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<title>Section 4 Model validation and interpretation | Multifunctional peptide engineering</title>
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<meta name="author" content="Renee Ti Chou and Henry T. Hsueh" />
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<ul class="summary">
<li><a href="./"><i>Multifunctional peptide engineering</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_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html"><i class="fa fa-check"></i><b>1</b> Melanin binding pilot peptide array</a>
<ul>
<li class="chapter" data-level="1.1" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html#overview"><i class="fa fa-check"></i><b>1.1</b> Overview</a></li>
<li class="chapter" data-level="1.2" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html#generating-ml-input"><i class="fa fa-check"></i><b>1.2</b> Generating ML input</a></li>
<li class="chapter" data-level="1.3" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html#training-initial-rf-model"><i class="fa fa-check"></i><b>1.3</b> Training initial RF model</a></li>
<li class="chapter" data-level="1.4" data-path="id_01_pilot_peptide_array.html"><a href="id_01_pilot_peptide_array.html#melanin-binding-variable-importance"><i class="fa fa-check"></i><b>1.4</b> Melanin binding variable importance</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html"><i class="fa fa-check"></i><b>2</b> Variable reduction</a>
<ul>
<li class="chapter" data-level="2.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#methods"><i class="fa fa-check"></i><b>2.1</b> Methods</a>
<ul>
<li class="chapter" data-level="2.1.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#regression"><i class="fa fa-check"></i><b>2.1.1</b> Regression</a></li>
<li class="chapter" data-level="2.1.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#classification"><i class="fa fa-check"></i><b>2.1.2</b> Classification</a>
<ul>
<li class="chapter" data-level="2.1.2.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#extension-to-multi-class-classification"><i class="fa fa-check"></i><b>2.1.2.1</b> Extension to multi-class classification</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="2.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#ml-input-generating-function"><i class="fa fa-check"></i><b>2.2</b> ML input generating function</a></li>
<li class="chapter" data-level="2.3" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#aic-functions"><i class="fa fa-check"></i><b>2.3</b> AIC functions</a></li>
<li class="chapter" data-level="2.4" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#melanin-binding-regression"><i class="fa fa-check"></i><b>2.4</b> Melanin binding (regression)</a>
<ul>
<li class="chapter" data-level="2.4.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-ml-input-1"><i class="fa fa-check"></i><b>2.4.1</b> Generating ML input</a></li>
<li class="chapter" data-level="2.4.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-importance"><i class="fa fa-check"></i><b>2.4.2</b> Variable importance</a></li>
<li class="chapter" data-level="2.4.3" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-reduction"><i class="fa fa-check"></i><b>2.4.3</b> Variable reduction</a></li>
<li class="chapter" data-level="2.4.4" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-train-test-splits"><i class="fa fa-check"></i><b>2.4.4</b> Generating train-test splits</a></li>
</ul></li>
<li class="chapter" data-level="2.5" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#cell-penetration-classification"><i class="fa fa-check"></i><b>2.5</b> Cell-penetration (classification)</a>
<ul>
<li class="chapter" data-level="2.5.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-ml-input-2"><i class="fa fa-check"></i><b>2.5.1</b> Generating ML input</a></li>
<li class="chapter" data-level="2.5.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-importance-1"><i class="fa fa-check"></i><b>2.5.2</b> Variable importance</a></li>
<li class="chapter" data-level="2.5.3" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-reduction-1"><i class="fa fa-check"></i><b>2.5.3</b> Variable reduction</a></li>
<li class="chapter" data-level="2.5.4" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-train-test-splits-1"><i class="fa fa-check"></i><b>2.5.4</b> Generating train-test splits</a></li>
</ul></li>
<li class="chapter" data-level="2.6" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#toxicity-classification"><i class="fa fa-check"></i><b>2.6</b> Toxicity (classification)</a>
<ul>
<li class="chapter" data-level="2.6.1" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-ml-input-3"><i class="fa fa-check"></i><b>2.6.1</b> Generating ML input</a></li>
<li class="chapter" data-level="2.6.2" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-importance-2"><i class="fa fa-check"></i><b>2.6.2</b> Variable importance</a></li>
<li class="chapter" data-level="2.6.3" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#variable-reduction-2"><i class="fa fa-check"></i><b>2.6.3</b> Variable reduction</a></li>
<li class="chapter" data-level="2.6.4" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#generating-train-test-splits-2"><i class="fa fa-check"></i><b>2.6.4</b> Generating train-test splits</a></li>
</ul></li>
<li class="chapter" data-level="2.7" data-path="id_02_variable_reduction.html"><a href="id_02_variable_reduction.html#plotting"><i class="fa fa-check"></i><b>2.7</b> Plotting</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="id_03_model_training.html"><a href="id_03_model_training.html"><i class="fa fa-check"></i><b>3</b> Model training</a>
<ul>
<li class="chapter" data-level="3.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#overview-1"><i class="fa fa-check"></i><b>3.1</b> Overview</a></li>
<li class="chapter" data-level="3.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#general-codefunctions"><i class="fa fa-check"></i><b>3.2</b> General code/functions</a></li>
<li class="chapter" data-level="3.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#melanin-binding-regression-1"><i class="fa fa-check"></i><b>3.3</b> Melanin binding (regression)</a>
<ul>
<li class="chapter" data-level="3.3.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-training"><i class="fa fa-check"></i><b>3.3.1</b> Model training</a></li>
<li class="chapter" data-level="3.3.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-cross-validation"><i class="fa fa-check"></i><b>3.3.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="3.3.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#training-on-whole-data-set"><i class="fa fa-check"></i><b>3.3.3</b> Training on whole data set</a></li>
<li class="chapter" data-level="3.3.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-evaluation"><i class="fa fa-check"></i><b>3.3.4</b> Model evaluation</a></li>
<li class="chapter" data-level="3.3.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-loop-model-selection"><i class="fa fa-check"></i><b>3.3.5</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="3.3.5.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-1"><i class="fa fa-check"></i><b>3.3.5.1</b> CV 1</a></li>
<li class="chapter" data-level="3.3.5.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-2"><i class="fa fa-check"></i><b>3.3.5.2</b> CV 2</a></li>
<li class="chapter" data-level="3.3.5.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-3"><i class="fa fa-check"></i><b>3.3.5.3</b> CV 3</a></li>
<li class="chapter" data-level="3.3.5.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-4"><i class="fa fa-check"></i><b>3.3.5.4</b> CV 4</a></li>
<li class="chapter" data-level="3.3.5.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-5"><i class="fa fa-check"></i><b>3.3.5.5</b> CV 5</a></li>
<li class="chapter" data-level="3.3.5.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-6"><i class="fa fa-check"></i><b>3.3.5.6</b> CV 6</a></li>
<li class="chapter" data-level="3.3.5.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-7"><i class="fa fa-check"></i><b>3.3.5.7</b> CV 7</a></li>
<li class="chapter" data-level="3.3.5.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-8"><i class="fa fa-check"></i><b>3.3.5.8</b> CV 8</a></li>
<li class="chapter" data-level="3.3.5.9" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-9"><i class="fa fa-check"></i><b>3.3.5.9</b> CV 9</a></li>
<li class="chapter" data-level="3.3.5.10" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-10"><i class="fa fa-check"></i><b>3.3.5.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="3.3.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-evaluation"><i class="fa fa-check"></i><b>3.3.6</b> Final evaluation</a></li>
<li class="chapter" data-level="3.3.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-model-selection"><i class="fa fa-check"></i><b>3.3.7</b> Final model selection</a></li>
<li class="chapter" data-level="3.3.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-reduced-sl"><i class="fa fa-check"></i><b>3.3.8</b> Final reduced SL</a></li>
</ul></li>
<li class="chapter" data-level="3.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cell-penetration-classification-1"><i class="fa fa-check"></i><b>3.4</b> Cell-penetration (classification)</a>
<ul>
<li class="chapter" data-level="3.4.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-training-1"><i class="fa fa-check"></i><b>3.4.1</b> Model training</a></li>
<li class="chapter" data-level="3.4.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-cross-validation-1"><i class="fa fa-check"></i><b>3.4.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="3.4.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#training-on-whole-data-set-1"><i class="fa fa-check"></i><b>3.4.3</b> Training on whole data set</a></li>
<li class="chapter" data-level="3.4.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-evaluation-1"><i class="fa fa-check"></i><b>3.4.4</b> Model evaluation</a></li>
<li class="chapter" data-level="3.4.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-loop-model-selection-1"><i class="fa fa-check"></i><b>3.4.5</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="3.4.5.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-1-1"><i class="fa fa-check"></i><b>3.4.5.1</b> CV 1</a></li>
<li class="chapter" data-level="3.4.5.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-2-1"><i class="fa fa-check"></i><b>3.4.5.2</b> CV 2</a></li>
<li class="chapter" data-level="3.4.5.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-3-1"><i class="fa fa-check"></i><b>3.4.5.3</b> CV 3</a></li>
<li class="chapter" data-level="3.4.5.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-4-1"><i class="fa fa-check"></i><b>3.4.5.4</b> CV 4</a></li>
<li class="chapter" data-level="3.4.5.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-5-1"><i class="fa fa-check"></i><b>3.4.5.5</b> CV 5</a></li>
<li class="chapter" data-level="3.4.5.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-6-1"><i class="fa fa-check"></i><b>3.4.5.6</b> CV 6</a></li>
<li class="chapter" data-level="3.4.5.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-7-1"><i class="fa fa-check"></i><b>3.4.5.7</b> CV 7</a></li>
<li class="chapter" data-level="3.4.5.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-8-1"><i class="fa fa-check"></i><b>3.4.5.8</b> CV 8</a></li>
<li class="chapter" data-level="3.4.5.9" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-9-1"><i class="fa fa-check"></i><b>3.4.5.9</b> CV 9</a></li>
<li class="chapter" data-level="3.4.5.10" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-10-1"><i class="fa fa-check"></i><b>3.4.5.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="3.4.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-evaluation-1"><i class="fa fa-check"></i><b>3.4.6</b> Final evaluation</a></li>
<li class="chapter" data-level="3.4.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-model-selection-1"><i class="fa fa-check"></i><b>3.4.7</b> Final model selection</a></li>
<li class="chapter" data-level="3.4.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-reduced-sl-1"><i class="fa fa-check"></i><b>3.4.8</b> Final reduced SL</a></li>
</ul></li>
<li class="chapter" data-level="3.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#toxicity-classification-1"><i class="fa fa-check"></i><b>3.5</b> Toxicity (classification)</a>
<ul>
<li class="chapter" data-level="3.5.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-training-2"><i class="fa fa-check"></i><b>3.5.1</b> Model training</a></li>
<li class="chapter" data-level="3.5.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-cross-validation-2"><i class="fa fa-check"></i><b>3.5.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="3.5.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#training-on-whole-data-set-2"><i class="fa fa-check"></i><b>3.5.3</b> Training on whole data set</a></li>
<li class="chapter" data-level="3.5.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#model-evaluation-2"><i class="fa fa-check"></i><b>3.5.4</b> Model evaluation</a></li>
<li class="chapter" data-level="3.5.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#inner-loop-model-selection-2"><i class="fa fa-check"></i><b>3.5.5</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="3.5.5.1" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-1-2"><i class="fa fa-check"></i><b>3.5.5.1</b> CV 1</a></li>
<li class="chapter" data-level="3.5.5.2" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-2-2"><i class="fa fa-check"></i><b>3.5.5.2</b> CV 2</a></li>
<li class="chapter" data-level="3.5.5.3" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-3-2"><i class="fa fa-check"></i><b>3.5.5.3</b> CV 3</a></li>
<li class="chapter" data-level="3.5.5.4" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-4-2"><i class="fa fa-check"></i><b>3.5.5.4</b> CV 4</a></li>
<li class="chapter" data-level="3.5.5.5" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-5-2"><i class="fa fa-check"></i><b>3.5.5.5</b> CV 5</a></li>
<li class="chapter" data-level="3.5.5.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-6-2"><i class="fa fa-check"></i><b>3.5.5.6</b> CV 6</a></li>
<li class="chapter" data-level="3.5.5.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-7-2"><i class="fa fa-check"></i><b>3.5.5.7</b> CV 7</a></li>
<li class="chapter" data-level="3.5.5.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-8-2"><i class="fa fa-check"></i><b>3.5.5.8</b> CV 8</a></li>
<li class="chapter" data-level="3.5.5.9" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-9-2"><i class="fa fa-check"></i><b>3.5.5.9</b> CV 9</a></li>
<li class="chapter" data-level="3.5.5.10" data-path="id_03_model_training.html"><a href="id_03_model_training.html#cv-10-2"><i class="fa fa-check"></i><b>3.5.5.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="3.5.6" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-evaluation-2"><i class="fa fa-check"></i><b>3.5.6</b> Final evaluation</a></li>
<li class="chapter" data-level="3.5.7" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-model-selection-2"><i class="fa fa-check"></i><b>3.5.7</b> Final model selection</a></li>
<li class="chapter" data-level="3.5.8" data-path="id_03_model_training.html"><a href="id_03_model_training.html#final-reduced-sl-2"><i class="fa fa-check"></i><b>3.5.8</b> Final reduced SL</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html"><i class="fa fa-check"></i><b>4</b> Model validation and interpretation</a>
<ul>
<li class="chapter" data-level="4.1" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#model-validation"><i class="fa fa-check"></i><b>4.1</b> Model validation</a>
<ul>
<li class="chapter" data-level="4.1.1" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melaning-binding"><i class="fa fa-check"></i><b>4.1.1</b> Melaning binding</a></li>
<li class="chapter" data-level="4.1.2" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melanin-binding-and-cell-penetration"><i class="fa fa-check"></i><b>4.1.2</b> Melanin binding and cell-penetration</a></li>
<li class="chapter" data-level="4.1.3" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melanin-induced-cells"><i class="fa fa-check"></i><b>4.1.3</b> Melanin-induced cells</a></li>
<li class="chapter" data-level="4.1.4" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#non-melanin-induced-cells"><i class="fa fa-check"></i><b>4.1.4</b> Non-melanin induced cells</a></li>
</ul></li>
<li class="chapter" data-level="4.2" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#overall-model-interpretation"><i class="fa fa-check"></i><b>4.2</b> Overall model interpretation</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melanin-binding-regression-2"><i class="fa fa-check"></i><b>4.2.1</b> Melanin binding (regression)</a></li>
<li class="chapter" data-level="4.2.2" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#cell-penetration-classification-2"><i class="fa fa-check"></i><b>4.2.2</b> Cell-penetration (classification)</a></li>
<li class="chapter" data-level="4.2.3" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#toxicity-classification-2"><i class="fa fa-check"></i><b>4.2.3</b> Toxicity (classification)</a></li>
</ul></li>
<li class="chapter" data-level="4.3" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#multifunctional-peptide-selection"><i class="fa fa-check"></i><b>4.3</b> Multifunctional peptide selection</a></li>
<li class="chapter" data-level="4.4" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#explanation-of-hr97-predictions"><i class="fa fa-check"></i><b>4.4</b> Explanation of HR97 predictions</a>
<ul>
<li class="chapter" data-level="4.4.1" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#melanin-binding"><i class="fa fa-check"></i><b>4.4.1</b> Melanin binding</a></li>
<li class="chapter" data-level="4.4.2" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#cell-penetration"><i class="fa fa-check"></i><b>4.4.2</b> Cell-penetration</a></li>
<li class="chapter" data-level="4.4.3" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#toxicity"><i class="fa fa-check"></i><b>4.4.3</b> Toxicity</a></li>
</ul></li>
<li class="chapter" data-level="4.5" data-path="id_04_model_validation_and_interpretation.html"><a href="id_04_model_validation_and_interpretation.html#peptide-design-space-visualization"><i class="fa fa-check"></i><b>4.5</b> Peptide design space visualization</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html"><i class="fa fa-check"></i><b>5</b> Adversarial computational control</a>
<ul>
<li class="chapter" data-level="5.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#general-codefunctions-1"><i class="fa fa-check"></i><b>5.1</b> General code/functions</a></li>
<li class="chapter" data-level="5.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#melanin-binding-regression-3"><i class="fa fa-check"></i><b>5.2</b> Melanin binding (regression)</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-training-3"><i class="fa fa-check"></i><b>5.2.1</b> Model training</a></li>
<li class="chapter" data-level="5.2.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-cross-validation-3"><i class="fa fa-check"></i><b>5.2.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="5.2.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-evaluation-3"><i class="fa fa-check"></i><b>5.2.3</b> Model evaluation</a></li>
<li class="chapter" data-level="5.2.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-loop-model-selection-3"><i class="fa fa-check"></i><b>5.2.4</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="5.2.4.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-1-3"><i class="fa fa-check"></i><b>5.2.4.1</b> CV 1</a></li>
<li class="chapter" data-level="5.2.4.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-2-3"><i class="fa fa-check"></i><b>5.2.4.2</b> CV 2</a></li>
<li class="chapter" data-level="5.2.4.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-3-3"><i class="fa fa-check"></i><b>5.2.4.3</b> CV 3</a></li>
<li class="chapter" data-level="5.2.4.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-4-3"><i class="fa fa-check"></i><b>5.2.4.4</b> CV 4</a></li>
<li class="chapter" data-level="5.2.4.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-5-3"><i class="fa fa-check"></i><b>5.2.4.5</b> CV 5</a></li>
<li class="chapter" data-level="5.2.4.6" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-6-3"><i class="fa fa-check"></i><b>5.2.4.6</b> CV 6</a></li>
<li class="chapter" data-level="5.2.4.7" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-7-3"><i class="fa fa-check"></i><b>5.2.4.7</b> CV 7</a></li>
<li class="chapter" data-level="5.2.4.8" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-8-3"><i class="fa fa-check"></i><b>5.2.4.8</b> CV 8</a></li>
<li class="chapter" data-level="5.2.4.9" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-9-3"><i class="fa fa-check"></i><b>5.2.4.9</b> CV 9</a></li>
<li class="chapter" data-level="5.2.4.10" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-10-3"><i class="fa fa-check"></i><b>5.2.4.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="5.2.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#final-evaluation-3"><i class="fa fa-check"></i><b>5.2.5</b> Final evaluation</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cell-penetration-classification-3"><i class="fa fa-check"></i><b>5.3</b> Cell-penetration (classification)</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-training-4"><i class="fa fa-check"></i><b>5.3.1</b> Model training</a></li>
<li class="chapter" data-level="5.3.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-cross-validation-4"><i class="fa fa-check"></i><b>5.3.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="5.3.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-evaluation-4"><i class="fa fa-check"></i><b>5.3.3</b> Model evaluation</a></li>
<li class="chapter" data-level="5.3.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-loop-model-selection-4"><i class="fa fa-check"></i><b>5.3.4</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="5.3.4.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-1-4"><i class="fa fa-check"></i><b>5.3.4.1</b> CV 1</a></li>
<li class="chapter" data-level="5.3.4.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-2-4"><i class="fa fa-check"></i><b>5.3.4.2</b> CV 2</a></li>
<li class="chapter" data-level="5.3.4.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-3-4"><i class="fa fa-check"></i><b>5.3.4.3</b> CV 3</a></li>
