" aria-hidden="true" tabindex="-1"></a> <span class="st">"P. vivax with heterologous positives"</span>,</span>
<span id="cb85-89"><a href="id_04_model_comparisons.html#cb85-89" aria-hidden="true" tabindex="-1"></a> <span class="st">"P. falciparum with heterologous positives"</span>,</span>
<span id="cb85-90"><a href="id_04_model_comparisons.html#cb85-90" aria-hidden="true" tabindex="-1"></a> <span class="st">"P. vivax with heterologous unlabeled"</span>,</span>
<span id="cb85-91"><a href="id_04_model_comparisons.html#cb85-91" aria-hidden="true" tabindex="-1"></a> <span class="st">"P. falciparum with heterologous unlabeled"</span></span>
<span id="cb85-92"><a href="id_04_model_comparisons.html#cb85-92" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb85-93"><a href="id_04_model_comparisons.html#cb85-93" aria-hidden="true" tabindex="-1"></a> chisq_pval, <span class="fu">do.call</span>(rbind, cramer_res)</span>
<span id="cb85-94"><a href="id_04_model_comparisons.html#cb85-94" aria-hidden="true" tabindex="-1"></a>))</span>
<span id="cb85-95"><a href="id_04_model_comparisons.html#cb85-95" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(df) <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"PURF model"</span>, <span class="st">"Chi-squared test p-value"</span>, <span class="st">"Cramer's V"</span>, <span class="st">"Lower CI"</span>, <span class="st">"Upper CI"</span>)</span>
<span id="cb85-96"><a href="id_04_model_comparisons.html#cb85-96" aria-hidden="true" tabindex="-1"></a>df<span class="sc">$</span><span class="st">`</span><span class="at">Chi-squared test p-value</span><span class="st">`</span> <span class="ot"><-</span> <span class="fu">sapply</span>(<span class="fu">as.numeric</span>(df<span class="sc">$</span><span class="st">`</span><span class="at">Chi-squared test p-value</span><span class="st">`</span>), scientific)</span>
<span id="cb85-97"><a href="id_04_model_comparisons.html#cb85-97" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(contingency_table) <span class="ot"><-</span> df<span class="sc">$</span><span class="st">`</span><span class="at">PURF model</span><span class="st">`</span></span>
<span id="cb85-98"><a href="id_04_model_comparisons.html#cb85-98" aria-hidden="true" tabindex="-1"></a><span class="fu">save</span>(contingency_table, df, <span class="at">file =</span> <span class="st">"./rdata/score_species_association.RData"</span>)</span></code></pre></div>
<div class="sourceCode" id="cb86"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb86-1"><a href="id_04_model_comparisons.html#cb86-1" aria-hidden="true" tabindex="-1"></a><span class="fu">load</span>(<span class="st">"./rdata/score_species_association.RData"</span>)</span>
<span id="cb86-2"><a href="id_04_model_comparisons.html#cb86-2" aria-hidden="true" tabindex="-1"></a>contingency_table</span></code></pre></div>
<pre><code>## $Combined
## species
## pred pf pv
## neg 2719 3814
## pos 2622 2639
##
## $`P. falciparum`
##
## pf pv
## neg 2897 3091
## pos 2444 3362
##
## $`P. vivax`
##
## pf pv
## neg 2451 3618
## pos 2890 2835
##
## $`P. falciparum with heterologous positives`
## species
## pred pf pv
## neg 2932 63
## pos 2409 6390
##
## $`P. vivax with heterologous positives`
## species
## pred pf pv
## neg 0 3695
## pos 5341 2758
##
## $`P. falciparum with heterologous unlabeled`
## species
## pred pf pv
## neg 108 6314
## pos 5233 139
##
## $`P. vivax with heterologous unlabeled`
## species
## pred pf pv
## neg 5133 1055
## pos 208 5398</code></pre>
<div class="sourceCode" id="cb88"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb88-1"><a href="id_04_model_comparisons.html#cb88-1" aria-hidden="true" tabindex="-1"></a>df <span class="sc">%>%</span></span>
<span id="cb88-2"><a href="id_04_model_comparisons.html#cb88-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">datatable</span>(<span class="at">rownames =</span> <span class="cn">FALSE</span>)</span></code></pre></div>
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-8f056c28eb67214a9e1d" style="width:100%;height:auto;"></div>
<script type="application/json" data-for="htmlwidget-8f056c28eb67214a9e1d">{"x":{"filter":"none","vertical":false,"data":[["Combined","P. falciparum","P. vivax","P. falciparum with heterologous positives","P. vivax with heterologous positives","P. falciparum with heterologous unlabeled","P. vivax with heterologous unlabeled"],["4.95 * 10^-19","7.08 * 10^-12","3.52 * 10^-28","0","0","0","0"],["0.08","0.06","0.10","0.62","0.61","0.96","0.80"],["0.06","0.05","0.08","0.61","0.60","0.95","0.78"],["0.10","0.08","0.12","0.63","0.62","0.96","0.80"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th>PURF model<\/th>\n <th>Chi-squared test p-value<\/th>\n <th>Cramer's V<\/th>\n <th>Lower CI<\/th>\n <th>Upper CI<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
</div>
<div id="tree-depth-analysis" class="section level2 hasAnchor" number="4.4">
<h2><span class="header-section-number">4.4</span> Tree depth analysis<a href="id_04_model_comparisons.html#tree-depth-analysis" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="analysis-3" class="section level3 hasAnchor" number="4.4.1">
