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microbiome · Nov 14, 2024 · 843f413 · 843f413
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diff --git a/docs/devel/pages/beta_diversity.html b/docs/devel/pages/beta_diversity.html
@@ -1127,7 +1127,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
 <td style="text-align: right;">6</td>
 <td style="text-align: right;">1.1157</td>
 <td style="text-align: right;">1.940</td>
-<td style="text-align: right;">0.038</td>
+<td style="text-align: right;">0.039</td>
 <td style="text-align: right;">3.991</td>
 <td style="text-align: right;">0.2795</td>
 </tr>
@@ -1136,7 +1136,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
 <td style="text-align: right;">4</td>
 <td style="text-align: right;">0.5837</td>
 <td style="text-align: right;">1.522</td>
-<td style="text-align: right;">0.139</td>
+<td style="text-align: right;">0.119</td>
 <td style="text-align: right;">3.991</td>
 <td style="text-align: right;">0.1463</td>
 </tr>
@@ -1145,7 +1145,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
 <td style="text-align: right;">1</td>
 <td style="text-align: right;">0.1679</td>
 <td style="text-align: right;">1.751</td>
-<td style="text-align: right;">0.093</td>
+<td style="text-align: right;">0.109</td>
 <td style="text-align: right;">3.991</td>
 <td style="text-align: right;">0.0421</td>
 </tr>
@@ -1254,7 +1254,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
 <td style="text-align: right;">0.0628</td>
 <td style="text-align: right;">2.7440</td>
 <td style="text-align: right;">999</td>
-<td style="text-align: right;">0.116</td>
+<td style="text-align: right;">0.104</td>
 <td style="text-align: right;">1.0288</td>
 <td style="text-align: right;">0.2440</td>
 </tr>
@@ -1265,7 +1265,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
 <td style="text-align: right;">0.0103</td>
 <td style="text-align: right;">0.4158</td>
 <td style="text-align: right;">999</td>
-<td style="text-align: right;">0.541</td>
+<td style="text-align: right;">0.519</td>
 <td style="text-align: right;">0.9283</td>
 <td style="text-align: right;">0.0111</td>
 </tr>
@@ -1276,7 +1276,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
 <td style="text-align: right;">0.0113</td>
 <td style="text-align: right;">17.0255</td>
 <td style="text-align: right;">999</td>
-<td style="text-align: right;">0.395</td>
+<td style="text-align: right;">0.415</td>
 <td style="text-align: right;">0.3319</td>
 <td style="text-align: right;">0.9860</td>
 </tr>

diff --git a/...igure-html/MDS plot based on the Bray-Curtis distances using rarefaction.-1.png b/...igure-html/MDS plot based on the Bray-Curtis distances using rarefaction.-1.png
diff --git a/docs/devel/pages/beta_diversity_files/figure-html/PC_correlation-1.png b/docs/devel/pages/beta_diversity_files/figure-html/PC_correlation-1.png
diff --git a/docs/devel/pages/beta_diversity_files/figure-html/plot-pca-1.png b/docs/devel/pages/beta_diversity_files/figure-html/plot-pca-1.png
diff --git a/docs/devel/pages/beta_diversity_files/figure-html/plot-rda-1.png b/docs/devel/pages/beta_diversity_files/figure-html/plot-rda-1.png
diff --git a/docs/devel/pages/beta_diversity_files/figure-html/plot-umap-1.png b/docs/devel/pages/beta_diversity_files/figure-html/plot-umap-1.png
diff --git a/docs/devel/pages/composition_files/figure-html/neatmap-1.png b/docs/devel/pages/composition_files/figure-html/neatmap-1.png
diff --git a/docs/devel/pages/extra_material.html b/docs/devel/pages/extra_material.html
@@ -1491,8 +1491,8 @@ <h1 class="title"><span id="sec-extras" class="quarto-section-identifier">Append
 <span><span class="co">##  </span></span>
 <span><span class="co">##  First  4  Cluster sizes:</span></span>
 <span><span class="co">##                     BC 1 BC 2 BC 3 BC 4</span></span>
-<span><span class="co">##  Number of Rows:      19   13   14    2</span></span>
-<span><span class="co">##  Number of Columns:   13   14   10   11</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="co">##  Number of Rows:      16   16   19    3</span></span>
+<span><span class="co">##  Number of Columns:   12   14    9    9</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>The object includes cluster information. However compared to <code>cobiclust</code>, <code>biclust</code> object includes only information about clusters that were found, not general cluster.</p>
 <p>Meaning that if one cluster size of 5 features was found out of 20 features, those 15 features do not belong to any cluster. That is why we have to create an additional cluster for features/samples that are not assigned into any cluster.</p>