<li class="chapter" data-level="5.3.4.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-4-4"><i class="fa fa-check"></i><b>5.3.4.4</b> CV 4</a></li>
<li class="chapter" data-level="5.3.4.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-5-4"><i class="fa fa-check"></i><b>5.3.4.5</b> CV 5</a></li>
<li class="chapter" data-level="5.3.4.6" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-6-4"><i class="fa fa-check"></i><b>5.3.4.6</b> CV 6</a></li>
<li class="chapter" data-level="5.3.4.7" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-7-4"><i class="fa fa-check"></i><b>5.3.4.7</b> CV 7</a></li>
<li class="chapter" data-level="5.3.4.8" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-8-4"><i class="fa fa-check"></i><b>5.3.4.8</b> CV 8</a></li>
<li class="chapter" data-level="5.3.4.9" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-9-4"><i class="fa fa-check"></i><b>5.3.4.9</b> CV 9</a></li>
<li class="chapter" data-level="5.3.4.10" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-10-4"><i class="fa fa-check"></i><b>5.3.4.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="5.3.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#final-evaluation-4"><i class="fa fa-check"></i><b>5.3.5</b> Final evaluation</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#toxicity-classification-3"><i class="fa fa-check"></i><b>5.4</b> Toxicity (classification)</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-training-5"><i class="fa fa-check"></i><b>5.4.1</b> Model training</a></li>
<li class="chapter" data-level="5.4.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-cross-validation-5"><i class="fa fa-check"></i><b>5.4.2</b> Inner cross-validation</a></li>
<li class="chapter" data-level="5.4.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#model-evaluation-5"><i class="fa fa-check"></i><b>5.4.3</b> Model evaluation</a></li>
<li class="chapter" data-level="5.4.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#inner-loop-model-selection-5"><i class="fa fa-check"></i><b>5.4.4</b> Inner loop model selection</a>
<ul>
<li class="chapter" data-level="5.4.4.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-1-5"><i class="fa fa-check"></i><b>5.4.4.1</b> CV 1</a></li>
<li class="chapter" data-level="5.4.4.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-2-5"><i class="fa fa-check"></i><b>5.4.4.2</b> CV 2</a></li>
<li class="chapter" data-level="5.4.4.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-3-5"><i class="fa fa-check"></i><b>5.4.4.3</b> CV 3</a></li>
<li class="chapter" data-level="5.4.4.4" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-4-5"><i class="fa fa-check"></i><b>5.4.4.4</b> CV 4</a></li>
<li class="chapter" data-level="5.4.4.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-5-5"><i class="fa fa-check"></i><b>5.4.4.5</b> CV 5</a></li>
<li class="chapter" data-level="5.4.4.6" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-6-5"><i class="fa fa-check"></i><b>5.4.4.6</b> CV 6</a></li>
<li class="chapter" data-level="5.4.4.7" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-7-5"><i class="fa fa-check"></i><b>5.4.4.7</b> CV 7</a></li>
<li class="chapter" data-level="5.4.4.8" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-8-5"><i class="fa fa-check"></i><b>5.4.4.8</b> CV 8</a></li>
<li class="chapter" data-level="5.4.4.9" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-9-5"><i class="fa fa-check"></i><b>5.4.4.9</b> CV 9</a></li>
<li class="chapter" data-level="5.4.4.10" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cv-10-5"><i class="fa fa-check"></i><b>5.4.4.10</b> CV 10</a></li>
</ul></li>
<li class="chapter" data-level="5.4.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#final-evaluation-5"><i class="fa fa-check"></i><b>5.4.5</b> Final evaluation</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#overall-model-interpretation-1"><i class="fa fa-check"></i><b>5.5</b> Overall model interpretation</a>
<ul>
<li class="chapter" data-level="5.5.1" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#melanin-binding-regression-4"><i class="fa fa-check"></i><b>5.5.1</b> Melanin binding (regression)</a></li>
<li class="chapter" data-level="5.5.2" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#cell-penetration-classification-4"><i class="fa fa-check"></i><b>5.5.2</b> Cell-penetration (classification)</a></li>
<li class="chapter" data-level="5.5.3" data-path="id_05_adversarial_computational_control.html"><a href="id_05_adversarial_computational_control.html#toxicity-classification-4"><i class="fa fa-check"></i><b>5.5.3</b> Toxicity (classification)</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html"><i class="fa fa-check"></i><b>6</b> Small data set demo</a>
<ul>
<li class="chapter" data-level="6.1" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#setup"><i class="fa fa-check"></i><b>6.1</b> Setup</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#load-libraries"><i class="fa fa-check"></i><b>6.1.1</b> Load libraries</a></li>
<li class="chapter" data-level="6.1.2" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#aic-functions-1"><i class="fa fa-check"></i><b>6.1.2</b> AIC functions</a></li>
<li class="chapter" data-level="6.1.3" data-path="id_06_small_data_set_demo.html"><a href="id_06_small_data_set_demo.html#model-parameters"><i class="fa fa-check"></i><b>6.1.3</b> Model parameters</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Multifunctional peptide engineering</a>
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<section class="normal" id="section-">
<div id="id_04_model_validation_and_interpretation" class="section level1 hasAnchor" number="4">
<h1><span class="header-section-number">Section 4</span> Model validation and interpretation<a href="id_04_model_validation_and_interpretation.html#id_04_model_validation_and_interpretation" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div class="sourceCode" id="cb77"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb77-1"><a href="id_04_model_validation_and_interpretation.html#cb77-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(h2o)</span>
<span id="cb77-2"><a href="id_04_model_validation_and_interpretation.html#cb77-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb77-3"><a href="id_04_model_validation_and_interpretation.html#cb77-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggpubr)</span>
<span id="cb77-4"><a href="id_04_model_validation_and_interpretation.html#cb77-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggbeeswarm)</span>
<span id="cb77-5"><a href="id_04_model_validation_and_interpretation.html#cb77-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(reticulate)</span>
<span id="cb77-6"><a href="id_04_model_validation_and_interpretation.html#cb77-6" aria-hidden="true" tabindex="-1"></a><span class="fu">use_condaenv</span>(<span class="st">"/Users/renee/Library/r-miniconda/envs/peptide_engineering/bin/python"</span>)</span>
<span id="cb77-7"><a href="id_04_model_validation_and_interpretation.html#cb77-7" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(reshape2)</span>
<span id="cb77-8"><a href="id_04_model_validation_and_interpretation.html#cb77-8" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(scales)</span>
<span id="cb77-9"><a href="id_04_model_validation_and_interpretation.html#cb77-9" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggforce)</span>
<span id="cb77-10"><a href="id_04_model_validation_and_interpretation.html#cb77-10" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(cowplot)</span>
<span id="cb77-11"><a href="id_04_model_validation_and_interpretation.html#cb77-11" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(plotly)</span>
<span id="cb77-12"><a href="id_04_model_validation_and_interpretation.html#cb77-12" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggrepel)</span></code></pre></div>
<div class="sourceCode" id="cb78"><pre class="sourceCode python fold-hide"><code class="sourceCode python"><span id="cb78-1"><a href="id_04_model_validation_and_interpretation.html#cb78-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> h2o</span>
<span id="cb78-2"><a href="id_04_model_validation_and_interpretation.html#cb78-2" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
<span id="cb78-3"><a href="id_04_model_validation_and_interpretation.html#cb78-3" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
<span id="cb78-4"><a href="id_04_model_validation_and_interpretation.html#cb78-4" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> shap</span>
<span id="cb78-5"><a href="id_04_model_validation_and_interpretation.html#cb78-5" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
<span id="cb78-6"><a href="id_04_model_validation_and_interpretation.html#cb78-6" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> session_info</span></code></pre></div>
<div id="model-validation" class="section level2 hasAnchor" number="4.1">
<h2><span class="header-section-number">4.1</span> Model validation<a href="id_04_model_validation_and_interpretation.html#model-validation" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="melaning-binding" class="section level3 hasAnchor" number="4.1.1">
<h3><span class="header-section-number">4.1.1</span> Melaning binding<a href="id_04_model_validation_and_interpretation.html#melaning-binding" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div class="sourceCode" id="cb79"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb79-1"><a href="id_04_model_validation_and_interpretation.html#cb79-1" aria-hidden="true" tabindex="-1"></a><span class="co"># ================</span></span>
<span id="cb79-2"><a href="id_04_model_validation_and_interpretation.html#cb79-2" aria-hidden="true" tabindex="-1"></a><span class="co"># predicted values</span></span>
<span id="cb79-3"><a href="id_04_model_validation_and_interpretation.html#cb79-3" aria-hidden="true" tabindex="-1"></a><span class="co"># ================</span></span>
<span id="cb79-4"><a href="id_04_model_validation_and_interpretation.html#cb79-4" aria-hidden="true" tabindex="-1"></a>mb_pred_ <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb79-5"><a href="id_04_model_validation_and_interpretation.html#cb79-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb79-6"><a href="id_04_model_validation_and_interpretation.html#cb79-6" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">0.0202</span>, <span class="fl">1.3650</span>, <span class="fl">2.1745</span>, <span class="fl">2.3456</span>, <span class="fl">2.5907</span>, <span class="fl">2.6903</span>, <span class="fl">2.9842</span>, <span class="fl">3.1325</span>, <span class="fl">3.5015</span>, <span class="fl">3.6640</span>, <span class="fl">3.7181</span>, <span class="fl">4.0701</span>,</span>
<span id="cb79-7"><a href="id_04_model_validation_and_interpretation.html#cb79-7" aria-hidden="true" tabindex="-1"></a> <span class="fl">0.3223</span>, <span class="fl">1.5153</span>, <span class="fl">2.1196</span>, <span class="fl">2.4047</span>, <span class="fl">2.5032</span>, <span class="fl">2.8177</span>, <span class="fl">3.0653</span>, <span class="fl">3.1491</span>, <span class="fl">3.5578</span>, <span class="fl">3.6465</span>, <span class="fl">3.5599</span>, <span class="fl">3.9509</span>,</span>
<span id="cb79-8"><a href="id_04_model_validation_and_interpretation.html#cb79-8" aria-hidden="true" tabindex="-1"></a> <span class="fl">0.6579</span>, <span class="fl">2.1797</span>, <span class="fl">1.9685</span>, <span class="fl">2.3709</span>, <span class="fl">2.6702</span>, <span class="fl">3.0694</span>, <span class="fl">2.9323</span>, <span class="fl">3.3150</span>, <span class="fl">3.4798</span>, <span class="fl">3.5661</span>, <span class="fl">3.6981</span>, <span class="fl">3.9730</span>,</span>
<span id="cb79-9"><a href="id_04_model_validation_and_interpretation.html#cb79-9" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">0.0589</span>, <span class="fl">1.3490</span>, <span class="fl">2.4402</span>, <span class="fl">2.1269</span>, <span class="fl">2.5097</span>, <span class="fl">2.6128</span>, <span class="fl">2.9359</span>, <span class="fl">3.3530</span>, <span class="fl">3.8094</span>, <span class="fl">3.5260</span>, <span class="fl">3.7525</span>, <span class="fl">3.8405</span>,</span>
<span id="cb79-10"><a href="id_04_model_validation_and_interpretation.html#cb79-10" aria-hidden="true" tabindex="-1"></a> <span class="fl">0.6532</span>, <span class="fl">1.3684</span>, <span class="fl">2.6170</span>, <span class="fl">2.5270</span>, <span class="fl">2.5228</span>, <span class="fl">2.9967</span>, <span class="fl">3.1125</span>, <span class="fl">3.2106</span>, <span class="fl">3.5952</span>, <span class="fl">3.7345</span>, <span class="fl">3.7353</span>, <span class="fl">3.8400</span>,</span>
<span id="cb79-11"><a href="id_04_model_validation_and_interpretation.html#cb79-11" aria-hidden="true" tabindex="-1"></a> <span class="fl">0.2941</span>, <span class="fl">1.1896</span>, <span class="fl">2.1987</span>, <span class="fl">2.7585</span>, <span class="fl">3.1348</span>, <span class="fl">2.9791</span>, <span class="fl">3.2625</span>, <span class="fl">3.0559</span>, <span class="fl">3.5153</span>, <span class="fl">3.6829</span>, <span class="fl">3.9875</span>, <span class="fl">4.0330</span>,</span>
<span id="cb79-12"><a href="id_04_model_validation_and_interpretation.html#cb79-12" aria-hidden="true" tabindex="-1"></a> <span class="fl">0.0156</span>, <span class="fl">1.1113</span>, <span class="fl">1.9551</span>, <span class="fl">2.3677</span>, <span class="fl">2.4250</span>, <span class="fl">4.0111</span>, <span class="fl">3.4891</span>, <span class="fl">3.6521</span>, <span class="fl">3.6634</span>, <span class="fl">3.2731</span>, <span class="fl">3.4504</span>, <span class="fl">3.7587</span>,</span>
<span id="cb79-13"><a href="id_04_model_validation_and_interpretation.html#cb79-13" aria-hidden="true" tabindex="-1"></a> <span class="fl">0.0209</span>, <span class="fl">1.9146</span>, <span class="fl">2.2865</span>, <span class="fl">2.5308</span>, <span class="fl">2.7193</span>, <span class="fl">3.0322</span>, <span class="fl">3.1020</span>, <span class="fl">3.3582</span>, <span class="fl">3.2993</span>, <span class="fl">3.8534</span>, <span class="fl">4.9542</span>, <span class="fl">3.5464</span></span>
<span id="cb79-14"><a href="id_04_model_validation_and_interpretation.html#cb79-14" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb79-15"><a href="id_04_model_validation_and_interpretation.html#cb79-15" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb79-16"><a href="id_04_model_validation_and_interpretation.html#cb79-16" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-17"><a href="id_04_model_validation_and_interpretation.html#cb79-17" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-18"><a href="id_04_model_validation_and_interpretation.html#cb79-18" aria-hidden="true" tabindex="-1"></a>new_mb_pred_ <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb79-19"><a href="id_04_model_validation_and_interpretation.html#cb79-19" aria-hidden="true" tabindex="-1"></a> <span class="fl">3.9318</span>, <span class="fl">3.9366</span>, <span class="fl">3.5531</span>, <span class="fl">3.4385</span>, <span class="fl">3.8434</span>, <span class="fl">3.3893</span>, <span class="fl">4.4159</span>, <span class="fl">4.7549</span>, <span class="fl">4.0004</span>, <span class="fl">3.2785</span>,</span>
<span id="cb79-20"><a href="id_04_model_validation_and_interpretation.html#cb79-20" aria-hidden="true" tabindex="-1"></a> <span class="fl">4.5784</span>, <span class="fl">4.6026</span>, <span class="fl">3.6229</span>, <span class="fl">3.8261</span>, <span class="fl">3.6111</span>, <span class="fl">5.0536</span>, <span class="fl">4.8169</span>, <span class="fl">5.9021</span>, <span class="fl">4.0992</span>, <span class="fl">4.3451</span>,</span>
<span id="cb79-21"><a href="id_04_model_validation_and_interpretation.html#cb79-21" aria-hidden="true" tabindex="-1"></a> <span class="fl">5.9626</span>, <span class="fl">4.2730</span>, <span class="fl">4.4115</span>, <span class="fl">4.8889</span>, <span class="fl">4.3264</span>, <span class="fl">4.4830</span>, <span class="fl">4.2847</span>, <span class="fl">4.6585</span>, <span class="fl">4.4568</span>, <span class="fl">4.8513</span>,</span>
<span id="cb79-22"><a href="id_04_model_validation_and_interpretation.html#cb79-22" aria-hidden="true" tabindex="-1"></a> <span class="fl">4.1523</span></span>
<span id="cb79-23"><a href="id_04_model_validation_and_interpretation.html#cb79-23" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-24"><a href="id_04_model_validation_and_interpretation.html#cb79-24" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-25"><a href="id_04_model_validation_and_interpretation.html#cb79-25" aria-hidden="true" tabindex="-1"></a>mb_pred <span class="ot"><-</span> <span class="fu">c</span>(<span class="fu">as.vector</span>(mb_pred_), new_mb_pred_)</span>
<span id="cb79-26"><a href="id_04_model_validation_and_interpretation.html#cb79-26" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">127</span>) {</span>
<span id="cb79-27"><a href="id_04_model_validation_and_interpretation.html#cb79-27" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (mb_pred[i] <span class="sc"><</span> <span class="dv">0</span>) mb_pred[i] <span class="ot"><-</span> <span class="cn">NA</span></span>
<span id="cb79-28"><a href="id_04_model_validation_and_interpretation.html#cb79-28" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb79-29"><a href="id_04_model_validation_and_interpretation.html#cb79-29" aria-hidden="true" tabindex="-1"></a><span class="co"># Re-scale to 0-100</span></span>
<span id="cb79-30"><a href="id_04_model_validation_and_interpretation.html#cb79-30" aria-hidden="true" tabindex="-1"></a><span class="fu">load</span>(<span class="at">file =</span> <span class="st">"./rdata/var_reduct_mb_train_test_splits.RData"</span>)</span>
<span id="cb79-31"><a href="id_04_model_validation_and_interpretation.html#cb79-31" aria-hidden="true" tabindex="-1"></a>mb_pred <span class="ot"><-</span> <span class="fu">rescale</span>(mb_pred, <span class="at">to =</span> <span class="fu">c</span>(<span class="dv">0</span>, <span class="dv">100</span>), <span class="at">from =</span> <span class="fu">range</span>(mb_data<span class="sc">$</span>log_intensity))</span>
<span id="cb79-32"><a href="id_04_model_validation_and_interpretation.html#cb79-32" aria-hidden="true" tabindex="-1"></a>mb_pred[mb_pred <span class="sc">></span> <span class="dv">100</span>] <span class="ot"><-</span> <span class="dv">100</span></span>
<span id="cb79-33"><a href="id_04_model_validation_and_interpretation.html#cb79-33" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-34"><a href="id_04_model_validation_and_interpretation.html#cb79-34" aria-hidden="true" tabindex="-1"></a><span class="co"># ===================</span></span>
<span id="cb79-35"><a href="id_04_model_validation_and_interpretation.html#cb79-35" aria-hidden="true" tabindex="-1"></a><span class="co"># Experimental values</span></span>
<span id="cb79-36"><a href="id_04_model_validation_and_interpretation.html#cb79-36" aria-hidden="true" tabindex="-1"></a><span class="co"># ===================</span></span>
<span id="cb79-37"><a href="id_04_model_validation_and_interpretation.html#cb79-37" aria-hidden="true" tabindex="-1"></a>replicate_1_1 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb79-38"><a href="id_04_model_validation_and_interpretation.html#cb79-38" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb79-39"><a href="id_04_model_validation_and_interpretation.html#cb79-39" aria-hidden="true" tabindex="-1"></a> <span class="fl">0.9775</span>, <span class="fl">50.1718</span>, <span class="fl">39.9822</span>, <span class="fl">66.0486</span>, <span class="fl">46.0249</span>, <span class="fl">40.8353</span>, <span class="fl">58.6552</span>, <span class="fl">72.8258</span>, <span class="fl">55.1955</span>, <span class="fl">59.8874</span>, <span class="fl">78.4182</span>, <span class="fl">77.8258</span>,</span>
<span id="cb79-40"><a href="id_04_model_validation_and_interpretation.html#cb79-40" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">3.6197</span>, <span class="fl">25.3377</span>, <span class="fl">56.6884</span>, <span class="fl">58.1339</span>, <span class="sc">-</span><span class="fl">0.8945</span>, <span class="fl">26.5936</span>, <span class="fl">64.4609</span>, <span class="fl">63.2050</span>, <span class="fl">68.3472</span>, <span class="fl">71.3566</span>, <span class="fl">80.4325</span>, <span class="fl">70.3140</span>,</span>
<span id="cb79-41"><a href="id_04_model_validation_and_interpretation.html#cb79-41" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">34.7571</span>, <span class="fl">26.0249</span>, <span class="fl">52.3519</span>, <span class="fl">70.4562</span>, <span class="fl">63.1813</span>, <span class="fl">69.1291</span>, <span class="fl">73.1339</span>, <span class="fl">65.6220</span>, <span class="fl">73.9396</span>, <span class="fl">76.5699</span>, <span class="fl">75.1955</span>, <span class="fl">76.0249</span>,</span>
<span id="cb79-42"><a href="id_04_model_validation_and_interpretation.html#cb79-42" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">1.3922</span>, <span class="fl">35.4325</span>, <span class="fl">4.0344</span>, <span class="fl">16.4514</span>, <span class="fl">28.4656</span>, <span class="fl">38.9870</span>, <span class="fl">71.5699</span>, <span class="fl">66.8306</span>, <span class="fl">71.0723</span>, <span class="fl">45.0059</span>, <span class="fl">83.4182</span>, <span class="fl">75.9301</span>,</span>
<span id="cb79-43"><a href="id_04_model_validation_and_interpretation.html#cb79-43" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">6.0604</span>, <span class="fl">19.9111</span>, <span class="fl">20.2666</span>, <span class="fl">39.2476</span>, <span class="fl">36.3329</span>, <span class="fl">70.1955</span>, <span class="fl">73.9633</span>, <span class="fl">72.4467</span>, <span class="fl">75.5746</span>, <span class="fl">59.9348</span>, <span class="fl">55.4799</span>, <span class="fl">75.8590</span>,</span>