<h3><span class="header-section-number">4.4.1</span> Analysis<a href="id_04_model_comparisons.html#analysis-3" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p><strong>In Python: </strong></p>
<div class="sourceCode" id="cb89"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb89-1"><a href="id_04_model_comparisons.html#cb89-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(reticulate)</span>
<span id="cb89-2"><a href="id_04_model_comparisons.html#cb89-2" aria-hidden="true" tabindex="-1"></a><span class="fu">use_condaenv</span>(<span class="st">"/Users/renee/Library/r-miniconda/envs/purf/bin/python"</span>)</span></code></pre></div>
<div class="sourceCode" id="cb90"><pre class="sourceCode python fold-hide"><code class="sourceCode python"><span id="cb90-1"><a href="id_04_model_comparisons.html#cb90-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
<span id="cb90-2"><a href="id_04_model_comparisons.html#cb90-2" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
<span id="cb90-3"><a href="id_04_model_comparisons.html#cb90-3" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pickle</span>
<span id="cb90-4"><a href="id_04_model_comparisons.html#cb90-4" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> purf.pu_ensemble <span class="im">import</span> PURandomForestClassifier</span>
<span id="cb90-5"><a href="id_04_model_comparisons.html#cb90-5" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> session_info</span></code></pre></div>
<div class="sourceCode" id="cb91"><pre class="sourceCode python fold-hide"><code class="sourceCode python"><span id="cb91-1"><a href="id_04_model_comparisons.html#cb91-1" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(<span class="st">'./pickle_data/pf_0.5_purf_tree_filtering.pkl'</span>, <span class="st">'rb'</span>) <span class="im">as</span> infile:</span>
<span id="cb91-2"><a href="id_04_model_comparisons.html#cb91-2" aria-hidden="true" tabindex="-1"></a> pf_single_model <span class="op">=</span> pickle.load(infile)</span>
<span id="cb91-3"><a href="id_04_model_comparisons.html#cb91-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb91-4"><a href="id_04_model_comparisons.html#cb91-4" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(<span class="st">'./pickle_data/pv_0.5_purf_tree_filtering.pkl'</span>, <span class="st">'rb'</span>) <span class="im">as</span> infile:</span>
<span id="cb91-5"><a href="id_04_model_comparisons.html#cb91-5" aria-hidden="true" tabindex="-1"></a> pv_single_model <span class="op">=</span> pickle.load(infile)</span>
<span id="cb91-6"><a href="id_04_model_comparisons.html#cb91-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb91-7"><a href="id_04_model_comparisons.html#cb91-7" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(<span class="st">'./pickle_data/pfpv_0.5_purf_tree_filtering.pkl'</span>, <span class="st">'rb'</span>) <span class="im">as</span> infile:</span>
<span id="cb91-8"><a href="id_04_model_comparisons.html#cb91-8" aria-hidden="true" tabindex="-1"></a> pfpv_combined_model <span class="op">=</span> pickle.load(infile)</span>
<span id="cb91-9"><a href="id_04_model_comparisons.html#cb91-9" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb91-10"><a href="id_04_model_comparisons.html#cb91-10" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(<span class="st">'./pickle_data/pf_pv_pos_purf.pkl'</span>, <span class="st">'rb'</span>) <span class="im">as</span> infile:</span>
<span id="cb91-11"><a href="id_04_model_comparisons.html#cb91-11" aria-hidden="true" tabindex="-1"></a> pf_pv_pos_model <span class="op">=</span> pickle.load(infile)</span>
<span id="cb91-12"><a href="id_04_model_comparisons.html#cb91-12" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb91-13"><a href="id_04_model_comparisons.html#cb91-13" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(<span class="st">'./pickle_data/pf_pv_unl_purf.pkl'</span>, <span class="st">'rb'</span>) <span class="im">as</span> infile:</span>
<span id="cb91-14"><a href="id_04_model_comparisons.html#cb91-14" aria-hidden="true" tabindex="-1"></a> pf_pv_unl_model <span class="op">=</span> pickle.load(infile)</span>
<span id="cb91-15"><a href="id_04_model_comparisons.html#cb91-15" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb91-16"><a href="id_04_model_comparisons.html#cb91-16" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(<span class="st">'./pickle_data/pv_pf_pos_purf.pkl'</span>, <span class="st">'rb'</span>) <span class="im">as</span> infile:</span>
<span id="cb91-17"><a href="id_04_model_comparisons.html#cb91-17" aria-hidden="true" tabindex="-1"></a> pv_pf_pos_model <span class="op">=</span> pickle.load(infile)</span>
<span id="cb91-18"><a href="id_04_model_comparisons.html#cb91-18" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb91-19"><a href="id_04_model_comparisons.html#cb91-19" aria-hidden="true" tabindex="-1"></a><span class="cf">with</span> <span class="bu">open</span>(<span class="st">'./pickle_data/pv_pf_unl_purf.pkl'</span>, <span class="st">'rb'</span>) <span class="im">as</span> infile:</span>
<span id="cb91-20"><a href="id_04_model_comparisons.html#cb91-20" aria-hidden="true" tabindex="-1"></a> pv_pf_unl_model <span class="op">=</span> pickle.load(infile)</span>
<span id="cb91-21"><a href="id_04_model_comparisons.html#cb91-21" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb91-22"><a href="id_04_model_comparisons.html#cb91-22" aria-hidden="true" tabindex="-1"></a>res <span class="op">=</span> pd.DataFrame({<span class="st">'pf_single_model'</span>: [tree.get_depth() <span class="cf">for</span> tree <span class="kw">in</span> pf_single_model[<span class="st">'model'</span>].estimators_],</span>
<span id="cb91-23"><a href="id_04_model_comparisons.html#cb91-23" aria-hidden="true" tabindex="-1"></a> <span class="st">'pv_single_model'</span>: [tree.get_depth() <span class="cf">for</span> tree <span class="kw">in</span> pv_single_model[<span class="st">'model'</span>].estimators_],</span>
<span id="cb91-24"><a href="id_04_model_comparisons.html#cb91-24" aria-hidden="true" tabindex="-1"></a> <span class="st">'pfpv_combined_model'</span>: [tree.get_depth() <span class="cf">for</span> tree <span class="kw">in</span> pfpv_combined_model[<span class="st">'model'</span>].estimators_],</span>
<span id="cb91-25"><a href="id_04_model_comparisons.html#cb91-25" aria-hidden="true" tabindex="-1"></a> <span class="st">'pf_pv_pos_model'</span>: [tree.get_depth() <span class="cf">for</span> tree <span class="kw">in</span> pf_pv_pos_model[<span class="st">'model'</span>].estimators_],</span>
<span id="cb91-26"><a href="id_04_model_comparisons.html#cb91-26" aria-hidden="true" tabindex="-1"></a> <span class="st">'pf_pv_unl_model'</span>: [tree.get_depth() <span class="cf">for</span> tree <span class="kw">in</span> pf_pv_unl_model[<span class="st">'model'</span>].estimators_],</span>
<span id="cb91-27"><a href="id_04_model_comparisons.html#cb91-27" aria-hidden="true" tabindex="-1"></a> <span class="st">'pv_pf_pos_model'</span>: [tree.get_depth() <span class="cf">for</span> tree <span class="kw">in</span> pv_pf_pos_model[<span class="st">'model'</span>].estimators_],</span>
<span id="cb91-28"><a href="id_04_model_comparisons.html#cb91-28" aria-hidden="true" tabindex="-1"></a> <span class="st">'pv_pf_unl_model'</span>: [tree.get_depth() <span class="cf">for</span> tree <span class="kw">in</span> pv_pf_unl_model[<span class="st">'model'</span>].estimators_]})</span>
<span id="cb91-29"><a href="id_04_model_comparisons.html#cb91-29" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb91-30"><a href="id_04_model_comparisons.html#cb91-30" aria-hidden="true" tabindex="-1"></a>res.to_csv(<span class="st">'./other_data/tree_depths.csv'</span>, index<span class="op">=</span><span class="va">False</span>)</span></code></pre></div>
<p><strong>In R</strong></p>
</div>
<div id="plotting-2" class="section level3 hasAnchor" number="4.4.2">
<h3><span class="header-section-number">4.4.2</span> Plotting<a href="id_04_model_comparisons.html#plotting-2" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div class="sourceCode" id="cb92"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb92-1"><a href="id_04_model_comparisons.html#cb92-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(psych)</span>
<span id="cb92-2"><a href="id_04_model_comparisons.html#cb92-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggrepel)</span></code></pre></div>
<div class="sourceCode" id="cb93"><pre class="sourceCode r fold-show"><code class="sourceCode r"><span id="cb93-1"><a href="id_04_model_comparisons.html#cb93-1" aria-hidden="true" tabindex="-1"></a>data <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"./other_data/tree_depths.csv"</span>)</span>
<span id="cb93-2"><a href="id_04_model_comparisons.html#cb93-2" aria-hidden="true" tabindex="-1"></a>proportion_positives <span class="ot"><-</span> <span class="fu">c</span>(<span class="dv">52</span> <span class="sc">/</span> <span class="dv">5393</span>, <span class="dv">90</span> <span class="sc">/</span> <span class="dv">5431</span>, <span class="dv">52</span> <span class="sc">/</span> <span class="dv">11846</span>, <span class="dv">38</span> <span class="sc">/</span> <span class="dv">6491</span>, <span class="dv">90</span> <span class="sc">/</span> <span class="dv">6543</span>, <span class="dv">38</span> <span class="sc">/</span> <span class="dv">11832</span>, <span class="dv">90</span> <span class="sc">/</span> <span class="dv">11884</span>)</span>
<span id="cb93-3"><a href="id_04_model_comparisons.html#cb93-3" aria-hidden="true" tabindex="-1"></a>mean_tree_depth <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb93-4"><a href="id_04_model_comparisons.html#cb93-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">mean</span>(data<span class="sc">$</span>pf_single_model), <span class="fu">mean</span>(data<span class="sc">$</span>pf_pv_pos_model), <span class="fu">mean</span>(data<span class="sc">$</span>pf_pv_unl_model),</span>
<span id="cb93-5"><a href="id_04_model_comparisons.html#cb93-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">mean</span>(data<span class="sc">$</span>pv_single_model), <span class="fu">mean</span>(data<span class="sc">$</span>pv_pf_pos_model), <span class="fu">mean</span>(data<span class="sc">$</span>pv_pf_unl_model),</span>