<span id="cb79-44"><a href="id_04_model_validation_and_interpretation.html#cb79-44" aria-hidden="true" tabindex="-1"></a> <span class="fl">1.9727</span>, <span class="fl">28.0628</span>, <span class="sc">-</span><span class="fl">29.7097</span>, <span class="fl">35.4562</span>, <span class="fl">58.8211</span>, <span class="fl">49.7927</span>, <span class="fl">61.7121</span>, <span class="fl">77.8732</span>, <span class="fl">77.2097</span>, <span class="fl">77.2571</span>, <span class="fl">54.8874</span>, <span class="fl">76.0249</span>,</span>
<span id="cb79-45"><a href="id_04_model_validation_and_interpretation.html#cb79-45" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">23.3353</span>, <span class="fl">33.2998</span>, <span class="fl">45.9064</span>, <span class="fl">36.1671</span>, <span class="fl">36.4751</span>, <span class="fl">74.5557</span>, <span class="fl">70.6220</span>, <span class="fl">48.2998</span>, <span class="fl">69.6742</span>, <span class="fl">76.9727</span>, <span class="fl">65.1244</span>, <span class="fl">75.9064</span>,</span>
<span id="cb79-46"><a href="id_04_model_validation_and_interpretation.html#cb79-46" aria-hidden="true" tabindex="-1"></a> <span class="fl">2.2571</span>, <span class="fl">27.1860</span>, <span class="sc">-</span><span class="fl">1.6055</span>, <span class="fl">42.3519</span>, <span class="fl">48.7500</span>, <span class="fl">47.8969</span>, <span class="fl">62.2334</span>, <span class="fl">70.6220</span>, <span class="fl">79.7927</span>, <span class="fl">75.9538</span>, <span class="fl">77.4467</span>, <span class="fl">81.0960</span></span>
<span id="cb79-47"><a href="id_04_model_validation_and_interpretation.html#cb79-47" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb79-48"><a href="id_04_model_validation_and_interpretation.html#cb79-48" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb79-49"><a href="id_04_model_validation_and_interpretation.html#cb79-49" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-50"><a href="id_04_model_validation_and_interpretation.html#cb79-50" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-51"><a href="id_04_model_validation_and_interpretation.html#cb79-51" aria-hidden="true" tabindex="-1"></a>replicate_1_2 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb79-52"><a href="id_04_model_validation_and_interpretation.html#cb79-52" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb79-53"><a href="id_04_model_validation_and_interpretation.html#cb79-53" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">7.7192</span>, <span class="fl">54.0818</span>, <span class="fl">45.1007</span>, <span class="fl">62.8495</span>, <span class="fl">50.1481</span>, <span class="fl">37.6126</span>, <span class="fl">59.5083</span>, <span class="fl">71.7121</span>, <span class="fl">57.7073</span>, <span class="fl">59.4135</span>, <span class="fl">77.0201</span>, <span class="fl">82.3756</span>,</span>
<span id="cb79-54"><a href="id_04_model_validation_and_interpretation.html#cb79-54" aria-hidden="true" tabindex="-1"></a> <span class="fl">21.4277</span>, <span class="fl">10.8353</span>, <span class="fl">54.6268</span>, <span class="fl">65.7168</span>, <span class="fl">15.6220</span>, <span class="fl">35.1007</span>, <span class="fl">64.8637</span>, <span class="fl">67.8258</span>, <span class="fl">66.5225</span>, <span class="fl">72.7073</span>, <span class="fl">83.1576</span>, <span class="fl">72.7784</span>,</span>
<span id="cb79-55"><a href="id_04_model_validation_and_interpretation.html#cb79-55" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">53.7855</span>, <span class="fl">2.6600</span>, <span class="fl">42.8732</span>, <span class="fl">32.9443</span>, <span class="fl">48.1576</span>, <span class="fl">71.0960</span>, <span class="fl">73.4656</span>, <span class="fl">66.9964</span>, <span class="fl">72.1386</span>, <span class="fl">78.6789</span>, <span class="fl">78.7500</span>, <span class="fl">77.1386</span>,</span>
<span id="cb79-56"><a href="id_04_model_validation_and_interpretation.html#cb79-56" aria-hidden="true" tabindex="-1"></a> <span class="fl">34.9822</span>, <span class="fl">37.1623</span>, <span class="fl">25.8590</span>, <span class="fl">34.7453</span>, <span class="fl">36.9964</span>, <span class="fl">54.2239</span>, <span class="fl">72.8969</span>, <span class="fl">67.5415</span>, <span class="fl">73.5604</span>, <span class="fl">52.8021</span>, <span class="fl">88.1339</span>, <span class="fl">80.0296</span>,</span>
<span id="cb79-57"><a href="id_04_model_validation_and_interpretation.html#cb79-57" aria-hidden="true" tabindex="-1"></a> <span class="fl">1.1434</span>, <span class="fl">30.6694</span>, <span class="fl">32.8969</span>, <span class="fl">45.5983</span>, <span class="fl">48.6552</span>, <span class="fl">70.5036</span>, <span class="fl">74.7927</span>, <span class="fl">76.0249</span>, <span class="fl">75.5983</span>, <span class="fl">62.6600</span>, <span class="fl">61.3803</span>, <span class="fl">81.4277</span>,</span>
<span id="cb79-58"><a href="id_04_model_validation_and_interpretation.html#cb79-58" aria-hidden="true" tabindex="-1"></a> <span class="fl">27.4467</span>, <span class="fl">30.3614</span>, <span class="fl">24.8164</span>, <span class="fl">25.8116</span>, <span class="fl">63.9633</span>, <span class="fl">49.7927</span>, <span class="fl">60.6457</span>, <span class="fl">79.8637</span>, <span class="fl">77.3282</span>, <span class="fl">79.8164</span>, <span class="fl">55.0770</span>, <span class="fl">77.1386</span>,</span>
<span id="cb79-59"><a href="id_04_model_validation_and_interpretation.html#cb79-59" aria-hidden="true" tabindex="-1"></a> <span class="fl">7.9206</span>, <span class="fl">44.0107</span>, <span class="fl">57.2571</span>, <span class="fl">50.1955</span>, <span class="fl">45.6220</span>, <span class="fl">76.2618</span>, <span class="fl">71.7358</span>, <span class="fl">51.6410</span>, <span class="fl">72.9680</span>, <span class="fl">76.6410</span>, <span class="fl">64.1291</span>, <span class="fl">76.5225</span>,</span>
<span id="cb79-60"><a href="id_04_model_validation_and_interpretation.html#cb79-60" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">3.7618</span>, <span class="fl">32.5178</span>, <span class="fl">28.9159</span>, <span class="fl">47.3756</span>, <span class="fl">50.5983</span>, <span class="fl">49.4609</span>, <span class="fl">62.7547</span>, <span class="fl">71.7358</span>, <span class="fl">83.3709</span>, <span class="fl">81.7832</span>, <span class="fl">83.3235</span>, <span class="fl">82.9917</span></span>
<span id="cb79-61"><a href="id_04_model_validation_and_interpretation.html#cb79-61" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb79-62"><a href="id_04_model_validation_and_interpretation.html#cb79-62" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb79-63"><a href="id_04_model_validation_and_interpretation.html#cb79-63" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-64"><a href="id_04_model_validation_and_interpretation.html#cb79-64" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-65"><a href="id_04_model_validation_and_interpretation.html#cb79-65" aria-hidden="true" tabindex="-1"></a>replicate_2_1 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb79-66"><a href="id_04_model_validation_and_interpretation.html#cb79-66" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb79-67"><a href="id_04_model_validation_and_interpretation.html#cb79-67" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">21.6291</span>, <span class="fl">12.7784</span>, <span class="fl">51.7595</span>, <span class="fl">30.0770</span>, <span class="fl">33.6078</span>, <span class="fl">28.2524</span>, <span class="fl">47.4467</span>, <span class="fl">51.8780</span>, <span class="fl">45.4088</span>, <span class="fl">64.9585</span>, <span class="fl">64.9585</span>, <span class="fl">69.3187</span>,</span>
<span id="cb79-68"><a href="id_04_model_validation_and_interpretation.html#cb79-68" aria-hidden="true" tabindex="-1"></a> <span class="fl">24.2476</span>, <span class="fl">7.0675</span>, <span class="fl">56.8780</span>, <span class="fl">71.7595</span>, <span class="fl">25.8116</span>, <span class="fl">40.1481</span>, <span class="fl">69.2476</span>, <span class="fl">71.3803</span>, <span class="fl">74.9585</span>, <span class="fl">73.1813</span>, <span class="fl">81.8069</span>, <span class="fl">74.8400</span>,</span>
<span id="cb79-69"><a href="id_04_model_validation_and_interpretation.html#cb79-69" aria-hidden="true" tabindex="-1"></a> <span class="fl">44.5557</span>, <span class="fl">31.2618</span>, <span class="fl">43.6552</span>, <span class="fl">39.0818</span>, <span class="fl">48.3235</span>, <span class="fl">67.8495</span>, <span class="fl">76.2855</span>, <span class="fl">64.5557</span>, <span class="fl">74.5083</span>, <span class="fl">76.0723</span>, <span class="fl">75.4799</span>, <span class="fl">75.5746</span>,</span>
<span id="cb79-70"><a href="id_04_model_validation_and_interpretation.html#cb79-70" aria-hidden="true" tabindex="-1"></a> <span class="fl">17.3045</span>, <span class="fl">45.8590</span>, <span class="sc">-</span><span class="fl">7.5533</span>, <span class="fl">34.7690</span>, <span class="fl">28.3945</span>, <span class="fl">41.9491</span>, <span class="fl">73.3709</span>, <span class="fl">69.8874</span>, <span class="fl">70.1244</span>, <span class="fl">62.9206</span>, <span class="fl">71.8306</span>, <span class="fl">78.6552</span>,</span>
<span id="cb79-71"><a href="id_04_model_validation_and_interpretation.html#cb79-71" aria-hidden="true" tabindex="-1"></a> <span class="fl">17.0675</span>, <span class="fl">34.8874</span>, <span class="fl">19.2002</span>, <span class="fl">35.7168</span>, <span class="fl">43.5130</span>, <span class="fl">2.1386</span>, <span class="fl">70.8353</span>, <span class="fl">50.4325</span>, <span class="fl">73.8922</span>, <span class="fl">68.7974</span>, <span class="fl">76.4277</span>, <span class="fl">77.3756</span>,</span>
<span id="cb79-72"><a href="id_04_model_validation_and_interpretation.html#cb79-72" aria-hidden="true" tabindex="-1"></a> <span class="fl">51.4751</span>, <span class="fl">2.5652</span>, <span class="fl">13.2998</span>, <span class="fl">25.7405</span>, <span class="fl">58.7500</span>, <span class="fl">50.5036</span>, <span class="fl">64.6979</span>, <span class="fl">76.6410</span>, <span class="fl">67.4467</span>, <span class="fl">80.3614</span>, <span class="fl">63.3945</span>, <span class="fl">75.5746</span>,</span>
<span id="cb79-73"><a href="id_04_model_validation_and_interpretation.html#cb79-73" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fl">41.2500</span>, <span class="fl">44.1528</span>, <span class="fl">51.4040</span>, <span class="fl">35.3377</span>, <span class="fl">57.3993</span>, <span class="fl">78.3945</span>, <span class="fl">72.7784</span>, <span class="fl">56.4751</span>, <span class="fl">75.5746</span>, <span class="fl">74.5320</span>, <span class="fl">68.5604</span>, <span class="fl">75.0533</span>,</span>
<span id="cb79-74"><a href="id_04_model_validation_and_interpretation.html#cb79-74" aria-hidden="true" tabindex="-1"></a> <span class="fl">15.5036</span>, <span class="fl">31.6173</span>, <span class="fl">11.4040</span>, <span class="fl">49.9111</span>, <span class="fl">49.6505</span>, <span class="fl">48.0865</span>, <span class="fl">61.4040</span>, <span class="fl">72.7784</span>, <span class="fl">79.9822</span>, <span class="fl">77.9443</span>, <span class="fl">71.5699</span>, <span class="fl">79.8164</span></span>
<span id="cb79-75"><a href="id_04_model_validation_and_interpretation.html#cb79-75" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb79-76"><a href="id_04_model_validation_and_interpretation.html#cb79-76" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb79-77"><a href="id_04_model_validation_and_interpretation.html#cb79-77" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-78"><a href="id_04_model_validation_and_interpretation.html#cb79-78" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-79"><a href="id_04_model_validation_and_interpretation.html#cb79-79" aria-hidden="true" tabindex="-1"></a>replicate_2_2 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb79-80"><a href="id_04_model_validation_and_interpretation.html#cb79-80" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb79-81"><a href="id_04_model_validation_and_interpretation.html#cb79-81" aria-hidden="true" tabindex="-1"></a> <span class="fl">13.5367</span>, <span class="fl">25.8827</span>, <span class="fl">48.0628</span>, <span class="fl">76.2855</span>, <span class="fl">58.0628</span>, <span class="fl">54.2713</span>, <span class="fl">69.7927</span>, <span class="fl">78.9633</span>, <span class="fl">55.6457</span>, <span class="fl">78.2287</span>, <span class="fl">80.5983</span>, <span class="fl">83.6789</span>,</span>
<span id="cb79-82"><a href="id_04_model_validation_and_interpretation.html#cb79-82" aria-hidden="true" tabindex="-1"></a> <span class="fl">51.5699</span>, <span class="fl">6.1671</span>, <span class="fl">50.8116</span>, <span class="fl">73.3472</span>, <span class="fl">28.4419</span>, <span class="fl">26.0960</span>, <span class="fl">73.4893</span>, <span class="fl">76.5699</span>, <span class="fl">74.5320</span>, <span class="fl">78.7263</span>, <span class="fl">85.4799</span>, <span class="fl">80.1718</span>,</span>
<span id="cb79-83"><a href="id_04_model_validation_and_interpretation.html#cb79-83" aria-hidden="true" tabindex="-1"></a> <span class="fl">41.7595</span>, <span class="fl">48.1339</span>, <span class="fl">39.0818</span>, <span class="fl">43.8211</span>, <span class="fl">47.9917</span>, <span class="fl">65.2429</span>, <span class="fl">79.1765</span>, <span class="fl">73.6078</span>, <span class="fl">78.5604</span>, <span class="fl">82.7547</span>, <span class="fl">81.2855</span>, <span class="fl">82.6126</span>,</span>
<span id="cb79-84"><a href="id_04_model_validation_and_interpretation.html#cb79-84" aria-hidden="true" tabindex="-1"></a> <span class="fl">38.0154</span>, <span class="fl">30.6931</span>, <span class="fl">42.3045</span>, <span class="fl">41.2145</span>, <span class="fl">30.7642</span>, <span class="fl">57.1386</span>, <span class="fl">75.6220</span>, <span class="fl">70.5746</span>, <span class="fl">72.1386</span>, <span class="fl">66.0960</span>, <span class="fl">78.2287</span>, <span class="fl">80.9775</span>,</span>
<span id="cb79-85"><a href="id_04_model_validation_and_interpretation.html#cb79-85" aria-hidden="true" tabindex="-1"></a> <span class="fl">19.6742</span>, <span class="fl">25.1481</span>, <span class="fl">36.0012</span>, <span class="fl">28.8685</span>, <span class="fl">33.3472</span>, <span class="fl">70.0533</span>, <span class="fl">73.1102</span>, <span class="fl">55.5509</span>, <span class="fl">73.3945</span>, <span class="fl">74.7216</span>, <span class="fl">80.4325</span>, <span class="fl">80.8827</span>,</span>
<span id="cb79-86"><a href="id_04_model_validation_and_interpretation.html#cb79-86" aria-hidden="true" tabindex="-1"></a> <span class="fl">46.7832</span>, <span class="fl">28.2050</span>, <span class="fl">30.6220</span>, <span class="fl">30.2903</span>, <span class="fl">60.5036</span>, <span class="fl">34.1291</span>, <span class="fl">66.9964</span>, <span class="fl">77.6363</span>, <span class="fl">76.3803</span>, <span class="fl">85.6694</span>, <span class="fl">68.1102</span>, <span class="fl">82.6126</span>,</span>
<span id="cb79-87"><a href="id_04_model_validation_and_interpretation.html#cb79-87" aria-hidden="true" tabindex="-1"></a> <span class="fl">6.4040</span>, <span class="fl">24.1528</span>, <span class="fl">64.3661</span>, <span class="fl">47.6126</span>, <span class="fl">63.5604</span>, <span class="fl">81.3566</span>, <span class="fl">79.8164</span>, <span class="fl">61.2382</span>, <span class="fl">78.0628</span>, <span class="fl">78.5604</span>, <span class="fl">70.7405</span>, <span class="fl">76.9017</span>,</span>
<span id="cb79-88"><a href="id_04_model_validation_and_interpretation.html#cb79-88" aria-hidden="true" tabindex="-1"></a> <span class="fl">25.3140</span>, <span class="fl">42.5889</span>, <span class="fl">40.6694</span>, <span class="fl">50.2192</span>, <span class="fl">53.0154</span>, <span class="fl">47.0912</span>, <span class="fl">66.6173</span>, <span class="fl">79.8164</span>, <span class="fl">83.3709</span>, <span class="fl">82.6363</span>, <span class="fl">77.1623</span>, <span class="fl">84.3898</span></span>
<span id="cb79-89"><a href="id_04_model_validation_and_interpretation.html#cb79-89" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb79-90"><a href="id_04_model_validation_and_interpretation.html#cb79-90" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb79-91"><a href="id_04_model_validation_and_interpretation.html#cb79-91" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-92"><a href="id_04_model_validation_and_interpretation.html#cb79-92" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-93"><a href="id_04_model_validation_and_interpretation.html#cb79-93" aria-hidden="true" tabindex="-1"></a>replicate_1_1 <span class="ot"><-</span> <span class="fu">as.vector</span>(replicate_1_1)</span>
<span id="cb79-94"><a href="id_04_model_validation_and_interpretation.html#cb79-94" aria-hidden="true" tabindex="-1"></a>replicate_1_2 <span class="ot"><-</span> <span class="fu">as.vector</span>(replicate_1_2)</span>
<span id="cb79-95"><a href="id_04_model_validation_and_interpretation.html#cb79-95" aria-hidden="true" tabindex="-1"></a>replicate_2_1 <span class="ot"><-</span> <span class="fu">as.vector</span>(replicate_2_1)</span>
<span id="cb79-96"><a href="id_04_model_validation_and_interpretation.html#cb79-96" aria-hidden="true" tabindex="-1"></a>replicate_2_2 <span class="ot"><-</span> <span class="fu">as.vector</span>(replicate_2_2)</span>
<span id="cb79-97"><a href="id_04_model_validation_and_interpretation.html#cb79-97" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-98"><a href="id_04_model_validation_and_interpretation.html#cb79-98" aria-hidden="true" tabindex="-1"></a>mb_true_ <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb79-99"><a href="id_04_model_validation_and_interpretation.html#cb79-99" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">96</span>) {</span>
<span id="cb79-100"><a href="id_04_model_validation_and_interpretation.html#cb79-100" aria-hidden="true" tabindex="-1"></a> res_ <span class="ot"><-</span> <span class="fu">mean</span>(<span class="fu">c</span>(</span>
<span id="cb79-101"><a href="id_04_model_validation_and_interpretation.html#cb79-101" aria-hidden="true" tabindex="-1"></a> <span class="fu">mean</span>(<span class="fu">c</span>(replicate_1_1[i], replicate_1_2[i])),</span>
<span id="cb79-102"><a href="id_04_model_validation_and_interpretation.html#cb79-102" aria-hidden="true" tabindex="-1"></a> <span class="fu">mean</span>(<span class="fu">c</span>(replicate_2_1[i], replicate_2_2[i]))</span>
<span id="cb79-103"><a href="id_04_model_validation_and_interpretation.html#cb79-103" aria-hidden="true" tabindex="-1"></a> ))</span>
<span id="cb79-104"><a href="id_04_model_validation_and_interpretation.html#cb79-104" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (res_ <span class="sc">>=</span> <span class="dv">0</span>) {</span>
<span id="cb79-105"><a href="id_04_model_validation_and_interpretation.html#cb79-105" aria-hidden="true" tabindex="-1"></a> mb_true_ <span class="ot"><-</span> <span class="fu">c</span>(mb_true_, res_)</span>
<span id="cb79-106"><a href="id_04_model_validation_and_interpretation.html#cb79-106" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb79-107"><a href="id_04_model_validation_and_interpretation.html#cb79-107" aria-hidden="true" tabindex="-1"></a> mb_true_ <span class="ot"><-</span> <span class="fu">c</span>(mb_true_, <span class="cn">NA</span>)</span>
<span id="cb79-108"><a href="id_04_model_validation_and_interpretation.html#cb79-108" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb79-109"><a href="id_04_model_validation_and_interpretation.html#cb79-109" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb79-110"><a href="id_04_model_validation_and_interpretation.html#cb79-110" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-111"><a href="id_04_model_validation_and_interpretation.html#cb79-111" aria-hidden="true" tabindex="-1"></a>new_replicate_1 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb79-112"><a href="id_04_model_validation_and_interpretation.html#cb79-112" aria-hidden="true" tabindex="-1"></a> <span class="fl">79.9064</span>, <span class="fl">80.2179</span>, <span class="fl">75.9474</span>, <span class="fl">79.1975</span>, <span class="fl">71.6238</span>, <span class="fl">53.5235</span>, <span class="fl">83.5678</span>, <span class="fl">81.2452</span>, <span class="fl">74.2512</span>, <span class="fl">68.4291</span>,</span>
<span id="cb79-113"><a href="id_04_model_validation_and_interpretation.html#cb79-113" aria-hidden="true" tabindex="-1"></a> <span class="fl">90.2855</span>, <span class="fl">89.2512</span>, <span class="fl">92.8356</span>, <span class="fl">80.2853</span>, <span class="fl">62.0912</span>, <span class="fl">89.2853</span>, <span class="fl">70.1267</span>, <span class="fl">90.2891</span>, <span class="fl">63.2853</span>, <span class="fl">70.6812</span>,</span>
<span id="cb79-114"><a href="id_04_model_validation_and_interpretation.html#cb79-114" aria-hidden="true" tabindex="-1"></a> <span class="fl">89.2582</span>, <span class="fl">85.2567</span>, <span class="fl">78.3682</span>, <span class="fl">90.5732</span>, <span class="fl">82.5253</span>, <span class="fl">84.2912</span>, <span class="fl">82.5923</span>, <span class="fl">90.8613</span>, <span class="fl">73.2862</span>, <span class="fl">90.4823</span>,</span>
<span id="cb79-115"><a href="id_04_model_validation_and_interpretation.html#cb79-115" aria-hidden="true" tabindex="-1"></a> <span class="fl">59.2715</span></span>
<span id="cb79-116"><a href="id_04_model_validation_and_interpretation.html#cb79-116" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-117"><a href="id_04_model_validation_and_interpretation.html#cb79-117" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-118"><a href="id_04_model_validation_and_interpretation.html#cb79-118" aria-hidden="true" tabindex="-1"></a>new_replicate_2 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb79-119"><a href="id_04_model_validation_and_interpretation.html#cb79-119" aria-hidden="true" tabindex="-1"></a> <span class="fl">77.6257</span>, <span class="fl">82.2692</span>, <span class="fl">71.8684</span>, <span class="fl">79.1338</span>, <span class="fl">67.7994</span>, <span class="fl">52.3258</span>, <span class="fl">88.2912</span>, <span class="fl">79.6823</span>, <span class="fl">78.5257</span>, <span class="fl">62.5212</span>,</span>
<span id="cb79-120"><a href="id_04_model_validation_and_interpretation.html#cb79-120" aria-hidden="true" tabindex="-1"></a> <span class="fl">81.2842</span>, <span class="fl">83.5812</span>, <span class="fl">90.2512</span>, <span class="fl">73.4821</span>, <span class="fl">63.6843</span>, <span class="fl">88.2965</span>, <span class="fl">72.0582</span>, <span class="fl">93.1925</span>, <span class="fl">62.9142</span>, <span class="fl">78.0396</span>,</span>
<span id="cb79-121"><a href="id_04_model_validation_and_interpretation.html#cb79-121" aria-hidden="true" tabindex="-1"></a> <span class="fl">86.9323</span>, <span class="fl">82.5323</span>, <span class="fl">72.6429</span>, <span class="fl">83.6736</span>, <span class="fl">89.5191</span>, <span class="fl">86.8432</span>, <span class="fl">81.5171</span>, <span class="fl">92.1856</span>, <span class="fl">92.6736</span>, <span class="fl">93.9124</span>,</span>
<span id="cb79-122"><a href="id_04_model_validation_and_interpretation.html#cb79-122" aria-hidden="true" tabindex="-1"></a> <span class="fl">95.3929</span></span>
<span id="cb79-123"><a href="id_04_model_validation_and_interpretation.html#cb79-123" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-124"><a href="id_04_model_validation_and_interpretation.html#cb79-124" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-125"><a href="id_04_model_validation_and_interpretation.html#cb79-125" aria-hidden="true" tabindex="-1"></a>new_replicate_3 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb79-126"><a href="id_04_model_validation_and_interpretation.html#cb79-126" aria-hidden="true" tabindex="-1"></a> <span class="fl">79.7602</span>, <span class="fl">83.5192</span>, <span class="fl">74.6645</span>, <span class="fl">80.8854</span>, <span class="fl">67.3918</span>, <span class="fl">49.5821</span>, <span class="fl">93.1263</span>, <span class="fl">84.2590</span>, <span class="fl">76.9253</span>, <span class="fl">60.4827</span>,</span>
<span id="cb79-127"><a href="id_04_model_validation_and_interpretation.html#cb79-127" aria-hidden="true" tabindex="-1"></a> <span class="fl">93.4825</span>, <span class="fl">85.9901</span>, <span class="fl">88.5705</span>, <span class="fl">79.0125</span>, <span class="fl">60.1825</span>, <span class="fl">90.5812</span>, <span class="fl">71.2281</span>, <span class="fl">89.9251</span>, <span class="fl">64.2681</span>, <span class="fl">72.5712</span>,</span>
<span id="cb79-128"><a href="id_04_model_validation_and_interpretation.html#cb79-128" aria-hidden="true" tabindex="-1"></a> <span class="fl">83.9235</span>, <span class="fl">84.2719</span>, <span class="fl">71.1281</span>, <span class="fl">95.2182</span>, <span class="fl">90.0191</span>, <span class="fl">89.1812</span>, <span class="fl">82.7195</span>, <span class="fl">89.9501</span>, <span class="fl">83.8581</span>, <span class="fl">85.3725</span>,</span>
<span id="cb79-129"><a href="id_04_model_validation_and_interpretation.html#cb79-129" aria-hidden="true" tabindex="-1"></a> <span class="fl">93.2801</span></span>
<span id="cb79-130"><a href="id_04_model_validation_and_interpretation.html#cb79-130" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb79-131"><a href="id_04_model_validation_and_interpretation.html#cb79-131" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-132"><a href="id_04_model_validation_and_interpretation.html#cb79-132" aria-hidden="true" tabindex="-1"></a>new_mb_true_ <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb79-133"><a href="id_04_model_validation_and_interpretation.html#cb79-133" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">31</span>) {</span>
<span id="cb79-134"><a href="id_04_model_validation_and_interpretation.html#cb79-134" aria-hidden="true" tabindex="-1"></a> res_ <span class="ot"><-</span> <span class="fu">mean</span>(<span class="fu">c</span>(new_replicate_1[i], new_replicate_2[i], new_replicate_3[i]))</span>
<span id="cb79-135"><a href="id_04_model_validation_and_interpretation.html#cb79-135" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (res_ <span class="sc">>=</span> <span class="dv">0</span>) {</span>
<span id="cb79-136"><a href="id_04_model_validation_and_interpretation.html#cb79-136" aria-hidden="true" tabindex="-1"></a> new_mb_true_ <span class="ot"><-</span> <span class="fu">c</span>(new_mb_true_, res_)</span>
<span id="cb79-137"><a href="id_04_model_validation_and_interpretation.html#cb79-137" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb79-138"><a href="id_04_model_validation_and_interpretation.html#cb79-138" aria-hidden="true" tabindex="-1"></a> new_mb_true_ <span class="ot"><-</span> <span class="fu">c</span>(new_mb_true_, <span class="cn">NA</span>)</span>
<span id="cb79-139"><a href="id_04_model_validation_and_interpretation.html#cb79-139" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb79-140"><a href="id_04_model_validation_and_interpretation.html#cb79-140" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb79-141"><a href="id_04_model_validation_and_interpretation.html#cb79-141" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb79-142"><a href="id_04_model_validation_and_interpretation.html#cb79-142" aria-hidden="true" tabindex="-1"></a>mb_true <span class="ot"><-</span> <span class="fu">c</span>(mb_true_, new_mb_true_)</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_validation_and_interpretation.html#cb80-1" aria-hidden="true" tabindex="-1"></a>mb_df <span class="ot"><-</span> <span class="fu">data.frame</span>(<span class="at">mb_pred =</span> mb_pred, <span class="at">mb_true =</span> mb_true)</span>
<span id="cb80-2"><a href="id_04_model_validation_and_interpretation.html#cb80-2" aria-hidden="true" tabindex="-1"></a>mb_df <span class="ot"><-</span> mb_df[<span class="fu">complete.cases</span>(mb_df), ]</span>
<span id="cb80-3"><a href="id_04_model_validation_and_interpretation.html#cb80-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb80-4"><a href="id_04_model_validation_and_interpretation.html#cb80-4" aria-hidden="true" tabindex="-1"></a>p1 <span class="ot"><-</span> <span class="fu">ggscatter</span>(mb_df,</span>
<span id="cb80-5"><a href="id_04_model_validation_and_interpretation.html#cb80-5" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"mb_pred"</span>, <span class="at">y =</span> <span class="st">"mb_true"</span>,</span>
<span id="cb80-6"><a href="id_04_model_validation_and_interpretation.html#cb80-6" aria-hidden="true" tabindex="-1"></a> <span class="at">alpha =</span> <span class="fl">0.8</span>, <span class="at">size =</span> <span class="fl">2.5</span>, <span class="at">stroke =</span> <span class="fl">0.2</span>, <span class="at">color =</span> <span class="st">"black"</span>, <span class="at">fill =</span> <span class="st">"grey70"</span>, <span class="at">shape =</span> <span class="dv">21</span>,</span>
<span id="cb80-7"><a href="id_04_model_validation_and_interpretation.html#cb80-7" aria-hidden="true" tabindex="-1"></a> <span class="at">add =</span> <span class="st">"reg.line"</span>, <span class="at">conf.int =</span> <span class="cn">TRUE</span>, <span class="at">conf.int.level =</span> <span class="fl">0.95</span>, <span class="at">cor.coef =</span> <span class="cn">TRUE</span>,</span>
<span id="cb80-8"><a href="id_04_model_validation_and_interpretation.html#cb80-8" aria-hidden="true" tabindex="-1"></a> <span class="at">add.params =</span> <span class="fu">list</span>(<span class="at">color =</span> <span class="st">"grey25"</span>, <span class="at">fill =</span> <span class="st">"grey70"</span>),</span>
<span id="cb80-9"><a href="id_04_model_validation_and_interpretation.html#cb80-9" aria-hidden="true" tabindex="-1"></a> <span class="at">cor.coeff.args =</span> <span class="fu">list</span>(</span>
<span id="cb80-10"><a href="id_04_model_validation_and_interpretation.html#cb80-10" aria-hidden="true" tabindex="-1"></a> <span class="at">method =</span> <span class="st">"pearson"</span>, <span class="at">label.x =</span> <span class="dv">2</span>, <span class="at">label.y =</span> <span class="dv">95</span>, <span class="at">label.sep =</span> <span class="st">"</span><span class="sc">\n</span><span class="st">"</span>,</span>
<span id="cb80-11"><a href="id_04_model_validation_and_interpretation.html#cb80-11" aria-hidden="true" tabindex="-1"></a> <span class="at">size =</span> <span class="fl">4.5</span></span>
<span id="cb80-12"><a href="id_04_model_validation_and_interpretation.html#cb80-12" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb80-13"><a href="id_04_model_validation_and_interpretation.html#cb80-13" aria-hidden="true" tabindex="-1"></a>) <span class="sc">+</span></span>
<span id="cb80-14"><a href="id_04_model_validation_and_interpretation.html#cb80-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb80-15"><a href="id_04_model_validation_and_interpretation.html#cb80-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb80-16"><a href="id_04_model_validation_and_interpretation.html#cb80-16" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb80-17"><a href="id_04_model_validation_and_interpretation.html#cb80-17" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb80-18"><a href="id_04_model_validation_and_interpretation.html#cb80-18" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.background =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb80-19"><a href="id_04_model_validation_and_interpretation.html#cb80-19" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.border =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb80-20"><a href="id_04_model_validation_and_interpretation.html#cb80-20" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.line =</span> <span class="fu">element_line</span>(<span class="at">color =</span> <span class="st">"black"</span>),</span>
<span id="cb80-21"><a href="id_04_model_validation_and_interpretation.html#cb80-21" 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 class="at">size =</span> <span class="dv">15</span>),</span>
<span id="cb80-22"><a href="id_04_model_validation_and_interpretation.html#cb80-22" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">15</span>),</span>
<span id="cb80-23"><a href="id_04_model_validation_and_interpretation.html#cb80-23" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">12</span>),</span>
<span id="cb80-24"><a href="id_04_model_validation_and_interpretation.html#cb80-24" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.y =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">12</span>)</span>
<span id="cb80-25"><a href="id_04_model_validation_and_interpretation.html#cb80-25" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb80-26"><a href="id_04_model_validation_and_interpretation.html#cb80-26" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">"Predicted peptide bound</span><span class="sc">\n</span><span class="st">to b-mNPs (%)"</span>) <span class="sc">+</span></span>
<span id="cb80-27"><a href="id_04_model_validation_and_interpretation.html#cb80-27" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"Measured peptide bound</span><span class="sc">\n</span><span class="st">to mNPs (%)"</span>) <span class="sc">+</span></span>
<span id="cb80-28"><a href="id_04_model_validation_and_interpretation.html#cb80-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlim</span>(<span class="sc">-</span><span class="dv">5</span>, <span class="dv">105</span>) <span class="sc">+</span></span>
<span id="cb80-29"><a href="id_04_model_validation_and_interpretation.html#cb80-29" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylim</span>(<span class="sc">-</span><span class="dv">5</span>, <span class="dv">105</span>)</span></code></pre></div>
<p><img src="figures/Fig%203%20mb%20validation.png" width="100%" style="display: block; margin: auto;" /></p>
</div>
<div id="melanin-binding-and-cell-penetration" class="section level3 hasAnchor" number="4.1.2">
<h3><span class="header-section-number">4.1.2</span> Melanin binding and cell-penetration<a href="id_04_model_validation_and_interpretation.html#melanin-binding-and-cell-penetration" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div class="sourceCode" id="cb81"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb81-1"><a href="id_04_model_validation_and_interpretation.html#cb81-1" aria-hidden="true" tabindex="-1"></a><span class="co"># ================</span></span>
<span id="cb81-2"><a href="id_04_model_validation_and_interpretation.html#cb81-2" aria-hidden="true" tabindex="-1"></a><span class="co"># predicted values</span></span>
<span id="cb81-3"><a href="id_04_model_validation_and_interpretation.html#cb81-3" aria-hidden="true" tabindex="-1"></a><span class="co"># ================</span></span>
<span id="cb81-4"><a href="id_04_model_validation_and_interpretation.html#cb81-4" aria-hidden="true" tabindex="-1"></a>cpp_pred_ <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb81-5"><a href="id_04_model_validation_and_interpretation.html#cb81-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb81-6"><a href="id_04_model_validation_and_interpretation.html#cb81-6" aria-hidden="true" tabindex="-1"></a> <span class="st">"Non-CPP"</span>, <span class="st">"Non-CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-7"><a href="id_04_model_validation_and_interpretation.html#cb81-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"Non-CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-8"><a href="id_04_model_validation_and_interpretation.html#cb81-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"Non-CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-9"><a href="id_04_model_validation_and_interpretation.html#cb81-9" aria-hidden="true" tabindex="-1"></a> <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-10"><a href="id_04_model_validation_and_interpretation.html#cb81-10" aria-hidden="true" tabindex="-1"></a> <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-11"><a href="id_04_model_validation_and_interpretation.html#cb81-11" aria-hidden="true" tabindex="-1"></a> <span class="st">"Non-CPP"</span>, <span class="st">"Non-CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-12"><a href="id_04_model_validation_and_interpretation.html#cb81-12" aria-hidden="true" tabindex="-1"></a> <span class="st">"Non-CPP"</span>, <span class="st">"Non-CPP"</span>, <span class="st">"Non-CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-13"><a href="id_04_model_validation_and_interpretation.html#cb81-13" aria-hidden="true" tabindex="-1"></a> <span class="st">"Non-CPP"</span>, <span class="st">"Non-CPP"</span>, <span class="st">"Non-CPP"</span>, <span class="st">"Non-CPP"</span>, <span class="st">"Non-CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span></span>
<span id="cb81-14"><a href="id_04_model_validation_and_interpretation.html#cb81-14" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb81-15"><a href="id_04_model_validation_and_interpretation.html#cb81-15" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb81-16"><a href="id_04_model_validation_and_interpretation.html#cb81-16" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-17"><a href="id_04_model_validation_and_interpretation.html#cb81-17" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-18"><a href="id_04_model_validation_and_interpretation.html#cb81-18" aria-hidden="true" tabindex="-1"></a>new_cpp_pred_ <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb81-19"><a href="id_04_model_validation_and_interpretation.html#cb81-19" aria-hidden="true" tabindex="-1"></a> <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-20"><a href="id_04_model_validation_and_interpretation.html#cb81-20" aria-hidden="true" tabindex="-1"></a> <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-21"><a href="id_04_model_validation_and_interpretation.html#cb81-21" aria-hidden="true" tabindex="-1"></a> <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>, <span class="st">"CPP"</span>,</span>
<span id="cb81-22"><a href="id_04_model_validation_and_interpretation.html#cb81-22" aria-hidden="true" tabindex="-1"></a> <span class="st">"CPP"</span></span>
<span id="cb81-23"><a href="id_04_model_validation_and_interpretation.html#cb81-23" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-24"><a href="id_04_model_validation_and_interpretation.html#cb81-24" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-25"><a href="id_04_model_validation_and_interpretation.html#cb81-25" aria-hidden="true" tabindex="-1"></a>cpp_pred <span class="ot"><-</span> <span class="fu">c</span>(<span class="fu">as.vector</span>(cpp_pred_), new_cpp_pred_)</span>
<span id="cb81-26"><a href="id_04_model_validation_and_interpretation.html#cb81-26" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-27"><a href="id_04_model_validation_and_interpretation.html#cb81-27" aria-hidden="true" tabindex="-1"></a><span class="co"># ===================</span></span>
<span id="cb81-28"><a href="id_04_model_validation_and_interpretation.html#cb81-28" aria-hidden="true" tabindex="-1"></a><span class="co"># Experimental values</span></span>
<span id="cb81-29"><a href="id_04_model_validation_and_interpretation.html#cb81-29" aria-hidden="true" tabindex="-1"></a><span class="co"># ===================</span></span>
<span id="cb81-30"><a href="id_04_model_validation_and_interpretation.html#cb81-30" aria-hidden="true" tabindex="-1"></a>non_induced_replicate_1 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb81-31"><a href="id_04_model_validation_and_interpretation.html#cb81-31" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb81-32"><a href="id_04_model_validation_and_interpretation.html#cb81-32" aria-hidden="true" tabindex="-1"></a> <span class="fl">31.3344</span>, <span class="fl">24.1344</span>, <span class="fl">25.3344</span>, <span class="fl">45.4944</span>, <span class="fl">16.0944</span>, <span class="fl">146.6544</span>, <span class="fl">20.2944</span>, <span class="fl">18.9744</span>, <span class="fl">15.3744</span>, <span class="fl">12.0144</span>, <span class="fl">19.8144</span>, <span class="fl">15.3744</span>,</span>
<span id="cb81-33"><a href="id_04_model_validation_and_interpretation.html#cb81-33" aria-hidden="true" tabindex="-1"></a> <span class="fl">20.8944</span>, <span class="fl">20.1744</span>, <span class="fl">17.2944</span>, <span class="fl">63.1344</span>, <span class="fl">15.6144</span>, <span class="fl">15.6144</span>, <span class="fl">32.4144</span>, <span class="fl">16.5744</span>, <span class="fl">17.7744</span>, <span class="fl">12.1344</span>, <span class="fl">14.7744</span>, <span class="fl">55.9344</span>,</span>
<span id="cb81-34"><a href="id_04_model_validation_and_interpretation.html#cb81-34" aria-hidden="true" tabindex="-1"></a> <span class="fl">19.4544</span>, <span class="fl">21.3744</span>, <span class="fl">29.1744</span>, <span class="fl">25.9344</span>, <span class="fl">89.5344</span>, <span class="fl">14.8944</span>, <span class="fl">19.9344</span>, <span class="fl">11.4144</span>, <span class="fl">29.5344</span>, <span class="fl">13.5744</span>, <span class="fl">13.3344</span>, <span class="fl">33.9744</span>,</span>
<span id="cb81-35"><a href="id_04_model_validation_and_interpretation.html#cb81-35" aria-hidden="true" tabindex="-1"></a> <span class="fl">13.2144</span>, <span class="fl">8.1744</span>, <span class="fl">29.7744</span>, <span class="sc">-</span><span class="fl">24.8256</span>, <span class="fl">14.2944</span>, <span class="fl">18.4944</span>, <span class="fl">15.7344</span>, <span class="fl">14.6544</span>, <span class="fl">14.1744</span>, <span class="fl">10.9344</span>, <span class="fl">9.1344</span>, <span class="fl">55.6944</span>,</span>
<span id="cb81-36"><a href="id_04_model_validation_and_interpretation.html#cb81-36" aria-hidden="true" tabindex="-1"></a> <span class="fl">13.9344</span>, <span class="fl">12.8544</span>, <span class="fl">36.7344</span>, <span class="fl">20.8944</span>, <span class="fl">15.2544</span>, <span class="fl">17.5344</span>, <span class="fl">13.3344</span>, <span class="fl">17.4144</span>, <span class="fl">20.7744</span>, <span class="fl">10.9344</span>, <span class="fl">15.8544</span>, <span class="fl">19.4544</span>,</span>
<span id="cb81-37"><a href="id_04_model_validation_and_interpretation.html#cb81-37" aria-hidden="true" tabindex="-1"></a> <span class="fl">10.4544</span>, <span class="fl">20.2944</span>, <span class="fl">25.9344</span>, <span class="fl">19.9344</span>, <span class="fl">18.8544</span>, <span class="fl">15.8544</span>, <span class="fl">15.7344</span>, <span class="fl">20.2944</span>, <span class="fl">13.4544</span>, <span class="fl">7.5744</span>, <span class="fl">11.7744</span>, <span class="fl">33.9744</span>,</span>
<span id="cb81-38"><a href="id_04_model_validation_and_interpretation.html#cb81-38" aria-hidden="true" tabindex="-1"></a> <span class="fl">17.7744</span>, <span class="fl">24.8544</span>, <span class="fl">23.6544</span>, <span class="fl">19.5744</span>, <span class="fl">19.9344</span>, <span class="fl">77.5344</span>, <span class="fl">24.0144</span>, <span class="fl">24.8544</span>, <span class="fl">24.4944</span>, <span class="fl">29.5344</span>, <span class="fl">31.5744</span>, <span class="fl">53.8944</span>,</span>
<span id="cb81-39"><a href="id_04_model_validation_and_interpretation.html#cb81-39" aria-hidden="true" tabindex="-1"></a> <span class="fl">9.7344</span>, <span class="fl">10.5744</span>, <span class="fl">25.3344</span>, <span class="fl">15.7344</span>, <span class="fl">27.9744</span>, <span class="fl">27.4944</span>, <span class="fl">19.6944</span>, <span class="fl">19.4544</span>, <span class="fl">27.4944</span>, <span class="fl">24.4944</span>, <span class="fl">24.6144</span>, <span class="fl">26.2944</span></span>