<span id="cb93-6"><a href="id_04_model_comparisons.html#cb93-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">mean</span>(data<span class="sc">$</span>pfpv_combined_model)</span>
<span id="cb93-7"><a href="id_04_model_comparisons.html#cb93-7" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb93-8"><a href="id_04_model_comparisons.html#cb93-8" aria-hidden="true" tabindex="-1"></a>sd_tree_depth <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb93-9"><a href="id_04_model_comparisons.html#cb93-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">sd</span>(data<span class="sc">$</span>pf_single_model), <span class="fu">sd</span>(data<span class="sc">$</span>pf_pv_pos_model), <span class="fu">sd</span>(data<span class="sc">$</span>pf_pv_unl_model),</span>
<span id="cb93-10"><a href="id_04_model_comparisons.html#cb93-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">sd</span>(data<span class="sc">$</span>pv_single_model), <span class="fu">sd</span>(data<span class="sc">$</span>pv_pf_pos_model), <span class="fu">sd</span>(data<span class="sc">$</span>pv_pf_unl_model),</span>
<span id="cb93-11"><a href="id_04_model_comparisons.html#cb93-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">sd</span>(data<span class="sc">$</span>pfpv_combined_model)</span>
<span id="cb93-12"><a href="id_04_model_comparisons.html#cb93-12" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb93-13"><a href="id_04_model_comparisons.html#cb93-13" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb93-14"><a href="id_04_model_comparisons.html#cb93-14" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-15"><a href="id_04_model_comparisons.html#cb93-15" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-16"><a href="id_04_model_comparisons.html#cb93-16" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"No transformation</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-17"><a href="id_04_model_comparisons.html#cb93-17" aria-hidden="true" tabindex="-1"></a><span class="do">## No transformation</span></span>
<span id="cb93-18"><a href="id_04_model_comparisons.html#cb93-18" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-19"><a href="id_04_model_comparisons.html#cb93-19" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-20"><a href="id_04_model_comparisons.html#cb93-20" aria-hidden="true" tabindex="-1"></a>res <span class="ot"><-</span> <span class="fu">lm</span>(mean_tree_depth <span class="sc">~</span> proportion_positives,</span>
<span id="cb93-21"><a href="id_04_model_comparisons.html#cb93-21" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> <span class="fu">data.frame</span>(</span>
<span id="cb93-22"><a href="id_04_model_comparisons.html#cb93-22" aria-hidden="true" tabindex="-1"></a> <span class="at">proportion_positives =</span> proportion_positives,</span>
<span id="cb93-23"><a href="id_04_model_comparisons.html#cb93-23" aria-hidden="true" tabindex="-1"></a> <span class="at">mean_tree_depth =</span> mean_tree_depth</span>
<span id="cb93-24"><a href="id_04_model_comparisons.html#cb93-24" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb93-25"><a href="id_04_model_comparisons.html#cb93-25" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb93-26"><a href="id_04_model_comparisons.html#cb93-26" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(res)</span>
<span id="cb93-27"><a href="id_04_model_comparisons.html#cb93-27" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-28"><a href="id_04_model_comparisons.html#cb93-28" aria-hidden="true" tabindex="-1"></a><span class="do">## Call:</span></span>
<span id="cb93-29"><a href="id_04_model_comparisons.html#cb93-29" aria-hidden="true" tabindex="-1"></a><span class="do">## lm(formula = mean_tree_depth ~ proportion_positives, data = data.frame(proportion_positives = proportion_positives, </span></span>
<span id="cb93-30"><a href="id_04_model_comparisons.html#cb93-30" aria-hidden="true" tabindex="-1"></a><span class="do">## mean_tree_depth = mean_tree_depth))</span></span>
<span id="cb93-31"><a href="id_04_model_comparisons.html#cb93-31" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-32"><a href="id_04_model_comparisons.html#cb93-32" aria-hidden="true" tabindex="-1"></a><span class="do">## Residuals:</span></span>
<span id="cb93-33"><a href="id_04_model_comparisons.html#cb93-33" aria-hidden="true" tabindex="-1"></a><span class="do">## 1 2 3 4 5 6 7 </span></span>
<span id="cb93-34"><a href="id_04_model_comparisons.html#cb93-34" aria-hidden="true" tabindex="-1"></a><span class="do">## -0.12948 -0.97473 -1.25954 0.10225 0.04435 -1.13048 3.34764 </span></span>
<span id="cb93-35"><a href="id_04_model_comparisons.html#cb93-35" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-36"><a href="id_04_model_comparisons.html#cb93-36" aria-hidden="true" tabindex="-1"></a><span class="do">## Coefficients:</span></span>
<span id="cb93-37"><a href="id_04_model_comparisons.html#cb93-37" aria-hidden="true" tabindex="-1"></a><span class="do">## Estimate Std. Error t value Pr(>|t|) </span></span>
<span id="cb93-38"><a href="id_04_model_comparisons.html#cb93-38" aria-hidden="true" tabindex="-1"></a><span class="do">## (Intercept) 3.269 1.411 2.317 0.0683 .</span></span>
<span id="cb93-39"><a href="id_04_model_comparisons.html#cb93-39" aria-hidden="true" tabindex="-1"></a><span class="do">## proportion_positives 366.882 143.355 2.559 0.0507 .</span></span>
<span id="cb93-40"><a href="id_04_model_comparisons.html#cb93-40" aria-hidden="true" tabindex="-1"></a><span class="do">## ---</span></span>
<span id="cb93-41"><a href="id_04_model_comparisons.html#cb93-41" aria-hidden="true" tabindex="-1"></a><span class="do">## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span></span>
<span id="cb93-42"><a href="id_04_model_comparisons.html#cb93-42" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-43"><a href="id_04_model_comparisons.html#cb93-43" aria-hidden="true" tabindex="-1"></a><span class="do">## Residual standard error: 1.735 on 5 degrees of freedom</span></span>
<span id="cb93-44"><a href="id_04_model_comparisons.html#cb93-44" aria-hidden="true" tabindex="-1"></a><span class="do">## Multiple R-squared: 0.5671, Adjusted R-squared: 0.4805 </span></span>
<span id="cb93-45"><a href="id_04_model_comparisons.html#cb93-45" aria-hidden="true" tabindex="-1"></a><span class="do">## F-statistic: 6.55 on 1 and 5 DF, p-value: 0.05069</span></span>
<span id="cb93-46"><a href="id_04_model_comparisons.html#cb93-46" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb93-47"><a href="id_04_model_comparisons.html#cb93-47" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-48"><a href="id_04_model_comparisons.html#cb93-48" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-49"><a href="id_04_model_comparisons.html#cb93-49" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"Log transform for tree depth</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-50"><a href="id_04_model_comparisons.html#cb93-50" aria-hidden="true" tabindex="-1"></a><span class="do">## Log transform for tree depth</span></span>
<span id="cb93-51"><a href="id_04_model_comparisons.html#cb93-51" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-52"><a href="id_04_model_comparisons.html#cb93-52" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-53"><a href="id_04_model_comparisons.html#cb93-53" aria-hidden="true" tabindex="-1"></a>res <span class="ot"><-</span> <span class="fu">lm</span>(mean_tree_depth <span class="sc">~</span> proportion_positives,</span>
<span id="cb93-54"><a href="id_04_model_comparisons.html#cb93-54" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> <span class="fu">data.frame</span>(</span>
<span id="cb93-55"><a href="id_04_model_comparisons.html#cb93-55" aria-hidden="true" tabindex="-1"></a> <span class="at">proportion_positives =</span> proportion_positives,</span>
<span id="cb93-56"><a href="id_04_model_comparisons.html#cb93-56" aria-hidden="true" tabindex="-1"></a> <span class="at">mean_tree_depth =</span> <span class="fu">log2</span>(mean_tree_depth)</span>
<span id="cb93-57"><a href="id_04_model_comparisons.html#cb93-57" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb93-58"><a href="id_04_model_comparisons.html#cb93-58" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb93-59"><a href="id_04_model_comparisons.html#cb93-59" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(res)</span>
<span id="cb93-60"><a href="id_04_model_comparisons.html#cb93-60" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-61"><a href="id_04_model_comparisons.html#cb93-61" aria-hidden="true" tabindex="-1"></a><span class="do">## Call:</span></span>
<span id="cb93-62"><a href="id_04_model_comparisons.html#cb93-62" aria-hidden="true" tabindex="-1"></a><span class="do">## lm(formula = mean_tree_depth ~ proportion_positives, data = data.frame(proportion_positives = proportion_positives, </span></span>
<span id="cb93-63"><a href="id_04_model_comparisons.html#cb93-63" aria-hidden="true" tabindex="-1"></a><span class="do">## mean_tree_depth = log2(mean_tree_depth)))</span></span>
<span id="cb93-64"><a href="id_04_model_comparisons.html#cb93-64" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-65"><a href="id_04_model_comparisons.html#cb93-65" aria-hidden="true" tabindex="-1"></a><span class="do">## Residuals:</span></span>
<span id="cb93-66"><a href="id_04_model_comparisons.html#cb93-66" aria-hidden="true" tabindex="-1"></a><span class="do">## 1 2 3 4 5 6 7 </span></span>
<span id="cb93-67"><a href="id_04_model_comparisons.html#cb93-67" aria-hidden="true" tabindex="-1"></a><span class="do">## 0.058792 -0.267279 -0.329568 0.140857 -0.004416 -0.344751 0.746365 </span></span>
<span id="cb93-68"><a href="id_04_model_comparisons.html#cb93-68" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-69"><a href="id_04_model_comparisons.html#cb93-69" aria-hidden="true" tabindex="-1"></a><span class="do">## Coefficients:</span></span>
<span id="cb93-70"><a href="id_04_model_comparisons.html#cb93-70" aria-hidden="true" tabindex="-1"></a><span class="do">## Estimate Std. Error t value Pr(>|t|) </span></span>