<span id="cb81-40"><a href="id_04_model_validation_and_interpretation.html#cb81-40" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb81-41"><a href="id_04_model_validation_and_interpretation.html#cb81-41" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb81-42"><a href="id_04_model_validation_and_interpretation.html#cb81-42" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-43"><a href="id_04_model_validation_and_interpretation.html#cb81-43" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-44"><a href="id_04_model_validation_and_interpretation.html#cb81-44" aria-hidden="true" tabindex="-1"></a>non_induced_replicate_2 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb81-45"><a href="id_04_model_validation_and_interpretation.html#cb81-45" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb81-46"><a href="id_04_model_validation_and_interpretation.html#cb81-46" aria-hidden="true" tabindex="-1"></a> <span class="fl">30.3744</span>, <span class="fl">28.4544</span>, <span class="fl">26.1744</span>, <span class="fl">30.0144</span>, <span class="fl">25.6944</span>, <span class="fl">131.5344</span>, <span class="fl">31.8144</span>, <span class="fl">21.9744</span>, <span class="fl">30.4944</span>, <span class="fl">20.2944</span>, <span class="fl">17.7744</span>, <span class="fl">26.7744</span>,</span>
<span id="cb81-47"><a href="id_04_model_validation_and_interpretation.html#cb81-47" aria-hidden="true" tabindex="-1"></a> <span class="fl">27.4944</span>, <span class="fl">20.6544</span>, <span class="fl">21.3744</span>, <span class="fl">44.2944</span>, <span class="fl">23.6544</span>, <span class="fl">28.5744</span>, <span class="fl">26.5344</span>, <span class="fl">22.0944</span>, <span class="fl">26.7744</span>, <span class="fl">17.5344</span>, <span class="fl">18.9744</span>, <span class="fl">63.0144</span>,</span>
<span id="cb81-48"><a href="id_04_model_validation_and_interpretation.html#cb81-48" aria-hidden="true" tabindex="-1"></a> <span class="fl">25.6944</span>, <span class="fl">22.8144</span>, <span class="fl">27.6144</span>, <span class="fl">26.7744</span>, <span class="fl">88.9344</span>, <span class="fl">30.8544</span>, <span class="fl">24.1344</span>, <span class="fl">10.9344</span>, <span class="fl">19.9344</span>, <span class="fl">19.5744</span>, <span class="fl">21.4944</span>, <span class="fl">25.2144</span>,</span>
<span id="cb81-49"><a href="id_04_model_validation_and_interpretation.html#cb81-49" aria-hidden="true" tabindex="-1"></a> <span class="fl">12.9744</span>, <span class="fl">15.0144</span>, <span class="fl">17.7744</span>, <span class="fl">14.8944</span>, <span class="fl">13.5744</span>, <span class="fl">24.4944</span>, <span class="fl">27.6144</span>, <span class="fl">13.9344</span>, <span class="fl">23.1744</span>, <span class="fl">17.7744</span>, <span class="fl">15.7344</span>, <span class="fl">45.6144</span>,</span>
<span id="cb81-50"><a href="id_04_model_validation_and_interpretation.html#cb81-50" aria-hidden="true" tabindex="-1"></a> <span class="fl">16.0944</span>, <span class="fl">23.1744</span>, <span class="fl">17.7744</span>, <span class="fl">15.7344</span>, <span class="fl">20.6544</span>, <span class="fl">27.6144</span>, <span class="fl">34.0944</span>, <span class="fl">24.6144</span>, <span class="fl">22.8144</span>, <span class="fl">14.4144</span>, <span class="fl">26.7744</span>, <span class="fl">25.6944</span>,</span>
<span id="cb81-51"><a href="id_04_model_validation_and_interpretation.html#cb81-51" aria-hidden="true" tabindex="-1"></a> <span class="fl">12.0144</span>, <span class="fl">31.8144</span>, <span class="fl">16.4544</span>, <span class="fl">21.6144</span>, <span class="fl">30.2544</span>, <span class="fl">18.7344</span>, <span class="fl">24.9744</span>, <span class="fl">29.7744</span>, <span class="fl">15.1344</span>, <span class="fl">15.1344</span>, <span class="fl">27.8544</span>, <span class="fl">25.2144</span>,</span>
<span id="cb81-52"><a href="id_04_model_validation_and_interpretation.html#cb81-52" aria-hidden="true" tabindex="-1"></a> <span class="fl">23.2944</span>, <span class="fl">28.2144</span>, <span class="fl">30.6144</span>, <span class="fl">22.0944</span>, <span class="fl">19.9344</span>, <span class="fl">63.0144</span>, <span class="fl">22.8144</span>, <span class="fl">22.2144</span>, <span class="fl">21.6144</span>, <span class="fl">19.9344</span>, <span class="fl">23.0544</span>, <span class="fl">30.9744</span>,</span>
<span id="cb81-53"><a href="id_04_model_validation_and_interpretation.html#cb81-53" aria-hidden="true" tabindex="-1"></a> <span class="fl">14.0544</span>, <span class="fl">23.7744</span>, <span class="fl">20.6544</span>, <span class="fl">11.0544</span>, <span class="fl">23.8944</span>, <span class="fl">31.4544</span>, <span class="fl">20.6544</span>, <span class="fl">15.4944</span>, <span class="fl">31.4544</span>, <span class="fl">26.0544</span>, <span class="fl">33.0144</span>, <span class="fl">37.0944</span></span>
<span id="cb81-54"><a href="id_04_model_validation_and_interpretation.html#cb81-54" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb81-55"><a href="id_04_model_validation_and_interpretation.html#cb81-55" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb81-56"><a href="id_04_model_validation_and_interpretation.html#cb81-56" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-57"><a href="id_04_model_validation_and_interpretation.html#cb81-57" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-58"><a href="id_04_model_validation_and_interpretation.html#cb81-58" aria-hidden="true" tabindex="-1"></a>non_induced_replicate_3 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb81-59"><a href="id_04_model_validation_and_interpretation.html#cb81-59" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb81-60"><a href="id_04_model_validation_and_interpretation.html#cb81-60" aria-hidden="true" tabindex="-1"></a> <span class="fl">27.3744</span>, <span class="fl">16.3344</span>, <span class="fl">17.5344</span>, <span class="fl">33.7344</span>, <span class="fl">13.8144</span>, <span class="fl">110.8944</span>, <span class="fl">33.4944</span>, <span class="fl">37.2144</span>, <span class="fl">34.8144</span>, <span class="fl">20.8944</span>, <span class="fl">39.4944</span>, <span class="fl">36.1344</span>,</span>
<span id="cb81-61"><a href="id_04_model_validation_and_interpretation.html#cb81-61" aria-hidden="true" tabindex="-1"></a> <span class="fl">15.9744</span>, <span class="fl">13.4544</span>, <span class="fl">18.6144</span>, <span class="fl">28.2144</span>, <span class="fl">13.0944</span>, <span class="fl">12.8544</span>, <span class="fl">46.3344</span>, <span class="fl">27.6144</span>, <span class="fl">64.6944</span>, <span class="fl">3.4944</span>, <span class="fl">25.5744</span>, <span class="fl">40.8144</span>,</span>
<span id="cb81-62"><a href="id_04_model_validation_and_interpretation.html#cb81-62" aria-hidden="true" tabindex="-1"></a> <span class="fl">13.8144</span>, <span class="fl">13.5744</span>, <span class="fl">35.7744</span>, <span class="fl">16.4544</span>, <span class="fl">54.4944</span>, <span class="fl">14.2944</span>, <span class="fl">30.7344</span>, <span class="fl">23.6544</span>, <span class="fl">41.0544</span>, <span class="fl">8.5344</span>, <span class="fl">23.1744</span>, <span class="fl">52.2144</span>,</span>
<span id="cb81-63"><a href="id_04_model_validation_and_interpretation.html#cb81-63" aria-hidden="true" tabindex="-1"></a> <span class="fl">32.5344</span>, <span class="fl">19.4544</span>, <span class="fl">27.2544</span>, <span class="fl">27.1344</span>, <span class="fl">20.5344</span>, <span class="fl">27.3744</span>, <span class="fl">30.6144</span>, <span class="fl">25.6944</span>, <span class="fl">27.1344</span>, <span class="fl">28.3344</span>, <span class="fl">29.4144</span>, <span class="fl">27.3744</span>,</span>
<span id="cb81-64"><a href="id_04_model_validation_and_interpretation.html#cb81-64" aria-hidden="true" tabindex="-1"></a> <span class="fl">30.0144</span>, <span class="fl">19.5744</span>, <span class="fl">31.3344</span>, <span class="fl">31.9344</span>, <span class="fl">25.6944</span>, <span class="fl">26.7744</span>, <span class="fl">36.4944</span>, <span class="fl">25.8144</span>, <span class="fl">35.2944</span>, <span class="fl">7.8144</span>, <span class="fl">45.1344</span>, <span class="fl">21.7344</span>,</span>
<span id="cb81-65"><a href="id_04_model_validation_and_interpretation.html#cb81-65" aria-hidden="true" tabindex="-1"></a> <span class="fl">19.4544</span>, <span class="fl">33.4944</span>, <span class="fl">22.8144</span>, <span class="fl">19.8144</span>, <span class="fl">21.9744</span>, <span class="fl">22.8144</span>, <span class="fl">24.8544</span>, <span class="fl">29.4144</span>, <span class="fl">31.3344</span>, <span class="fl">33.3744</span>, <span class="fl">42.9744</span>, <span class="fl">52.2144</span>,</span>
<span id="cb81-66"><a href="id_04_model_validation_and_interpretation.html#cb81-66" aria-hidden="true" tabindex="-1"></a> <span class="fl">12.4944</span>, <span class="fl">15.3744</span>, <span class="fl">27.3744</span>, <span class="fl">10.4544</span>, <span class="fl">7.9344</span>, <span class="fl">64.3344</span>, <span class="fl">36.0144</span>, <span class="fl">68.7744</span>, <span class="fl">27.6144</span>, <span class="fl">41.0544</span>, <span class="fl">47.5344</span>, <span class="fl">70.2144</span>,</span>
<span id="cb81-67"><a href="id_04_model_validation_and_interpretation.html#cb81-67" aria-hidden="true" tabindex="-1"></a> <span class="fl">20.4144</span>, <span class="fl">10.8144</span>, <span class="fl">28.0944</span>, <span class="fl">20.5344</span>, <span class="fl">29.0544</span>, <span class="fl">37.2144</span>, <span class="fl">27.9744</span>, <span class="fl">14.1744</span>, <span class="fl">37.2144</span>, <span class="fl">29.4144</span>, <span class="fl">23.1744</span>, <span class="fl">25.5744</span></span>
<span id="cb81-68"><a href="id_04_model_validation_and_interpretation.html#cb81-68" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb81-69"><a href="id_04_model_validation_and_interpretation.html#cb81-69" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb81-70"><a href="id_04_model_validation_and_interpretation.html#cb81-70" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-71"><a href="id_04_model_validation_and_interpretation.html#cb81-71" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-72"><a href="id_04_model_validation_and_interpretation.html#cb81-72" aria-hidden="true" tabindex="-1"></a>non_induced_true_ <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb81-73"><a href="id_04_model_validation_and_interpretation.html#cb81-73" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">96</span>) {</span>
<span id="cb81-74"><a href="id_04_model_validation_and_interpretation.html#cb81-74" aria-hidden="true" tabindex="-1"></a> res_ <span class="ot"><-</span> <span class="fu">mean</span>(<span class="fu">c</span>(non_induced_replicate_1[i], non_induced_replicate_2[i], non_induced_replicate_3[i]))</span>
<span id="cb81-75"><a href="id_04_model_validation_and_interpretation.html#cb81-75" aria-hidden="true" tabindex="-1"></a> non_induced_true_ <span class="ot"><-</span> <span class="fu">c</span>(non_induced_true_, res_)</span>
<span id="cb81-76"><a href="id_04_model_validation_and_interpretation.html#cb81-76" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb81-77"><a href="id_04_model_validation_and_interpretation.html#cb81-77" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-78"><a href="id_04_model_validation_and_interpretation.html#cb81-78" aria-hidden="true" tabindex="-1"></a>induced_replicate_1 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb81-79"><a href="id_04_model_validation_and_interpretation.html#cb81-79" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb81-80"><a href="id_04_model_validation_and_interpretation.html#cb81-80" aria-hidden="true" tabindex="-1"></a> <span class="fl">171.4944</span>, <span class="fl">32.1744</span>, <span class="fl">23.6544</span>, <span class="fl">24.7344</span>, <span class="fl">47.1744</span>, <span class="fl">404.5344</span>, <span class="fl">224.2944</span>, <span class="fl">71.8944</span>, <span class="fl">442.4544</span>, <span class="fl">394.5744</span>, <span class="fl">294.8544</span>, <span class="fl">464.8944</span>,</span>
<span id="cb81-81"><a href="id_04_model_validation_and_interpretation.html#cb81-81" aria-hidden="true" tabindex="-1"></a> <span class="fl">39.4944</span>, <span class="fl">24.2544</span>, <span class="fl">59.4144</span>, <span class="fl">55.6944</span>, <span class="fl">31.9344</span>, <span class="fl">182.2944</span>, <span class="fl">195.2544</span>, <span class="fl">434.1744</span>, <span class="fl">486.8544</span>, <span class="fl">406.8144</span>, <span class="fl">25.4544</span>, <span class="fl">524.5344</span>,</span>
<span id="cb81-82"><a href="id_04_model_validation_and_interpretation.html#cb81-82" aria-hidden="true" tabindex="-1"></a> <span class="fl">28.8144</span>, <span class="fl">76.2144</span>, <span class="fl">160.6944</span>, <span class="fl">32.6544</span>, <span class="fl">424.8144</span>, <span class="fl">60.4944</span>, <span class="fl">474.1344</span>, <span class="fl">281.2944</span>, <span class="fl">240.2544</span>, <span class="fl">226.8144</span>, <span class="fl">386.1744</span>, <span class="fl">235.2144</span>,</span>
<span id="cb81-83"><a href="id_04_model_validation_and_interpretation.html#cb81-83" aria-hidden="true" tabindex="-1"></a> <span class="fl">20.7744</span>, <span class="fl">28.9344</span>, <span class="fl">43.6944</span>, <span class="fl">34.2144</span>, <span class="fl">20.6544</span>, <span class="fl">45.9744</span>, <span class="fl">297.0144</span>, <span class="fl">30.9744</span>, <span class="fl">540.3744</span>, <span class="fl">235.4544</span>, <span class="fl">618.3744</span>, <span class="fl">395.7744</span>,</span>
<span id="cb81-84"><a href="id_04_model_validation_and_interpretation.html#cb81-84" aria-hidden="true" tabindex="-1"></a> <span class="fl">24.7344</span>, <span class="fl">13.9344</span>, <span class="fl">30.2544</span>, <span class="fl">23.5344</span>, <span class="fl">14.8944</span>, <span class="fl">17.1744</span>, <span class="fl">40.5744</span>, <span class="fl">132.4944</span>, <span class="fl">410.4144</span>, <span class="fl">53.2944</span>, <span class="fl">352.8144</span>, <span class="fl">427.2144</span>,</span>
<span id="cb81-85"><a href="id_04_model_validation_and_interpretation.html#cb81-85" aria-hidden="true" tabindex="-1"></a> <span class="fl">13.3344</span>, <span class="fl">224.2944</span>, <span class="fl">28.2144</span>, <span class="fl">48.0144</span>, <span class="fl">62.5344</span>, <span class="fl">25.6944</span>, <span class="fl">352.6944</span>, <span class="fl">245.6544</span>, <span class="fl">80.8944</span>, <span class="fl">313.5744</span>, <span class="fl">414.6144</span>, <span class="fl">235.2144</span>,</span>
<span id="cb81-86"><a href="id_04_model_validation_and_interpretation.html#cb81-86" aria-hidden="true" tabindex="-1"></a> <span class="fl">20.8944</span>, <span class="fl">29.8944</span>, <span class="fl">36.9744</span>, <span class="fl">19.6944</span>, <span class="fl">12.7344</span>, <span class="fl">422.1744</span>, <span class="fl">341.8944</span>, <span class="fl">120.2544</span>, <span class="fl">333.6144</span>, <span class="fl">281.2944</span>, <span class="fl">534.7344</span>, <span class="fl">356.2944</span>,</span>
<span id="cb81-87"><a href="id_04_model_validation_and_interpretation.html#cb81-87" aria-hidden="true" tabindex="-1"></a> <span class="fl">15.7344</span>, <span class="fl">66.4944</span>, <span class="fl">33.3744</span>, <span class="fl">21.0144</span>, <span class="fl">73.5744</span>, <span class="fl">17.8944</span>, <span class="fl">108.9744</span>, <span class="fl">116.1744</span>, <span class="fl">618.3744</span>, <span class="fl">538.0944</span>, <span class="fl">554.0544</span>, <span class="fl">502.4544</span></span>
<span id="cb81-88"><a href="id_04_model_validation_and_interpretation.html#cb81-88" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb81-89"><a href="id_04_model_validation_and_interpretation.html#cb81-89" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb81-90"><a href="id_04_model_validation_and_interpretation.html#cb81-90" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-91"><a href="id_04_model_validation_and_interpretation.html#cb81-91" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-92"><a href="id_04_model_validation_and_interpretation.html#cb81-92" aria-hidden="true" tabindex="-1"></a>induced_replicate_2 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb81-93"><a href="id_04_model_validation_and_interpretation.html#cb81-93" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb81-94"><a href="id_04_model_validation_and_interpretation.html#cb81-94" aria-hidden="true" tabindex="-1"></a> <span class="fl">39.1344</span>, <span class="fl">30.1344</span>, <span class="fl">34.5744</span>, <span class="fl">367.2144</span>, <span class="fl">36.7344</span>, <span class="fl">185.4144</span>, <span class="fl">192.9744</span>, <span class="fl">434.2944</span>, <span class="fl">376.2144</span>, <span class="fl">305.4144</span>, <span class="fl">192.9744</span>, <span class="fl">420.6144</span>,</span>
<span id="cb81-95"><a href="id_04_model_validation_and_interpretation.html#cb81-95" aria-hidden="true" tabindex="-1"></a> <span class="fl">41.4144</span>, <span class="fl">19.4544</span>, <span class="fl">101.6544</span>, <span class="fl">370.0944</span>, <span class="fl">43.9344</span>, <span class="fl">231.1344</span>, <span class="fl">110.1744</span>, <span class="fl">476.8944</span>, <span class="fl">395.6544</span>, <span class="fl">315.6144</span>, <span class="fl">75.9744</span>, <span class="fl">435.2544</span>,</span>
<span id="cb81-96"><a href="id_04_model_validation_and_interpretation.html#cb81-96" aria-hidden="true" tabindex="-1"></a> <span class="fl">26.8944</span>, <span class="fl">60.6144</span>, <span class="fl">29.8944</span>, <span class="fl">200.1744</span>, <span class="fl">460.5744</span>, <span class="fl">265.9344</span>, <span class="fl">541.6944</span>, <span class="fl">310.2144</span>, <span class="fl">282.6144</span>, <span class="fl">404.4144</span>, <span class="fl">168.9744</span>, <span class="fl">196.2144</span>,</span>
<span id="cb81-97"><a href="id_04_model_validation_and_interpretation.html#cb81-97" aria-hidden="true" tabindex="-1"></a> <span class="fl">12.6144</span>, <span class="fl">137.7744</span>, <span class="fl">16.0944</span>, <span class="fl">16.2144</span>, <span class="fl">47.8944</span>, <span class="fl">24.7344</span>, <span class="fl">274.4544</span>, <span class="fl">62.0544</span>, <span class="fl">247.9344</span>, <span class="fl">209.2944</span>, <span class="fl">393.4944</span>, <span class="fl">423.3744</span>,</span>
<span id="cb81-98"><a href="id_04_model_validation_and_interpretation.html#cb81-98" aria-hidden="true" tabindex="-1"></a> <span class="fl">22.2144</span>, <span class="fl">21.3744</span>, <span class="fl">11.1744</span>, <span class="fl">9.1344</span>, <span class="fl">128.4144</span>, <span class="fl">19.6944</span>, <span class="fl">58.9344</span>, <span class="fl">233.1744</span>, <span class="fl">437.4144</span>, <span class="fl">58.6944</span>, <span class="fl">361.0944</span>, <span class="fl">458.8944</span>,</span>
<span id="cb81-99"><a href="id_04_model_validation_and_interpretation.html#cb81-99" aria-hidden="true" tabindex="-1"></a> <span class="fl">16.8144</span>, <span class="fl">33.3744</span>, <span class="fl">12.3744</span>, <span class="fl">24.3744</span>, <span class="fl">134.1744</span>, <span class="fl">25.9344</span>, <span class="fl">364.4544</span>, <span class="fl">207.8544</span>, <span class="fl">91.2144</span>, <span class="fl">383.6544</span>, <span class="fl">434.0544</span>, <span class="fl">196.2144</span>,</span>
<span id="cb81-100"><a href="id_04_model_validation_and_interpretation.html#cb81-100" aria-hidden="true" tabindex="-1"></a> <span class="fl">11.8944</span>, <span class="fl">21.7344</span>, <span class="fl">17.4144</span>, <span class="fl">16.8144</span>, <span class="fl">19.9344</span>, <span class="fl">525.4944</span>, <span class="fl">422.4144</span>, <span class="fl">519.9744</span>, <span class="fl">379.5744</span>, <span class="fl">282.6144</span>, <span class="fl">616.9344</span>, <span class="fl">450.0144</span>,</span>
<span id="cb81-101"><a href="id_04_model_validation_and_interpretation.html#cb81-101" aria-hidden="true" tabindex="-1"></a> <span class="fl">19.2144</span>, <span class="fl">42.7344</span>, <span class="fl">19.4544</span>, <span class="fl">25.9344</span>, <span class="fl">54.7344</span>, <span class="fl">42.9744</span>, <span class="fl">73.2144</span>, <span class="fl">135.4944</span>, <span class="fl">524.0544</span>, <span class="fl">471.7344</span>, <span class="fl">528.4944</span>, <span class="fl">511.0944</span></span>
<span id="cb81-102"><a href="id_04_model_validation_and_interpretation.html#cb81-102" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb81-103"><a href="id_04_model_validation_and_interpretation.html#cb81-103" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb81-104"><a href="id_04_model_validation_and_interpretation.html#cb81-104" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-105"><a href="id_04_model_validation_and_interpretation.html#cb81-105" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-106"><a href="id_04_model_validation_and_interpretation.html#cb81-106" aria-hidden="true" tabindex="-1"></a>induced_replicate_3 <span class="ot"><-</span> <span class="fu">matrix</span>(</span>
<span id="cb81-107"><a href="id_04_model_validation_and_interpretation.html#cb81-107" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(</span>
<span id="cb81-108"><a href="id_04_model_validation_and_interpretation.html#cb81-108" aria-hidden="true" tabindex="-1"></a> <span class="fl">30.3744</span>, <span class="fl">20.2944</span>, <span class="fl">233.8944</span>, <span class="fl">83.8944</span>, <span class="fl">24.2544</span>, <span class="fl">25.3344</span>, <span class="fl">136.2144</span>, <span class="fl">374.8944</span>, <span class="fl">334.5744</span>, <span class="fl">399.6144</span>, <span class="fl">383.6544</span>, <span class="fl">544.6944</span>,</span>
<span id="cb81-109"><a href="id_04_model_validation_and_interpretation.html#cb81-109" aria-hidden="true" tabindex="-1"></a> <span class="fl">18.9744</span>, <span class="fl">21.1344</span>, <span class="fl">20.0544</span>, <span class="fl">401.7744</span>, <span class="fl">22.6944</span>, <span class="fl">62.7744</span>, <span class="fl">51.4944</span>, <span class="fl">430.6944</span>, <span class="fl">303.7344</span>, <span class="fl">466.6944</span>, <span class="fl">329.6544</span>, <span class="fl">567.7344</span>,</span>