<span id="cb93-71"><a href="id_04_model_comparisons.html#cb93-71" aria-hidden="true" tabindex="-1"></a><span class="do">## (Intercept) 1.772 0.341 5.197 0.00348 **</span></span>
<span id="cb93-72"><a href="id_04_model_comparisons.html#cb93-72" aria-hidden="true" tabindex="-1"></a><span class="do">## proportion_positives 94.203 34.650 2.719 0.04184 * </span></span>
<span id="cb93-73"><a href="id_04_model_comparisons.html#cb93-73" aria-hidden="true" tabindex="-1"></a><span class="do">## ---</span></span>
<span id="cb93-74"><a href="id_04_model_comparisons.html#cb93-74" aria-hidden="true" tabindex="-1"></a><span class="do">## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span></span>
<span id="cb93-75"><a href="id_04_model_comparisons.html#cb93-75" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-76"><a href="id_04_model_comparisons.html#cb93-76" aria-hidden="true" tabindex="-1"></a><span class="do">## Residual standard error: 0.4194 on 5 degrees of freedom</span></span>
<span id="cb93-77"><a href="id_04_model_comparisons.html#cb93-77" aria-hidden="true" tabindex="-1"></a><span class="do">## Multiple R-squared: 0.5965, Adjusted R-squared: 0.5158 </span></span>
<span id="cb93-78"><a href="id_04_model_comparisons.html#cb93-78" aria-hidden="true" tabindex="-1"></a><span class="do">## F-statistic: 7.391 on 1 and 5 DF, p-value: 0.04184</span></span>
<span id="cb93-79"><a href="id_04_model_comparisons.html#cb93-79" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb93-80"><a href="id_04_model_comparisons.html#cb93-80" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-81"><a href="id_04_model_comparisons.html#cb93-81" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-82"><a href="id_04_model_comparisons.html#cb93-82" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"Logit transform for proportion positives</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-83"><a href="id_04_model_comparisons.html#cb93-83" aria-hidden="true" tabindex="-1"></a><span class="do">## Logit transform for proportion positives</span></span>
<span id="cb93-84"><a href="id_04_model_comparisons.html#cb93-84" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-85"><a href="id_04_model_comparisons.html#cb93-85" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-86"><a href="id_04_model_comparisons.html#cb93-86" aria-hidden="true" tabindex="-1"></a>res <span class="ot"><-</span> <span class="fu">lm</span>(mean_tree_depth <span class="sc">~</span> proportion_positives,</span>
<span id="cb93-87"><a href="id_04_model_comparisons.html#cb93-87" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> <span class="fu">data.frame</span>(</span>
<span id="cb93-88"><a href="id_04_model_comparisons.html#cb93-88" aria-hidden="true" tabindex="-1"></a> <span class="at">proportion_positives =</span> <span class="fu">logit</span>(proportion_positives),</span>
<span id="cb93-89"><a href="id_04_model_comparisons.html#cb93-89" aria-hidden="true" tabindex="-1"></a> <span class="at">mean_tree_depth =</span> mean_tree_depth</span>
<span id="cb93-90"><a href="id_04_model_comparisons.html#cb93-90" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb93-91"><a href="id_04_model_comparisons.html#cb93-91" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb93-92"><a href="id_04_model_comparisons.html#cb93-92" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(res)</span>
<span id="cb93-93"><a href="id_04_model_comparisons.html#cb93-93" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-94"><a href="id_04_model_comparisons.html#cb93-94" aria-hidden="true" tabindex="-1"></a><span class="do">## Call:</span></span>
<span id="cb93-95"><a href="id_04_model_comparisons.html#cb93-95" aria-hidden="true" tabindex="-1"></a><span class="do">## lm(formula = mean_tree_depth ~ proportion_positives, data = data.frame(proportion_positives = logit(proportion_positives), </span></span>
<span id="cb93-96"><a href="id_04_model_comparisons.html#cb93-96" aria-hidden="true" tabindex="-1"></a><span class="do">## mean_tree_depth = mean_tree_depth))</span></span>
<span id="cb93-97"><a href="id_04_model_comparisons.html#cb93-97" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-98"><a href="id_04_model_comparisons.html#cb93-98" aria-hidden="true" tabindex="-1"></a><span class="do">## Residuals:</span></span>
<span id="cb93-99"><a href="id_04_model_comparisons.html#cb93-99" aria-hidden="true" tabindex="-1"></a><span class="do">## 1 2 3 4 5 6 7 </span></span>
<span id="cb93-100"><a href="id_04_model_comparisons.html#cb93-100" aria-hidden="true" tabindex="-1"></a><span class="do">## -0.6182 -0.7549 -1.0271 -0.0954 -0.1369 -0.2818 2.9143 </span></span>
<span id="cb93-101"><a href="id_04_model_comparisons.html#cb93-101" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-102"><a href="id_04_model_comparisons.html#cb93-102" aria-hidden="true" tabindex="-1"></a><span class="do">## Coefficients:</span></span>
<span id="cb93-103"><a href="id_04_model_comparisons.html#cb93-103" aria-hidden="true" tabindex="-1"></a><span class="do">## Estimate Std. Error t value Pr(>|t|) </span></span>
<span id="cb93-104"><a href="id_04_model_comparisons.html#cb93-104" aria-hidden="true" tabindex="-1"></a><span class="do">## (Intercept) 22.7794 4.8653 4.682 0.00542 **</span></span>
<span id="cb93-105"><a href="id_04_model_comparisons.html#cb93-105" aria-hidden="true" tabindex="-1"></a><span class="do">## proportion_positives 3.3428 0.9906 3.375 0.01979 * </span></span>
<span id="cb93-106"><a href="id_04_model_comparisons.html#cb93-106" aria-hidden="true" tabindex="-1"></a><span class="do">## ---</span></span>
<span id="cb93-107"><a href="id_04_model_comparisons.html#cb93-107" aria-hidden="true" tabindex="-1"></a><span class="do">## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span></span>
<span id="cb93-108"><a href="id_04_model_comparisons.html#cb93-108" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-109"><a href="id_04_model_comparisons.html#cb93-109" aria-hidden="true" tabindex="-1"></a><span class="do">## Residual standard error: 1.457 on 5 degrees of freedom</span></span>
<span id="cb93-110"><a href="id_04_model_comparisons.html#cb93-110" aria-hidden="true" tabindex="-1"></a><span class="do">## Multiple R-squared: 0.6949, Adjusted R-squared: 0.6339 </span></span>
<span id="cb93-111"><a href="id_04_model_comparisons.html#cb93-111" aria-hidden="true" tabindex="-1"></a><span class="do">## F-statistic: 11.39 on 1 and 5 DF, p-value: 0.01979</span></span>
<span id="cb93-112"><a href="id_04_model_comparisons.html#cb93-112" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb93-113"><a href="id_04_model_comparisons.html#cb93-113" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-114"><a href="id_04_model_comparisons.html#cb93-114" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-115"><a href="id_04_model_comparisons.html#cb93-115" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"Arc-sine transform for proportion positives</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-116"><a href="id_04_model_comparisons.html#cb93-116" aria-hidden="true" tabindex="-1"></a><span class="do">## Arc-sine transform for proportion positives</span></span>
<span id="cb93-117"><a href="id_04_model_comparisons.html#cb93-117" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-118"><a href="id_04_model_comparisons.html#cb93-118" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-119"><a href="id_04_model_comparisons.html#cb93-119" aria-hidden="true" tabindex="-1"></a>res <span class="ot"><-</span> <span class="fu">lm</span>(mean_tree_depth <span class="sc">~</span> proportion_positives,</span>
<span id="cb93-120"><a href="id_04_model_comparisons.html#cb93-120" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> <span class="fu">data.frame</span>(</span>
<span id="cb93-121"><a href="id_04_model_comparisons.html#cb93-121" aria-hidden="true" tabindex="-1"></a> <span class="at">proportion_positives =</span> <span class="fu">asin</span>(<span class="fu">sqrt</span>(proportion_positives)),</span>
<span id="cb93-122"><a href="id_04_model_comparisons.html#cb93-122" aria-hidden="true" tabindex="-1"></a> <span class="at">mean_tree_depth =</span> mean_tree_depth</span>
<span id="cb93-123"><a href="id_04_model_comparisons.html#cb93-123" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb93-124"><a href="id_04_model_comparisons.html#cb93-124" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb93-125"><a href="id_04_model_comparisons.html#cb93-125" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(res)</span>
<span id="cb93-126"><a href="id_04_model_comparisons.html#cb93-126" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-127"><a href="id_04_model_comparisons.html#cb93-127" aria-hidden="true" tabindex="-1"></a><span class="do">## Call:</span></span>
<span id="cb93-128"><a href="id_04_model_comparisons.html#cb93-128" aria-hidden="true" tabindex="-1"></a><span class="do">## lm(formula = mean_tree_depth ~ proportion_positives, data = data.frame(proportion_positives = asin(sqrt(proportion_positives)), </span></span>
<span id="cb93-129"><a href="id_04_model_comparisons.html#cb93-129" aria-hidden="true" tabindex="-1"></a><span class="do">## mean_tree_depth = mean_tree_depth))</span></span>
<span id="cb93-130"><a href="id_04_model_comparisons.html#cb93-130" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-131"><a href="id_04_model_comparisons.html#cb93-131" aria-hidden="true" tabindex="-1"></a><span class="do">## Residuals:</span></span>
<span id="cb93-132"><a href="id_04_model_comparisons.html#cb93-132" aria-hidden="true" tabindex="-1"></a><span class="do">## 1 2 3 4 5 6 7 </span></span>
<span id="cb93-133"><a href="id_04_model_comparisons.html#cb93-133" aria-hidden="true" tabindex="-1"></a><span class="do">## -0.37586 -0.90400 -1.11266 0.04187 -0.08305 -0.72069 3.15439 </span></span>
<span id="cb93-134"><a href="id_04_model_comparisons.html#cb93-134" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-135"><a href="id_04_model_comparisons.html#cb93-135" aria-hidden="true" tabindex="-1"></a><span class="do">## Coefficients:</span></span>
<span id="cb93-136"><a href="id_04_model_comparisons.html#cb93-136" aria-hidden="true" tabindex="-1"></a><span class="do">## Estimate Std. Error t value Pr(>|t|) </span></span>