<span id="cb81-110"><a href="id_04_model_validation_and_interpretation.html#cb81-110" aria-hidden="true" tabindex="-1"></a> <span class="fl">21.8544</span>, <span class="fl">75.3744</span>, <span class="fl">51.9744</span>, <span class="fl">150.3744</span>, <span class="fl">411.4944</span>, <span class="fl">122.0544</span>, <span class="fl">458.2944</span>, <span class="fl">127.8144</span>, <span class="fl">38.4144</span>, <span class="fl">269.8944</span>, <span class="fl">51.9744</span>, <span class="fl">366.9744</span>,</span>
<span id="cb81-111"><a href="id_04_model_validation_and_interpretation.html#cb81-111" aria-hidden="true" tabindex="-1"></a> <span class="fl">12.1344</span>, <span class="fl">6.6144</span>, <span class="fl">8.8944</span>, <span class="fl">16.8144</span>, <span class="fl">13.3344</span>, <span class="fl">24.4944</span>, <span class="fl">276.9744</span>, <span class="fl">77.4144</span>, <span class="fl">163.6944</span>, <span class="fl">297.8544</span>, <span class="fl">423.9744</span>, <span class="fl">492.8544</span>,</span>
<span id="cb81-112"><a href="id_04_model_validation_and_interpretation.html#cb81-112" aria-hidden="true" tabindex="-1"></a> <span class="fl">13.9344</span>, <span class="fl">1.9344</span>, <span class="fl">10.4544</span>, <span class="fl">10.5744</span>, <span class="fl">19.0944</span>, <span class="fl">17.6544</span>, <span class="fl">33.0144</span>, <span class="fl">86.7744</span>, <span class="fl">43.2144</span>, <span class="fl">316.0944</span>, <span class="fl">382.8144</span>, <span class="fl">351.9744</span>,</span>
<span id="cb81-113"><a href="id_04_model_validation_and_interpretation.html#cb81-113" aria-hidden="true" tabindex="-1"></a> <span class="fl">1.4544</span>, <span class="fl">136.2144</span>, <span class="fl">9.9744</span>, <span class="fl">13.4544</span>, <span class="fl">101.5344</span>, <span class="fl">18.1344</span>, <span class="fl">403.9344</span>, <span class="fl">183.0144</span>, <span class="fl">389.7744</span>, <span class="fl">70.4544</span>, <span class="fl">444.1344</span>, <span class="fl">149.2944</span>,</span>
<span id="cb81-114"><a href="id_04_model_validation_and_interpretation.html#cb81-114" aria-hidden="true" tabindex="-1"></a> <span class="fl">7.5744</span>, <span class="fl">15.3744</span>, <span class="fl">141.7344</span>, <span class="fl">15.0144</span>, <span class="fl">12.1344</span>, <span class="fl">423.4944</span>, <span class="fl">422.7744</span>, <span class="fl">94.8144</span>, <span class="fl">269.8944</span>, <span class="fl">289.2144</span>, <span class="fl">473.7744</span>, <span class="fl">364.5744</span>,</span>
<span id="cb81-115"><a href="id_04_model_validation_and_interpretation.html#cb81-115" aria-hidden="true" tabindex="-1"></a> <span class="fl">0.8544</span>, <span class="fl">25.5744</span>, <span class="fl">14.4144</span>, <span class="fl">8.4144</span>, <span class="fl">37.3344</span>, <span class="fl">37.2144</span>, <span class="fl">250.5744</span>, <span class="fl">159.3744</span>, <span class="fl">608.5344</span>, <span class="fl">466.2144</span>, <span class="fl">524.4144</span>, <span class="fl">510.4944</span></span>
<span id="cb81-116"><a href="id_04_model_validation_and_interpretation.html#cb81-116" aria-hidden="true" tabindex="-1"></a> ),</span>
<span id="cb81-117"><a href="id_04_model_validation_and_interpretation.html#cb81-117" aria-hidden="true" tabindex="-1"></a> <span class="at">nrow =</span> <span class="dv">8</span>, <span class="at">byrow =</span> <span class="cn">TRUE</span></span>
<span id="cb81-118"><a href="id_04_model_validation_and_interpretation.html#cb81-118" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-119"><a href="id_04_model_validation_and_interpretation.html#cb81-119" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-120"><a href="id_04_model_validation_and_interpretation.html#cb81-120" aria-hidden="true" tabindex="-1"></a>induced_true_ <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb81-121"><a href="id_04_model_validation_and_interpretation.html#cb81-121" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">96</span>) {</span>
<span id="cb81-122"><a href="id_04_model_validation_and_interpretation.html#cb81-122" aria-hidden="true" tabindex="-1"></a> res_ <span class="ot"><-</span> <span class="fu">mean</span>(<span class="fu">c</span>(induced_replicate_1[i], induced_replicate_2[i], induced_replicate_3[i]))</span>
<span id="cb81-123"><a href="id_04_model_validation_and_interpretation.html#cb81-123" aria-hidden="true" tabindex="-1"></a> induced_true_ <span class="ot"><-</span> <span class="fu">c</span>(induced_true_, res_)</span>
<span id="cb81-124"><a href="id_04_model_validation_and_interpretation.html#cb81-124" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb81-125"><a href="id_04_model_validation_and_interpretation.html#cb81-125" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-126"><a href="id_04_model_validation_and_interpretation.html#cb81-126" aria-hidden="true" tabindex="-1"></a>new_non_induced_replicate_1 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb81-127"><a href="id_04_model_validation_and_interpretation.html#cb81-127" aria-hidden="true" tabindex="-1"></a> <span class="fl">94.6865</span>, <span class="fl">84.2145</span>, <span class="fl">58.6890</span>, <span class="fl">69.1610</span>, <span class="fl">35.1270</span>, <span class="fl">12.4261</span>, <span class="fl">19.8169</span>, <span class="fl">12.4261</span>, <span class="fl">12.4368</span>, <span class="fl">19.8169</span>,</span>
<span id="cb81-128"><a href="id_04_model_validation_and_interpretation.html#cb81-128" aria-hidden="true" tabindex="-1"></a> <span class="fl">12.4261</span>, <span class="fl">19.8169</span>, <span class="fl">12.4368</span>, <span class="fl">10.1149</span>, <span class="fl">8.6644</span>, <span class="fl">38.8384</span>, <span class="fl">12.0117</span>, <span class="fl">23.1802</span>, <span class="fl">9.9236</span>, <span class="fl">10.7153</span>,</span>
<span id="cb81-129"><a href="id_04_model_validation_and_interpretation.html#cb81-129" aria-hidden="true" tabindex="-1"></a> <span class="fl">55.7665</span>, <span class="fl">14.1476</span>, <span class="fl">24.8167</span>, <span class="fl">11.4644</span>, <span class="fl">21.2568</span>, <span class="fl">41.3144</span>, <span class="fl">11.8948</span>, <span class="fl">17.2878</span>, <span class="fl">21.1505</span>, <span class="fl">12.9894</span>,</span>
<span id="cb81-130"><a href="id_04_model_validation_and_interpretation.html#cb81-130" aria-hidden="true" tabindex="-1"></a> <span class="fl">20.8902</span></span>
<span id="cb81-131"><a href="id_04_model_validation_and_interpretation.html#cb81-131" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-132"><a href="id_04_model_validation_and_interpretation.html#cb81-132" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-133"><a href="id_04_model_validation_and_interpretation.html#cb81-133" aria-hidden="true" tabindex="-1"></a>new_non_induced_replicate_2 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb81-134"><a href="id_04_model_validation_and_interpretation.html#cb81-134" aria-hidden="true" tabindex="-1"></a> <span class="fl">88.1415</span>, <span class="fl">77.0150</span>, <span class="fl">52.1440</span>, <span class="fl">43.6355</span>, <span class="fl">35.1270</span>, <span class="fl">11.6132</span>, <span class="fl">28.8335</span>, <span class="fl">11.6132</span>, <span class="fl">13.2019</span>, <span class="fl">28.8335</span>,</span>
<span id="cb81-135"><a href="id_04_model_validation_and_interpretation.html#cb81-135" aria-hidden="true" tabindex="-1"></a> <span class="fl">11.6132</span>, <span class="fl">28.8335</span>, <span class="fl">13.2019</span>, <span class="fl">11.6717</span>, <span class="fl">10.0671</span>, <span class="fl">30.3106</span>, <span class="fl">13.4888</span>, <span class="fl">34.5612</span>, <span class="fl">12.9309</span>, <span class="fl">12.6759</span>,</span>
<span id="cb81-136"><a href="id_04_model_validation_and_interpretation.html#cb81-136" aria-hidden="true" tabindex="-1"></a> <span class="fl">42.8393</span>, <span class="fl">17.0753</span>, <span class="fl">38.7481</span>, <span class="fl">11.7673</span>, <span class="fl">24.1153</span>, <span class="fl">35.5229</span>, <span class="fl">13.7651</span>, <span class="fl">22.8933</span>, <span class="fl">25.4702</span>, <span class="fl">14.9234</span>,</span>
<span id="cb81-137"><a href="id_04_model_validation_and_interpretation.html#cb81-137" aria-hidden="true" tabindex="-1"></a> <span class="fl">29.0832</span></span>
<span id="cb81-138"><a href="id_04_model_validation_and_interpretation.html#cb81-138" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-139"><a href="id_04_model_validation_and_interpretation.html#cb81-139" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-140"><a href="id_04_model_validation_and_interpretation.html#cb81-140" aria-hidden="true" tabindex="-1"></a>new_non_induced_replicate_3 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb81-141"><a href="id_04_model_validation_and_interpretation.html#cb81-141" aria-hidden="true" tabindex="-1"></a> <span class="fl">64.5795</span>, <span class="fl">63.2705</span>, <span class="fl">48.2170</span>, <span class="fl">52.1440</span>, <span class="fl">27.9275</span>, <span class="fl">15.0881</span>, <span class="fl">40.0817</span>, <span class="fl">15.0881</span>, <span class="fl">13.9936</span>, <span class="fl">40.0817</span>,</span>
<span id="cb81-142"><a href="id_04_model_validation_and_interpretation.html#cb81-142" aria-hidden="true" tabindex="-1"></a> <span class="fl">15.0881</span>, <span class="fl">40.0817</span>, <span class="fl">13.9936</span>, <span class="fl">8.5847</span>, <span class="fl">13.4835</span>, <span class="fl">64.9266</span>, <span class="fl">13.2444</span>, <span class="fl">56.1065</span>, <span class="fl">10.6090</span>, <span class="fl">13.8660</span>,</span>
<span id="cb81-143"><a href="id_04_model_validation_and_interpretation.html#cb81-143" aria-hidden="true" tabindex="-1"></a> <span class="fl">69.1400</span>, <span class="fl">21.0974</span>, <span class="fl">67.0891</span>, <span class="fl">10.8056</span>, <span class="fl">25.8900</span>, <span class="fl">55.3361</span>, <span class="fl">16.4695</span>, <span class="fl">24.6201</span>, <span class="fl">42.7755</span>, <span class="fl">14.1317</span>,</span>
<span id="cb81-144"><a href="id_04_model_validation_and_interpretation.html#cb81-144" aria-hidden="true" tabindex="-1"></a> <span class="fl">49.6828</span></span>
<span id="cb81-145"><a href="id_04_model_validation_and_interpretation.html#cb81-145" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-146"><a href="id_04_model_validation_and_interpretation.html#cb81-146" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-147"><a href="id_04_model_validation_and_interpretation.html#cb81-147" aria-hidden="true" tabindex="-1"></a>new_non_induced_true_ <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb81-148"><a href="id_04_model_validation_and_interpretation.html#cb81-148" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">31</span>) {</span>
<span id="cb81-149"><a href="id_04_model_validation_and_interpretation.html#cb81-149" aria-hidden="true" tabindex="-1"></a> res_ <span class="ot"><-</span> <span class="fu">mean</span>(<span class="fu">c</span>(new_non_induced_replicate_1[i], new_non_induced_replicate_2[i], new_non_induced_replicate_3[i]))</span>
<span id="cb81-150"><a href="id_04_model_validation_and_interpretation.html#cb81-150" aria-hidden="true" tabindex="-1"></a> new_non_induced_true_ <span class="ot"><-</span> <span class="fu">c</span>(new_non_induced_true_, res_)</span>
<span id="cb81-151"><a href="id_04_model_validation_and_interpretation.html#cb81-151" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb81-152"><a href="id_04_model_validation_and_interpretation.html#cb81-152" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-153"><a href="id_04_model_validation_and_interpretation.html#cb81-153" aria-hidden="true" tabindex="-1"></a>new_induced_replicate_1 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb81-154"><a href="id_04_model_validation_and_interpretation.html#cb81-154" aria-hidden="true" tabindex="-1"></a> <span class="fl">775.3412</span>, <span class="fl">608.3964</span>, <span class="fl">376.3855</span>, <span class="fl">403.2684</span>, <span class="fl">450.2610</span>, <span class="fl">104.3842</span>, <span class="fl">610.9376</span>, <span class="fl">104.3842</span>, <span class="fl">206.0770</span>, <span class="fl">610.9376</span>,</span>
<span id="cb81-155"><a href="id_04_model_validation_and_interpretation.html#cb81-155" aria-hidden="true" tabindex="-1"></a> <span class="fl">104.3842</span>, <span class="fl">610.9376</span>, <span class="fl">206.0770</span>, <span class="fl">61.42746</span>, <span class="fl">63.9640</span>, <span class="fl">725.5767</span>, <span class="fl">182.7868</span>, <span class="fl">436.4094</span>, <span class="fl">89.5931</span>, <span class="fl">105.8666</span>,</span>
<span id="cb81-156"><a href="id_04_model_validation_and_interpretation.html#cb81-156" aria-hidden="true" tabindex="-1"></a> <span class="fl">643.6163</span>, <span class="fl">295.6471</span>, <span class="fl">536.2245</span>, <span class="fl">141.8066</span>, <span class="fl">415.8205</span>, <span class="fl">549.5332</span>, <span class="fl">258.9823</span>, <span class="fl">532.0408</span>, <span class="fl">386.370</span>, <span class="fl">313.6335</span>,</span>
<span id="cb81-157"><a href="id_04_model_validation_and_interpretation.html#cb81-157" aria-hidden="true" tabindex="-1"></a> <span class="fl">596.1610</span></span>
<span id="cb81-158"><a href="id_04_model_validation_and_interpretation.html#cb81-158" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-159"><a href="id_04_model_validation_and_interpretation.html#cb81-159" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-160"><a href="id_04_model_validation_and_interpretation.html#cb81-160" aria-hidden="true" tabindex="-1"></a>new_induced_replicate_2 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb81-161"><a href="id_04_model_validation_and_interpretation.html#cb81-161" aria-hidden="true" tabindex="-1"></a> <span class="fl">720.8794</span>, <span class="fl">670.3267</span>, <span class="fl">402.6897</span>, <span class="fl">361.0000</span>, <span class="fl">423.5832</span>, <span class="fl">95.4568</span>, <span class="fl">353.5596</span>, <span class="fl">95.4568</span>, <span class="fl">173.0359</span>, <span class="fl">353.5596</span>,</span>
<span id="cb81-162"><a href="id_04_model_validation_and_interpretation.html#cb81-162" aria-hidden="true" tabindex="-1"></a> <span class="fl">95.4568</span>, <span class="fl">353.5596</span>, <span class="fl">173.0359</span>, <span class="fl">70.6842</span>, <span class="fl">58.2979</span>, <span class="fl">560.2724</span>, <span class="fl">235.8898</span>, <span class="fl">367.2965</span>, <span class="fl">83.7953</span>, <span class="fl">102.8688</span>,</span>
<span id="cb81-163"><a href="id_04_model_validation_and_interpretation.html#cb81-163" aria-hidden="true" tabindex="-1"></a> <span class="fl">552.6956</span>, <span class="fl">249.6267</span>, <span class="fl">461.8738</span>, <span class="fl">114.8928</span>, <span class="fl">335.8037</span>, <span class="fl">455.3512</span>, <span class="fl">205.2205</span>, <span class="fl">327.7658</span>, <span class="fl">417.4017</span>, <span class="fl">186.3116</span>,</span>
<span id="cb81-164"><a href="id_04_model_validation_and_interpretation.html#cb81-164" aria-hidden="true" tabindex="-1"></a> <span class="fl">851.0120</span></span>
<span id="cb81-165"><a href="id_04_model_validation_and_interpretation.html#cb81-165" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-166"><a href="id_04_model_validation_and_interpretation.html#cb81-166" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-167"><a href="id_04_model_validation_and_interpretation.html#cb81-167" aria-hidden="true" tabindex="-1"></a>new_induced_replicate_3 <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb81-168"><a href="id_04_model_validation_and_interpretation.html#cb81-168" aria-hidden="true" tabindex="-1"></a> <span class="fl">783.3711</span>, <span class="fl">690.3612</span>, <span class="fl">393.6819</span>, <span class="fl">493.6712</span>, <span class="fl">480.9125</span>, <span class="fl">86.2659</span>, <span class="fl">417.0393</span>, <span class="fl">86.2659</span>, <span class="fl">159.3978</span>, <span class="fl">417.0393</span>,</span>
<span id="cb81-169"><a href="id_04_model_validation_and_interpretation.html#cb81-169" aria-hidden="true" tabindex="-1"></a> <span class="fl">86.2659</span>, <span class="fl">417.0393</span>, <span class="fl">159.3978</span>, <span class="fl">60.1427</span>, <span class="fl">53.6201</span>, <span class="fl">512.8355</span>, <span class="fl">120.0977</span>, <span class="fl">394.4739</span>, <span class="fl">100.9911</span>, <span class="fl">112.4550</span>,</span>
<span id="cb81-170"><a href="id_04_model_validation_and_interpretation.html#cb81-170" aria-hidden="true" tabindex="-1"></a> <span class="fl">577.1388</span>, <span class="fl">243.4006</span>, <span class="fl">552.0697</span>, <span class="fl">118.0552</span>, <span class="fl">376.5862</span>, <span class="fl">513.8896</span>, <span class="fl">224.0635</span>, <span class="fl">387.4242</span>, <span class="fl">380.8028</span>, <span class="fl">221.7246</span>,</span>
<span id="cb81-171"><a href="id_04_model_validation_and_interpretation.html#cb81-171" aria-hidden="true" tabindex="-1"></a> <span class="fl">766.4130</span></span>
<span id="cb81-172"><a href="id_04_model_validation_and_interpretation.html#cb81-172" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb81-173"><a href="id_04_model_validation_and_interpretation.html#cb81-173" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-174"><a href="id_04_model_validation_and_interpretation.html#cb81-174" aria-hidden="true" tabindex="-1"></a>new_induced_true_ <span class="ot"><-</span> <span class="fu">c</span>()</span>
<span id="cb81-175"><a href="id_04_model_validation_and_interpretation.html#cb81-175" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">31</span>) {</span>
<span id="cb81-176"><a href="id_04_model_validation_and_interpretation.html#cb81-176" aria-hidden="true" tabindex="-1"></a> res_ <span class="ot"><-</span> <span class="fu">mean</span>(<span class="fu">c</span>(new_induced_replicate_1[i], new_induced_replicate_2[i], new_induced_replicate_3[i]))</span>
<span id="cb81-177"><a href="id_04_model_validation_and_interpretation.html#cb81-177" aria-hidden="true" tabindex="-1"></a> new_induced_true_ <span class="ot"><-</span> <span class="fu">c</span>(new_induced_true_, res_)</span>
<span id="cb81-178"><a href="id_04_model_validation_and_interpretation.html#cb81-178" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb81-179"><a href="id_04_model_validation_and_interpretation.html#cb81-179" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb81-180"><a href="id_04_model_validation_and_interpretation.html#cb81-180" aria-hidden="true" tabindex="-1"></a>cpp_true_non_induced <span class="ot"><-</span> <span class="fu">c</span>(non_induced_true_, new_non_induced_true_)</span>
<span id="cb81-181"><a href="id_04_model_validation_and_interpretation.html#cb81-181" aria-hidden="true" tabindex="-1"></a>cpp_true_induced <span class="ot"><-</span> <span class="fu">c</span>(induced_true_, new_induced_true_)</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_validation_and_interpretation.html#cb82-1" aria-hidden="true" tabindex="-1"></a>mb_cp_df <span class="ot"><-</span> <span class="fu">data.frame</span>(</span>
<span id="cb82-2"><a href="id_04_model_validation_and_interpretation.html#cb82-2" aria-hidden="true" tabindex="-1"></a> <span class="at">mb_true =</span> <span class="fu">rep</span>(mb_true, <span class="dv">2</span>),</span>
<span id="cb82-3"><a href="id_04_model_validation_and_interpretation.html#cb82-3" aria-hidden="true" tabindex="-1"></a> <span class="at">cpp_true =</span> <span class="fu">c</span>(cpp_true_non_induced, cpp_true_induced),</span>
<span id="cb82-4"><a href="id_04_model_validation_and_interpretation.html#cb82-4" aria-hidden="true" tabindex="-1"></a> <span class="at">mb_pred =</span> <span class="fu">rep</span>(mb_pred, <span class="dv">2</span>),</span>
<span id="cb82-5"><a href="id_04_model_validation_and_interpretation.html#cb82-5" aria-hidden="true" tabindex="-1"></a> <span class="at">cpp_pred =</span> <span class="fu">factor</span>(<span class="fu">rep</span>(cpp_pred, <span class="dv">2</span>), <span class="at">levels =</span> <span class="fu">c</span>(<span class="st">"Non-CPP"</span>, <span class="st">"CPP"</span>)),</span>
<span id="cb82-6"><a href="id_04_model_validation_and_interpretation.html#cb82-6" aria-hidden="true" tabindex="-1"></a> <span class="at">cell_group =</span> <span class="fu">as.factor</span>(<span class="fu">c</span>(</span>
<span id="cb82-7"><a href="id_04_model_validation_and_interpretation.html#cb82-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">rep</span>(<span class="st">"Non-induced"</span>, <span class="fu">length</span>(cpp_true_non_induced)),</span>
<span id="cb82-8"><a href="id_04_model_validation_and_interpretation.html#cb82-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">rep</span>(<span class="st">"Induced"</span>, <span class="fu">length</span>(cpp_true_induced))</span>
<span id="cb82-9"><a href="id_04_model_validation_and_interpretation.html#cb82-9" aria-hidden="true" tabindex="-1"></a> ))</span>
<span id="cb82-10"><a href="id_04_model_validation_and_interpretation.html#cb82-10" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="melanin-induced-cells" class="section level3 hasAnchor" number="4.1.3">
<h3><span class="header-section-number">4.1.3</span> Melanin-induced cells<a href="id_04_model_validation_and_interpretation.html#melanin-induced-cells" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div class="sourceCode" id="cb83"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb83-1"><a href="id_04_model_validation_and_interpretation.html#cb83-1" aria-hidden="true" tabindex="-1"></a>mb_cp_df<span class="sc">$</span>log_cpp_true <span class="ot"><-</span> <span class="fu">log10</span>(mb_cp_df<span class="sc">$</span>cpp_true)</span>
<span id="cb83-2"><a href="id_04_model_validation_and_interpretation.html#cb83-2" aria-hidden="true" tabindex="-1"></a>p2_1 <span class="ot"><-</span> <span class="fu">ggscatter</span>(mb_cp_df[mb_cp_df<span class="sc">$</span>cell_group <span class="sc">==</span> <span class="st">"Induced"</span>, ],</span>
<span id="cb83-3"><a href="id_04_model_validation_and_interpretation.html#cb83-3" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"mb_true"</span>, <span class="at">y =</span> <span class="st">"log_cpp_true"</span>,</span>
<span id="cb83-4"><a href="id_04_model_validation_and_interpretation.html#cb83-4" aria-hidden="true" tabindex="-1"></a> <span class="at">alpha =</span> <span class="fl">0.7</span>, <span class="at">size =</span> <span class="dv">3</span>, <span class="at">stroke =</span> <span class="fl">0.3</span>, <span class="at">color =</span> <span class="st">"black"</span>, <span class="at">fill =</span> <span class="st">"cpp_pred"</span>, <span class="at">shape =</span> <span class="st">"cpp_pred"</span>,</span>
<span id="cb83-5"><a href="id_04_model_validation_and_interpretation.html#cb83-5" aria-hidden="true" tabindex="-1"></a> <span class="at">add =</span> <span class="st">"reg.line"</span>, <span class="at">conf.int =</span> <span class="cn">TRUE</span>, <span class="at">conf.int.level =</span> <span class="fl">0.95</span>, <span class="at">cor.coef =</span> <span class="cn">TRUE</span>,</span>
<span id="cb83-6"><a href="id_04_model_validation_and_interpretation.html#cb83-6" aria-hidden="true" tabindex="-1"></a> <span class="at">add.params =</span> <span class="fu">list</span>(<span class="at">color =</span> <span class="st">"grey25"</span>),</span>
<span id="cb83-7"><a href="id_04_model_validation_and_interpretation.html#cb83-7" aria-hidden="true" tabindex="-1"></a> <span class="at">cor.coeff.args =</span> <span class="fu">list</span>(</span>
<span id="cb83-8"><a href="id_04_model_validation_and_interpretation.html#cb83-8" aria-hidden="true" tabindex="-1"></a> <span class="at">method =</span> <span class="st">"pearson"</span>, <span class="at">label.x =</span> <span class="fl">2.2</span>, <span class="at">label.y =</span> <span class="fl">2.85</span>, <span class="at">label.sep =</span> <span class="st">"</span><span class="sc">\n</span><span class="st">"</span>,</span>
<span id="cb83-9"><a href="id_04_model_validation_and_interpretation.html#cb83-9" aria-hidden="true" tabindex="-1"></a> <span class="at">size =</span> <span class="dv">5</span></span>
<span id="cb83-10"><a href="id_04_model_validation_and_interpretation.html#cb83-10" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb83-11"><a href="id_04_model_validation_and_interpretation.html#cb83-11" aria-hidden="true" tabindex="-1"></a>) <span class="sc">+</span></span>
<span id="cb83-12"><a href="id_04_model_validation_and_interpretation.html#cb83-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">facet_grid</span>(. <span class="sc">~</span> cpp_pred) <span class="sc">+</span></span>
<span id="cb83-13"><a href="id_04_model_validation_and_interpretation.html#cb83-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#1f77b4"</span>, <span class="st">"#d62728"</span>)) <span class="sc">+</span></span>
<span id="cb83-14"><a href="id_04_model_validation_and_interpretation.html#cb83-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_shape_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="dv">24</span>, <span class="dv">21</span>)) <span class="sc">+</span></span>
<span id="cb83-15"><a href="id_04_model_validation_and_interpretation.html#cb83-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(</span>
<span id="cb83-16"><a href="id_04_model_validation_and_interpretation.html#cb83-16" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> <span class="fu">c</span>(<span class="fl">0.63</span>, <span class="dv">3</span>),</span>
<span id="cb83-17"><a href="id_04_model_validation_and_interpretation.html#cb83-17" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, <span class="fu">log10</span>(<span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>) <span class="sc">/</span> <span class="dv">2</span>)),</span>
<span id="cb83-18"><a href="id_04_model_validation_and_interpretation.html#cb83-18" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">sapply</span>(</span>
<span id="cb83-19"><a href="id_04_model_validation_and_interpretation.html#cb83-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>), <span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>) <span class="sc">/</span> <span class="dv">2</span>),</span>
<span id="cb83-20"><a href="id_04_model_validation_and_interpretation.html#cb83-20" aria-hidden="true" tabindex="-1"></a> <span class="cf">function</span>(x) <span class="fu">format</span>(x, <span class="at">big.mark =</span> <span class="st">","</span>, <span class="at">scientific =</span> <span class="cn">FALSE</span>)</span>
<span id="cb83-21"><a href="id_04_model_validation_and_interpretation.html#cb83-21" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb83-22"><a href="id_04_model_validation_and_interpretation.html#cb83-22" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb83-23"><a href="id_04_model_validation_and_interpretation.html#cb83-23" aria-hidden="true" tabindex="-1"></a> <span class="fu">annotation_logticks</span>(<span class="at">sides =</span> <span class="st">"l"</span>) <span class="sc">+</span></span>
<span id="cb83-24"><a href="id_04_model_validation_and_interpretation.html#cb83-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="st">"none"</span>, <span class="at">shape =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb83-25"><a href="id_04_model_validation_and_interpretation.html#cb83-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb83-26"><a href="id_04_model_validation_and_interpretation.html#cb83-26" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb83-27"><a href="id_04_model_validation_and_interpretation.html#cb83-27" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb83-28"><a href="id_04_model_validation_and_interpretation.html#cb83-28" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb83-29"><a href="id_04_model_validation_and_interpretation.html#cb83-29" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">17</span>),</span>
<span id="cb83-30"><a href="id_04_model_validation_and_interpretation.html#cb83-30" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.y =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">17</span>),</span>
<span id="cb83-31"><a href="id_04_model_validation_and_interpretation.html#cb83-31" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">20</span>),</span>
<span id="cb83-32"><a href="id_04_model_validation_and_interpretation.html#cb83-32" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.border =</span> <span class="fu">element_rect</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb83-33"><a href="id_04_model_validation_and_interpretation.html#cb83-33" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb83-34"><a href="id_04_model_validation_and_interpretation.html#cb83-34" 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 class="at">size =</span> <span class="dv">22</span>)</span>
<span id="cb83-35"><a href="id_04_model_validation_and_interpretation.html#cb83-35" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb83-36"><a href="id_04_model_validation_and_interpretation.html#cb83-36" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">"Peptide bound to mNPs (%)"</span>) <span class="sc">+</span></span>
<span id="cb83-37"><a href="id_04_model_validation_and_interpretation.html#cb83-37" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"Peptide (pMol / 100K cells)"</span>)</span>
<span id="cb83-38"><a href="id_04_model_validation_and_interpretation.html#cb83-38" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb83-39"><a href="id_04_model_validation_and_interpretation.html#cb83-39" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">1</span>)</span>
<span id="cb83-40"><a href="id_04_model_validation_and_interpretation.html#cb83-40" aria-hidden="true" tabindex="-1"></a>pos <span class="ot"><-</span> <span class="fu">position_jitter</span>(<span class="at">width =</span> <span class="fl">0.1</span>, <span class="at">seed =</span> <span class="dv">16</span>)</span>
<span id="cb83-41"><a href="id_04_model_validation_and_interpretation.html#cb83-41" aria-hidden="true" tabindex="-1"></a>p2_2 <span class="ot"><-</span> <span class="fu">ggplot</span>(mb_cp_df[mb_cp_df<span class="sc">$</span>cell_group <span class="sc">==</span> <span class="st">"Induced"</span>, ], <span class="fu">aes</span>(<span class="at">x =</span> cpp_pred, <span class="at">y =</span> log_cpp_true)) <span class="sc">+</span></span>
<span id="cb83-42"><a href="id_04_model_validation_and_interpretation.html#cb83-42" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="fu">aes</span>(<span class="at">color =</span> cpp_pred), <span class="at">outlier.color =</span> <span class="cn">NA</span>, <span class="at">lwd =</span> <span class="fl">1.5</span>, <span class="at">show.legend =</span> <span class="cn">FALSE</span>) <span class="sc">+</span></span>
<span id="cb83-43"><a href="id_04_model_validation_and_interpretation.html#cb83-43" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_beeswarm</span>(<span class="fu">aes</span>(<span class="at">fill =</span> cpp_pred, <span class="at">shape =</span> cpp_pred),</span>
<span id="cb83-44"><a href="id_04_model_validation_and_interpretation.html#cb83-44" aria-hidden="true" tabindex="-1"></a> <span class="at">color =</span> <span class="st">"black"</span>, <span class="at">alpha =</span> <span class="fl">0.7</span>, <span class="at">size =</span> <span class="dv">3</span>,</span>
<span id="cb83-45"><a href="id_04_model_validation_and_interpretation.html#cb83-45" aria-hidden="true" tabindex="-1"></a> <span class="at">stroke =</span> <span class="fl">0.3</span>, <span class="at">cex =</span> <span class="dv">2</span>, <span class="at">priority =</span> <span class="st">"random"</span></span>
<span id="cb83-46"><a href="id_04_model_validation_and_interpretation.html#cb83-46" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb83-47"><a href="id_04_model_validation_and_interpretation.html#cb83-47" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_compare_means</span>(</span>
<span id="cb83-48"><a href="id_04_model_validation_and_interpretation.html#cb83-48" aria-hidden="true" tabindex="-1"></a> <span class="at">label =</span> <span class="st">"p.signif"</span>, <span class="at">size =</span> <span class="dv">5</span>, <span class="at">method =</span> <span class="st">"wilcox.test"</span>, <span class="at">label.x.npc =</span> <span class="fl">0.2</span>,</span>
<span id="cb83-49"><a href="id_04_model_validation_and_interpretation.html#cb83-49" aria-hidden="true" tabindex="-1"></a> <span class="at">label.y =</span> <span class="fl">2.92</span>, <span class="at">hide.ns =</span> <span class="cn">TRUE</span></span>
<span id="cb83-50"><a href="id_04_model_validation_and_interpretation.html#cb83-50" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb83-51"><a href="id_04_model_validation_and_interpretation.html#cb83-51" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_compare_means</span>(</span>
<span id="cb83-52"><a href="id_04_model_validation_and_interpretation.html#cb83-52" aria-hidden="true" tabindex="-1"></a> <span class="at">label =</span> <span class="st">"p.format"</span>, <span class="at">size =</span> <span class="dv">5</span>, <span class="at">method =</span> <span class="st">"wilcox.test"</span>, <span class="at">label.x.npc =</span> <span class="fl">0.2</span>,</span>
<span id="cb83-53"><a href="id_04_model_validation_and_interpretation.html#cb83-53" aria-hidden="true" tabindex="-1"></a> <span class="at">label.y =</span> <span class="fl">2.82</span>, <span class="at">hide.ns =</span> <span class="cn">TRUE</span></span>
<span id="cb83-54"><a href="id_04_model_validation_and_interpretation.html#cb83-54" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb83-55"><a href="id_04_model_validation_and_interpretation.html#cb83-55" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#cae6fa"</span>, <span class="st">"#f5b8b8"</span>)) <span class="sc">+</span></span>
<span id="cb83-56"><a href="id_04_model_validation_and_interpretation.html#cb83-56" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#1f77b4"</span>, <span class="st">"#d62728"</span>)) <span class="sc">+</span></span>
<span id="cb83-57"><a href="id_04_model_validation_and_interpretation.html#cb83-57" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_shape_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="dv">24</span>, <span class="dv">21</span>)) <span class="sc">+</span></span>
<span id="cb83-58"><a href="id_04_model_validation_and_interpretation.html#cb83-58" 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">override.aes =</span> <span class="fu">list</span>(<span class="at">shape =</span> <span class="fu">c</span>(<span class="dv">24</span>, <span class="dv">21</span>))), <span class="at">shape =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb83-59"><a href="id_04_model_validation_and_interpretation.html#cb83-59" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(</span>
<span id="cb83-60"><a href="id_04_model_validation_and_interpretation.html#cb83-60" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> <span class="fu">c</span>(<span class="fl">0.63</span>, <span class="dv">3</span>),</span>
<span id="cb83-61"><a href="id_04_model_validation_and_interpretation.html#cb83-61" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, <span class="fu">log10</span>(<span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>) <span class="sc">/</span> <span class="dv">2</span>)),</span>
<span id="cb83-62"><a href="id_04_model_validation_and_interpretation.html#cb83-62" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>), <span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>) <span class="sc">/</span> <span class="dv">2</span>)</span>
<span id="cb83-63"><a href="id_04_model_validation_and_interpretation.html#cb83-63" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb83-64"><a href="id_04_model_validation_and_interpretation.html#cb83-64" aria-hidden="true" tabindex="-1"></a> <span class="fu">annotation_logticks</span>(<span class="at">sides =</span> <span class="st">"l"</span>) <span class="sc">+</span></span>
<span id="cb83-65"><a href="id_04_model_validation_and_interpretation.html#cb83-65" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb83-66"><a href="id_04_model_validation_and_interpretation.html#cb83-66" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb83-67"><a href="id_04_model_validation_and_interpretation.html#cb83-67" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb83-68"><a href="id_04_model_validation_and_interpretation.html#cb83-68" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb83-69"><a href="id_04_model_validation_and_interpretation.html#cb83-69" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.border =</span> <span class="fu">element_rect</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb83-70"><a href="id_04_model_validation_and_interpretation.html#cb83-70" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">20</span>),</span>
<span id="cb83-71"><a href="id_04_model_validation_and_interpretation.html#cb83-71" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">18</span>),</span>
<span id="cb83-72"><a href="id_04_model_validation_and_interpretation.html#cb83-72" 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 class="at">size =</span> <span class="dv">15</span>),</span>
<span id="cb83-73"><a href="id_04_model_validation_and_interpretation.html#cb83-73" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb83-74"><a href="id_04_model_validation_and_interpretation.html#cb83-74" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb83-75"><a href="id_04_model_validation_and_interpretation.html#cb83-75" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.ticks.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb83-76"><a href="id_04_model_validation_and_interpretation.html#cb83-76" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">unit</span>(<span class="fu">c</span>(<span class="fl">1.15</span>, <span class="fl">0.15</span>, <span class="fl">0.53</span>, <span class="dv">0</span>), <span class="st">"cm"</span>),</span>
<span id="cb83-77"><a href="id_04_model_validation_and_interpretation.html#cb83-77" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="fu">c</span>(<span class="fl">0.5</span>, <span class="fl">1.05</span>),</span>
<span id="cb83-78"><a href="id_04_model_validation_and_interpretation.html#cb83-78" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.direction =</span> <span class="st">"horizontal"</span>,</span>
<span id="cb83-79"><a href="id_04_model_validation_and_interpretation.html#cb83-79" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.key =</span> <span class="fu">element_rect</span>(<span class="at">fill =</span> <span class="cn">NA</span>)</span>
<span id="cb83-80"><a href="id_04_model_validation_and_interpretation.html#cb83-80" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb83-81"><a href="id_04_model_validation_and_interpretation.html#cb83-81" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">""</span>) <span class="sc">+</span></span>
<span id="cb83-82"><a href="id_04_model_validation_and_interpretation.html#cb83-82" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">fill =</span> <span class="st">""</span>, <span class="at">color =</span> <span class="st">""</span>, <span class="at">shape =</span> <span class="st">""</span>)</span>
<span id="cb83-83"><a href="id_04_model_validation_and_interpretation.html#cb83-83" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb83-84"><a href="id_04_model_validation_and_interpretation.html#cb83-84" aria-hidden="true" tabindex="-1"></a>p2 <span class="ot"><-</span> <span class="fu">ggarrange</span>(p2_1, p2_2, <span class="at">widths =</span> <span class="fu">c</span>(<span class="fl">2.39</span>, <span class="fl">1.02</span>))</span></code></pre></div>
<p><img src="figures/Fig%203%20mb%20vs%20cpp%20induced%20cells.png" width="100%" style="display: block; margin: auto;" /></p>
</div>
<div id="non-melanin-induced-cells" class="section level3 hasAnchor" number="4.1.4">
<h3><span class="header-section-number">4.1.4</span> Non-melanin induced cells<a href="id_04_model_validation_and_interpretation.html#non-melanin-induced-cells" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div class="sourceCode" id="cb84"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb84-1"><a href="id_04_model_validation_and_interpretation.html#cb84-1" aria-hidden="true" tabindex="-1"></a>p3_1 <span class="ot"><-</span> <span class="fu">ggscatter</span>(mb_cp_df[mb_cp_df<span class="sc">$</span>cell_group <span class="sc">==</span> <span class="st">"Non-induced"</span>, ],</span>
<span id="cb84-2"><a href="id_04_model_validation_and_interpretation.html#cb84-2" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"mb_true"</span>, <span class="at">y =</span> <span class="st">"log_cpp_true"</span>,</span>
<span id="cb84-3"><a href="id_04_model_validation_and_interpretation.html#cb84-3" aria-hidden="true" tabindex="-1"></a> <span class="at">alpha =</span> <span class="fl">0.7</span>, <span class="at">size =</span> <span class="dv">3</span>, <span class="at">stroke =</span> <span class="fl">0.3</span>, <span class="at">color =</span> <span class="st">"black"</span>, <span class="at">fill =</span> <span class="st">"cpp_pred"</span>, <span class="at">shape =</span> <span class="st">"cpp_pred"</span>,</span>
<span id="cb84-4"><a href="id_04_model_validation_and_interpretation.html#cb84-4" aria-hidden="true" tabindex="-1"></a> <span class="at">add =</span> <span class="st">"reg.line"</span>, <span class="at">conf.int =</span> <span class="cn">TRUE</span>, <span class="at">conf.int.level =</span> <span class="fl">0.95</span>, <span class="at">cor.coef =</span> <span class="cn">TRUE</span>,</span>
<span id="cb84-5"><a href="id_04_model_validation_and_interpretation.html#cb84-5" aria-hidden="true" tabindex="-1"></a> <span class="at">add.params =</span> <span class="fu">list</span>(<span class="at">color =</span> <span class="st">"grey25"</span>),</span>
<span id="cb84-6"><a href="id_04_model_validation_and_interpretation.html#cb84-6" aria-hidden="true" tabindex="-1"></a> <span class="at">cor.coeff.args =</span> <span class="fu">list</span>(</span>
<span id="cb84-7"><a href="id_04_model_validation_and_interpretation.html#cb84-7" aria-hidden="true" tabindex="-1"></a> <span class="at">method =</span> <span class="st">"pearson"</span>, <span class="at">label.x =</span> <span class="fl">2.2</span>, <span class="at">label.y =</span> <span class="fl">2.85</span>, <span class="at">label.sep =</span> <span class="st">"</span><span class="sc">\n</span><span class="st">"</span>,</span>
<span id="cb84-8"><a href="id_04_model_validation_and_interpretation.html#cb84-8" aria-hidden="true" tabindex="-1"></a> <span class="at">size =</span> <span class="dv">5</span></span>
<span id="cb84-9"><a href="id_04_model_validation_and_interpretation.html#cb84-9" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb84-10"><a href="id_04_model_validation_and_interpretation.html#cb84-10" aria-hidden="true" tabindex="-1"></a>) <span class="sc">+</span></span>
<span id="cb84-11"><a href="id_04_model_validation_and_interpretation.html#cb84-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">facet_grid</span>(. <span class="sc">~</span> cpp_pred) <span class="sc">+</span></span>
<span id="cb84-12"><a href="id_04_model_validation_and_interpretation.html#cb84-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#1f77b4"</span>, <span class="st">"#d62728"</span>)) <span class="sc">+</span></span>
<span id="cb84-13"><a href="id_04_model_validation_and_interpretation.html#cb84-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_shape_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="dv">24</span>, <span class="dv">21</span>)) <span class="sc">+</span></span>
<span id="cb84-14"><a href="id_04_model_validation_and_interpretation.html#cb84-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(</span>
<span id="cb84-15"><a href="id_04_model_validation_and_interpretation.html#cb84-15" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> <span class="fu">c</span>(<span class="fl">0.63</span>, <span class="dv">3</span>),</span>