<span id="cb93-137"><a href="id_04_model_comparisons.html#cb93-137" aria-hidden="true" tabindex="-1"></a><span class="do">## (Intercept) -0.06706 2.29355 -0.029 0.9778 </span></span>
<span id="cb93-138"><a href="id_04_model_comparisons.html#cb93-138" aria-hidden="true" tabindex="-1"></a><span class="do">## proportion_positives 72.39644 24.52407 2.952 0.0318 *</span></span>
<span id="cb93-139"><a href="id_04_model_comparisons.html#cb93-139" aria-hidden="true" tabindex="-1"></a><span class="do">## ---</span></span>
<span id="cb93-140"><a href="id_04_model_comparisons.html#cb93-140" aria-hidden="true" tabindex="-1"></a><span class="do">## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</span></span>
<span id="cb93-141"><a href="id_04_model_comparisons.html#cb93-141" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-142"><a href="id_04_model_comparisons.html#cb93-142" aria-hidden="true" tabindex="-1"></a><span class="do">## Residual standard error: 1.592 on 5 degrees of freedom</span></span>
<span id="cb93-143"><a href="id_04_model_comparisons.html#cb93-143" aria-hidden="true" tabindex="-1"></a><span class="do">## Multiple R-squared: 0.6354, Adjusted R-squared: 0.5625 </span></span>
<span id="cb93-144"><a href="id_04_model_comparisons.html#cb93-144" aria-hidden="true" tabindex="-1"></a><span class="do">## F-statistic: 8.715 on 1 and 5 DF, p-value: 0.03181</span></span>
<span id="cb93-145"><a href="id_04_model_comparisons.html#cb93-145" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb93-146"><a href="id_04_model_comparisons.html#cb93-146" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-147"><a href="id_04_model_comparisons.html#cb93-147" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-148"><a href="id_04_model_comparisons.html#cb93-148" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"Logit transform for proportion positives & log transform for tree depth </span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-149"><a href="id_04_model_comparisons.html#cb93-149" aria-hidden="true" tabindex="-1"></a><span class="do">## Logit transform for proportion positives & log transform for tree depth</span></span>
<span id="cb93-150"><a href="id_04_model_comparisons.html#cb93-150" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span><span class="sc">\n</span><span class="st">"</span>)</span>
<span id="cb93-151"><a href="id_04_model_comparisons.html#cb93-151" aria-hidden="true" tabindex="-1"></a><span class="do">## ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~</span></span>
<span id="cb93-152"><a href="id_04_model_comparisons.html#cb93-152" aria-hidden="true" tabindex="-1"></a>res <span class="ot"><-</span> <span class="fu">lm</span>(mean_tree_depth <span class="sc">~</span> proportion_positives,</span>
<span id="cb93-153"><a href="id_04_model_comparisons.html#cb93-153" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> <span class="fu">data.frame</span>(</span>
<span id="cb93-154"><a href="id_04_model_comparisons.html#cb93-154" aria-hidden="true" tabindex="-1"></a> <span class="at">proportion_positives =</span> <span class="fu">logit</span>(proportion_positives),</span>
<span id="cb93-155"><a href="id_04_model_comparisons.html#cb93-155" aria-hidden="true" tabindex="-1"></a> <span class="at">mean_tree_depth =</span> <span class="fu">log2</span>(mean_tree_depth)</span>
<span id="cb93-156"><a href="id_04_model_comparisons.html#cb93-156" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb93-157"><a href="id_04_model_comparisons.html#cb93-157" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb93-158"><a href="id_04_model_comparisons.html#cb93-158" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(res)</span>
<span id="cb93-159"><a href="id_04_model_comparisons.html#cb93-159" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-160"><a href="id_04_model_comparisons.html#cb93-160" aria-hidden="true" tabindex="-1"></a><span class="do">## Call:</span></span>
<span id="cb93-161"><a href="id_04_model_comparisons.html#cb93-161" aria-hidden="true" tabindex="-1"></a><span class="do">## lm(formula = mean_tree_depth ~ proportion_positives, data = data.frame(proportion_positives = logit(proportion_positives), </span></span>
<span id="cb93-162"><a href="id_04_model_comparisons.html#cb93-162" aria-hidden="true" tabindex="-1"></a><span class="do">## mean_tree_depth = log2(mean_tree_depth)))</span></span>
<span id="cb93-163"><a href="id_04_model_comparisons.html#cb93-163" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>
<span id="cb93-164"><a href="id_04_model_comparisons.html#cb93-164" aria-hidden="true" tabindex="-1"></a><span class="do">## Residuals:</span></span>
<span id="cb93-165"><a href="id_04_model_comparisons.html#cb93-165" aria-hidden="true" tabindex="-1"></a><span class="do">## 1 2 3 4 5 6 7 </span></span>
<span id="cb93-166"><a href="id_04_model_comparisons.html#cb93-166" aria-hidden="true" tabindex="-1"></a><span class="do">## -0.06899 -0.21823 -0.26484 0.09247 -0.05659 -0.11887 0.63505 </span></span>
<span id="cb93-167"><a href="id_04_model_comparisons.html#cb93-167" aria-hidden="true" tabindex="-1"></a><span class="do">## </span></span>