<span id="cb84-16"><a href="id_04_model_validation_and_interpretation.html#cb84-16" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, <span class="fu">log10</span>(<span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>) <span class="sc">/</span> <span class="dv">2</span>)),</span>
<span id="cb84-17"><a href="id_04_model_validation_and_interpretation.html#cb84-17" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">sapply</span>(</span>
<span id="cb84-18"><a href="id_04_model_validation_and_interpretation.html#cb84-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>), <span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>) <span class="sc">/</span> <span class="dv">2</span>),</span>
<span id="cb84-19"><a href="id_04_model_validation_and_interpretation.html#cb84-19" aria-hidden="true" tabindex="-1"></a> <span class="cf">function</span>(x) <span class="fu">format</span>(x, <span class="at">big.mark =</span> <span class="st">","</span>, <span class="at">scientific =</span> <span class="cn">FALSE</span>)</span>
<span id="cb84-20"><a href="id_04_model_validation_and_interpretation.html#cb84-20" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb84-21"><a href="id_04_model_validation_and_interpretation.html#cb84-21" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb84-22"><a href="id_04_model_validation_and_interpretation.html#cb84-22" aria-hidden="true" tabindex="-1"></a> <span class="fu">annotation_logticks</span>(<span class="at">sides =</span> <span class="st">"l"</span>) <span class="sc">+</span></span>
<span id="cb84-23"><a href="id_04_model_validation_and_interpretation.html#cb84-23" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">fill =</span> <span class="st">"none"</span>, <span class="at">shape =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb84-24"><a href="id_04_model_validation_and_interpretation.html#cb84-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb84-25"><a href="id_04_model_validation_and_interpretation.html#cb84-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb84-26"><a href="id_04_model_validation_and_interpretation.html#cb84-26" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb84-27"><a href="id_04_model_validation_and_interpretation.html#cb84-27" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb84-28"><a href="id_04_model_validation_and_interpretation.html#cb84-28" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">17</span>),</span>
<span id="cb84-29"><a href="id_04_model_validation_and_interpretation.html#cb84-29" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.y =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">17</span>),</span>
<span id="cb84-30"><a href="id_04_model_validation_and_interpretation.html#cb84-30" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">20</span>),</span>
<span id="cb84-31"><a href="id_04_model_validation_and_interpretation.html#cb84-31" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.border =</span> <span class="fu">element_rect</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb84-32"><a href="id_04_model_validation_and_interpretation.html#cb84-32" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb84-33"><a href="id_04_model_validation_and_interpretation.html#cb84-33" 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 class="at">size =</span> <span class="dv">22</span>)</span>
<span id="cb84-34"><a href="id_04_model_validation_and_interpretation.html#cb84-34" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb84-35"><a href="id_04_model_validation_and_interpretation.html#cb84-35" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">"Peptide bound to mNPs (%)"</span>) <span class="sc">+</span></span>
<span id="cb84-36"><a href="id_04_model_validation_and_interpretation.html#cb84-36" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"Peptide (pMol / 100K cells)"</span>)</span>
<span id="cb84-37"><a href="id_04_model_validation_and_interpretation.html#cb84-37" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb84-38"><a href="id_04_model_validation_and_interpretation.html#cb84-38" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">1</span>)</span>
<span id="cb84-39"><a href="id_04_model_validation_and_interpretation.html#cb84-39" aria-hidden="true" tabindex="-1"></a>pos <span class="ot"><-</span> <span class="fu">position_jitter</span>(<span class="at">width =</span> <span class="fl">0.1</span>, <span class="at">seed =</span> <span class="dv">16</span>)</span>
<span id="cb84-40"><a href="id_04_model_validation_and_interpretation.html#cb84-40" aria-hidden="true" tabindex="-1"></a>p3_2 <span class="ot"><-</span> <span class="fu">ggplot</span>(mb_cp_df[mb_cp_df<span class="sc">$</span>cell_group <span class="sc">==</span> <span class="st">"Non-induced"</span>, ], <span class="fu">aes</span>(<span class="at">x =</span> cpp_pred, <span class="at">y =</span> log_cpp_true)) <span class="sc">+</span></span>
<span id="cb84-41"><a href="id_04_model_validation_and_interpretation.html#cb84-41" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_boxplot</span>(<span class="fu">aes</span>(<span class="at">color =</span> cpp_pred), <span class="at">outlier.color =</span> <span class="cn">NA</span>, <span class="at">lwd =</span> <span class="fl">1.5</span>, <span class="at">show.legend =</span> <span class="cn">FALSE</span>) <span class="sc">+</span></span>
<span id="cb84-42"><a href="id_04_model_validation_and_interpretation.html#cb84-42" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_beeswarm</span>(<span class="fu">aes</span>(<span class="at">fill =</span> cpp_pred, <span class="at">shape =</span> cpp_pred),</span>
<span id="cb84-43"><a href="id_04_model_validation_and_interpretation.html#cb84-43" aria-hidden="true" tabindex="-1"></a> <span class="at">color =</span> <span class="st">"black"</span>, <span class="at">alpha =</span> <span class="fl">0.7</span>, <span class="at">size =</span> <span class="dv">3</span>,</span>
<span id="cb84-44"><a href="id_04_model_validation_and_interpretation.html#cb84-44" aria-hidden="true" tabindex="-1"></a> <span class="at">stroke =</span> <span class="fl">0.3</span>, <span class="at">cex =</span> <span class="dv">2</span>, <span class="at">priority =</span> <span class="st">"random"</span></span>
<span id="cb84-45"><a href="id_04_model_validation_and_interpretation.html#cb84-45" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb84-46"><a href="id_04_model_validation_and_interpretation.html#cb84-46" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_compare_means</span>(</span>
<span id="cb84-47"><a href="id_04_model_validation_and_interpretation.html#cb84-47" aria-hidden="true" tabindex="-1"></a> <span class="at">label =</span> <span class="st">"p.signif"</span>, <span class="at">size =</span> <span class="dv">5</span>, <span class="at">method =</span> <span class="st">"wilcox.test"</span>, <span class="at">label.x.npc =</span> <span class="fl">0.2</span>,</span>
<span id="cb84-48"><a href="id_04_model_validation_and_interpretation.html#cb84-48" aria-hidden="true" tabindex="-1"></a> <span class="at">label.y =</span> <span class="fl">2.92</span>, <span class="at">hide.ns =</span> <span class="cn">TRUE</span></span>
<span id="cb84-49"><a href="id_04_model_validation_and_interpretation.html#cb84-49" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb84-50"><a href="id_04_model_validation_and_interpretation.html#cb84-50" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_compare_means</span>(</span>
<span id="cb84-51"><a href="id_04_model_validation_and_interpretation.html#cb84-51" aria-hidden="true" tabindex="-1"></a> <span class="at">label =</span> <span class="st">"p.format"</span>, <span class="at">size =</span> <span class="dv">5</span>, <span class="at">method =</span> <span class="st">"wilcox.test"</span>, <span class="at">label.x.npc =</span> <span class="fl">0.2</span>,</span>
<span id="cb84-52"><a href="id_04_model_validation_and_interpretation.html#cb84-52" aria-hidden="true" tabindex="-1"></a> <span class="at">label.y =</span> <span class="fl">2.82</span>, <span class="at">hide.ns =</span> <span class="cn">TRUE</span></span>
<span id="cb84-53"><a href="id_04_model_validation_and_interpretation.html#cb84-53" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb84-54"><a href="id_04_model_validation_and_interpretation.html#cb84-54" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#cae6fa"</span>, <span class="st">"#f5b8b8"</span>)) <span class="sc">+</span></span>
<span id="cb84-55"><a href="id_04_model_validation_and_interpretation.html#cb84-55" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"#1f77b4"</span>, <span class="st">"#d62728"</span>)) <span class="sc">+</span></span>
<span id="cb84-56"><a href="id_04_model_validation_and_interpretation.html#cb84-56" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_shape_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="dv">24</span>, <span class="dv">21</span>)) <span class="sc">+</span></span>
<span id="cb84-57"><a href="id_04_model_validation_and_interpretation.html#cb84-57" 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">override.aes =</span> <span class="fu">list</span>(<span class="at">shape =</span> <span class="fu">c</span>(<span class="dv">24</span>, <span class="dv">21</span>))), <span class="at">shape =</span> <span class="st">"none"</span>) <span class="sc">+</span></span>
<span id="cb84-58"><a href="id_04_model_validation_and_interpretation.html#cb84-58" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_continuous</span>(</span>
<span id="cb84-59"><a href="id_04_model_validation_and_interpretation.html#cb84-59" aria-hidden="true" tabindex="-1"></a> <span class="at">limits =</span> <span class="fu">c</span>(<span class="fl">0.63</span>, <span class="dv">3</span>),</span>
<span id="cb84-60"><a href="id_04_model_validation_and_interpretation.html#cb84-60" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>, <span class="fu">log10</span>(<span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>) <span class="sc">/</span> <span class="dv">2</span>)),</span>
<span id="cb84-61"><a href="id_04_model_validation_and_interpretation.html#cb84-61" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>), <span class="dv">10</span><span class="sc">^</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">4</span>) <span class="sc">/</span> <span class="dv">2</span>)</span>
<span id="cb84-62"><a href="id_04_model_validation_and_interpretation.html#cb84-62" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb84-63"><a href="id_04_model_validation_and_interpretation.html#cb84-63" aria-hidden="true" tabindex="-1"></a> <span class="fu">annotation_logticks</span>(<span class="at">sides =</span> <span class="st">"l"</span>) <span class="sc">+</span></span>
<span id="cb84-64"><a href="id_04_model_validation_and_interpretation.html#cb84-64" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
<span id="cb84-65"><a href="id_04_model_validation_and_interpretation.html#cb84-65" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(</span>
<span id="cb84-66"><a href="id_04_model_validation_and_interpretation.html#cb84-66" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb84-67"><a href="id_04_model_validation_and_interpretation.html#cb84-67" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb84-68"><a href="id_04_model_validation_and_interpretation.html#cb84-68" aria-hidden="true" tabindex="-1"></a> <span class="at">panel.border =</span> <span class="fu">element_rect</span>(<span class="at">colour =</span> <span class="st">"black"</span>),</span>
<span id="cb84-69"><a href="id_04_model_validation_and_interpretation.html#cb84-69" aria-hidden="true" tabindex="-1"></a> <span class="at">strip.text =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">20</span>),</span>
<span id="cb84-70"><a href="id_04_model_validation_and_interpretation.html#cb84-70" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">colour =</span> <span class="st">"black"</span>, <span class="at">size =</span> <span class="dv">18</span>),</span>
<span id="cb84-71"><a href="id_04_model_validation_and_interpretation.html#cb84-71" 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 class="at">size =</span> <span class="dv">15</span>),</span>
<span id="cb84-72"><a href="id_04_model_validation_and_interpretation.html#cb84-72" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.title.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb84-73"><a href="id_04_model_validation_and_interpretation.html#cb84-73" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.text.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb84-74"><a href="id_04_model_validation_and_interpretation.html#cb84-74" aria-hidden="true" tabindex="-1"></a> <span class="at">axis.ticks.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb84-75"><a href="id_04_model_validation_and_interpretation.html#cb84-75" aria-hidden="true" tabindex="-1"></a> <span class="at">plot.margin =</span> <span class="fu">unit</span>(<span class="fu">c</span>(<span class="fl">1.15</span>, <span class="fl">0.15</span>, <span class="fl">0.53</span>, <span class="dv">0</span>), <span class="st">"cm"</span>),</span>
<span id="cb84-76"><a href="id_04_model_validation_and_interpretation.html#cb84-76" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="fu">c</span>(<span class="fl">0.5</span>, <span class="fl">1.05</span>),</span>
<span id="cb84-77"><a href="id_04_model_validation_and_interpretation.html#cb84-77" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.direction =</span> <span class="st">"horizontal"</span>,</span>
<span id="cb84-78"><a href="id_04_model_validation_and_interpretation.html#cb84-78" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.key =</span> <span class="fu">element_rect</span>(<span class="at">fill =</span> <span class="cn">NA</span>)</span>
<span id="cb84-79"><a href="id_04_model_validation_and_interpretation.html#cb84-79" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb84-80"><a href="id_04_model_validation_and_interpretation.html#cb84-80" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">""</span>) <span class="sc">+</span></span>
<span id="cb84-81"><a href="id_04_model_validation_and_interpretation.html#cb84-81" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">fill =</span> <span class="st">""</span>, <span class="at">color =</span> <span class="st">""</span>, <span class="at">shape =</span> <span class="st">""</span>)</span>
<span id="cb84-82"><a href="id_04_model_validation_and_interpretation.html#cb84-82" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb84-83"><a href="id_04_model_validation_and_interpretation.html#cb84-83" aria-hidden="true" tabindex="-1"></a>p3 <span class="ot"><-</span> <span class="fu">ggarrange</span>(p3_1, p3_2, <span class="at">widths =</span> <span class="fu">c</span>(<span class="fl">2.39</span>, <span class="fl">1.02</span>))</span></code></pre></div>
<p><img src="figures/Supplementary%20Fig%205%20mb%20vs%20cpp%20non-induced%20cells.png" width="100%" style="display: block; margin: auto;" /></p>
</div>
</div>
<div id="overall-model-interpretation" class="section level2 hasAnchor" number="4.2">
<h2><span class="header-section-number">4.2</span> Overall model interpretation<a href="id_04_model_validation_and_interpretation.html#overall-model-interpretation" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="melanin-binding-regression-2" class="section level3 hasAnchor" number="4.2.1">
<h3><span class="header-section-number">4.2.1</span> Melanin binding (regression)<a href="id_04_model_validation_and_interpretation.html#melanin-binding-regression-2" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div class="sourceCode" id="cb85"><pre class="sourceCode r fold-hide"><code class="sourceCode r"><span id="cb85-1"><a href="id_04_model_validation_and_interpretation.html#cb85-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Save train and test sets in csv format</span></span>
<span id="cb85-2"><a href="id_04_model_validation_and_interpretation.html#cb85-2" aria-hidden="true" tabindex="-1"></a><span class="fu">load</span>(<span class="at">file =</span> <span class="st">"./rdata/var_reduct_mb_train_test_splits.RData"</span>)</span>
<span id="cb85-3"><a href="id_04_model_validation_and_interpretation.html#cb85-3" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="dv">1</span><span class="sc">:</span><span class="dv">10</span>) {</span>
<span id="cb85-4"><a href="id_04_model_validation_and_interpretation.html#cb85-4" aria-hidden="true" tabindex="-1"></a> prefix <span class="ot"><-</span> <span class="fu">paste0</span>(<span class="st">"outer_"</span>, i)</span>
<span id="cb85-5"><a href="id_04_model_validation_and_interpretation.html#cb85-5" aria-hidden="true" tabindex="-1"></a> exp_dir <span class="ot"><-</span> <span class="fu">paste0</span>(<span class="st">"/Users/renee/Downloads/melanin_binding/"</span>, prefix)</span>
<span id="cb85-6"><a href="id_04_model_validation_and_interpretation.html#cb85-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">write.csv</span>(outer_splits[[i]]<span class="sc">$</span>train, <span class="at">file =</span> <span class="fu">paste0</span>(exp_dir, <span class="st">"/train_set.csv"</span>))</span>
<span id="cb85-7"><a href="id_04_model_validation_and_interpretation.html#cb85-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">write.csv</span>(outer_splits[[i]]<span class="sc">$</span>test, <span class="at">file =</span> <span class="fu">paste0</span>(exp_dir, <span class="st">"/test_set.csv"</span>))</span>
<span id="cb85-8"><a href="id_04_model_validation_and_interpretation.html#cb85-8" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb85-9"><a href="id_04_model_validation_and_interpretation.html#cb85-9" aria-hidden="true" tabindex="-1"></a>exp_dir <span class="ot"><-</span> <span class="fu">paste0</span>(<span class="st">"/Users/renee/Downloads/melanin_binding/whole_data_set"</span>)</span>
<span id="cb85-10"><a href="id_04_model_validation_and_interpretation.html#cb85-10" aria-hidden="true" tabindex="-1"></a><span class="fu">write.csv</span>(mb_data, <span class="at">file =</span> <span class="fu">paste0</span>(exp_dir, <span class="st">"/train_set.csv"</span>))</span></code></pre></div>
<div class="sourceCode" id="cb86"><pre class="sourceCode python fold-hide"><code class="sourceCode python"><span id="cb86-1"><a href="id_04_model_validation_and_interpretation.html#cb86-1" aria-hidden="true" tabindex="-1"></a>h2o.init(nthreads<span class="op">=-</span><span class="dv">1</span>)</span>
<span id="cb86-2"><a href="id_04_model_validation_and_interpretation.html#cb86-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb86-3"><a href="id_04_model_validation_and_interpretation.html#cb86-3" aria-hidden="true" tabindex="-1"></a>dir_path <span class="op">=</span> <span class="st">'/Users/renee/Downloads/melanin_binding'</span></span>
<span id="cb86-4"><a href="id_04_model_validation_and_interpretation.html#cb86-4" aria-hidden="true" tabindex="-1"></a>model_names <span class="op">=</span> [<span class="st">'superlearner_iter_3'</span>, <span class="st">'superlearner_iter_2'</span>, <span class="st">'superlearner_iter_2'</span>, <span class="st">'superlearner_iter_3'</span>, </span>
<span id="cb86-5"><a href="id_04_model_validation_and_interpretation.html#cb86-5" aria-hidden="true" tabindex="-1"></a> <span class="st">'superlearner_iter_3'</span>, <span class="st">'superlearner_iter_3'</span>, <span class="st">'superlearner_iter_3'</span>, <span class="st">'superlearner_iter_3'</span>, </span>
<span id="cb86-6"><a href="id_04_model_validation_and_interpretation.html#cb86-6" aria-hidden="true" tabindex="-1"></a> <span class="st">'superlearner_iter_4'</span>, <span class="st">'superlearner_iter_3'</span>]</span>
<span id="cb86-7"><a href="id_04_model_validation_and_interpretation.html#cb86-7" aria-hidden="true" tabindex="-1"></a>shap_res <span class="op">=</span> []</span>
<span id="cb86-8"><a href="id_04_model_validation_and_interpretation.html#cb86-8" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> i <span class="kw">in</span> <span class="bu">range</span>(<span class="dv">10</span>):</span>
<span id="cb86-9"><a href="id_04_model_validation_and_interpretation.html#cb86-9" aria-hidden="true" tabindex="-1"></a> <span class="bu">print</span>(<span class="st">'Iter '</span> <span class="op">+</span> <span class="bu">str</span>(i <span class="op">+</span> <span class="dv">1</span>) <span class="op">+</span> <span class="st">':'</span>)</span>
<span id="cb86-10"><a href="id_04_model_validation_and_interpretation.html#cb86-10" aria-hidden="true" tabindex="-1"></a> train <span class="op">=</span> pd.read_csv(dir_path <span class="op">+</span> <span class="st">'/outer_'</span> <span class="op">+</span> <span class="bu">str</span>(i <span class="op">+</span> <span class="dv">1</span>) <span class="op">+</span> <span class="st">'/train_set.csv'</span>, index_col<span class="op">=</span><span class="dv">0</span>)</span>
<span id="cb86-11"><a href="id_04_model_validation_and_interpretation.html#cb86-11" aria-hidden="true" tabindex="-1"></a> X_train <span class="op">=</span> train.iloc[:, :<span class="op">-</span><span class="dv">1</span>]</span>
<span id="cb86-12"><a href="id_04_model_validation_and_interpretation.html#cb86-12" aria-hidden="true" tabindex="-1"></a> test <span class="op">=</span> pd.read_csv(dir_path <span class="op">+</span> <span class="st">'/outer_'</span> <span class="op">+</span> <span class="bu">str</span>(i <span class="op">+</span> <span class="dv">1</span>) <span class="op">+</span> <span class="st">'/test_set.csv'</span>, index_col<span class="op">=</span><span class="dv">0</span>)</span>
<span id="cb86-13"><a href="id_04_model_validation_and_interpretation.html#cb86-13" aria-hidden="true" tabindex="-1"></a> X_test <span class="op">=</span> test.iloc[:, :<span class="op">-</span><span class="dv">1</span>]</span>
<span id="cb86-14"><a href="id_04_model_validation_and_interpretation.html#cb86-14" aria-hidden="true" tabindex="-1"></a> model <span class="op">=</span> h2o.load_model(dir_path <span class="op">+</span> <span class="st">'/outer_'</span> <span class="op">+</span> <span class="bu">str</span>(i <span class="op">+</span> <span class="dv">1</span>) <span class="op">+</span> <span class="st">'/'</span> <span class="op">+</span> model_names[i])</span>