diff --git a/docs/devel/pages/extra_material_files/figure-html/biclust_7-1.png b/docs/devel/pages/extra_material_files/figure-html/biclust_7-1.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/biclust_7-2.png b/docs/devel/pages/extra_material_files/figure-html/biclust_7-2.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/biclust_7-3.png b/docs/devel/pages/extra_material_files/figure-html/biclust_7-3.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/biclust_7-4.png b/docs/devel/pages/extra_material_files/figure-html/biclust_7-4.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/biclust_7-5.png b/docs/devel/pages/extra_material_files/figure-html/biclust_7-5.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/biclust_7-6.png b/docs/devel/pages/extra_material_files/figure-html/biclust_7-6.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/biclust_9-1.png b/docs/devel/pages/extra_material_files/figure-html/biclust_9-1.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/cobiclust_3b-1.png b/docs/devel/pages/extra_material_files/figure-html/cobiclust_3b-1.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/unnamed-chunk-35-1.png b/docs/devel/pages/extra_material_files/figure-html/unnamed-chunk-35-1.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/unnamed-chunk-38-1.png b/docs/devel/pages/extra_material_files/figure-html/unnamed-chunk-38-1.png
diff --git a/docs/devel/pages/extra_material_files/figure-html/unnamed-chunk-39-1.png b/docs/devel/pages/extra_material_files/figure-html/unnamed-chunk-39-1.png
diff --git a/docs/devel/pages/integrated_learner.html b/docs/devel/pages/integrated_learner.html
@@ -751,7 +751,7 @@ <h1 class="title"><span id="sec-multi-omics-integration" class="quarto-section-i
 <span><span class="co">##  Running base model for layer  2 ... </span></span>
 <span><span class="co">##  Running stacked model...</span></span>
 <span><span class="co">##  Running concatenated model...</span></span>
-<span><span class="co">##  Time for model fit : 1.611 minutes </span></span>
+<span><span class="co">##  Time for model fit : 1.619 minutes </span></span>
 <span><span class="co">##  ========================================</span></span>
 <span><span class="co">##  Model fit for individual layers: SL.randomForest </span></span>
 <span><span class="co">##  Model fit for stacked layer: SL.nnls.auc </span></span>

diff --git a/docs/devel/pages/introductory_workflow_dutch_version.html b/docs/devel/pages/introductory_workflow_dutch_version.html
diff --git a/docs/devel/pages/introductory_workflow_files/figure-html/showPCoA-1.png b/docs/devel/pages/introductory_workflow_files/figure-html/showPCoA-1.png
diff --git a/docs/devel/pages/introductory_workflow_french_version.html b/docs/devel/pages/introductory_workflow_french_version.html
diff --git a/docs/devel/pages/machine_learning.html b/docs/devel/pages/machine_learning.html
@@ -708,26 +708,26 @@ <h1 class="title"><span id="sec-machine_learning" class="quarto-section-identifi
 <span><span class="co">##  </span></span>
 <span><span class="co">##            Reference</span></span>
 <span><span class="co">##  Prediction T2D healthy</span></span>
-<span><span class="co">##     T2D      82      49</span></span>
-<span><span class="co">##     healthy  54     106</span></span>
+<span><span class="co">##     T2D      86      47</span></span>
+<span><span class="co">##     healthy  50     108</span></span>
 <span><span class="co">##                                          </span></span>
-<span><span class="co">##                 Accuracy : 0.646         </span></span>
-<span><span class="co">##                   95% CI : (0.588, 0.701)</span></span>
+<span><span class="co">##                 Accuracy : 0.667         </span></span>
+<span><span class="co">##                   95% CI : (0.609, 0.721)</span></span>
 <span><span class="co">##      No Information Rate : 0.533         </span></span>
-<span><span class="co">##      P-Value [Acc &gt; NIR] : 5.86e-05      </span></span>
+<span><span class="co">##      P-Value [Acc &gt; NIR] : 2.37e-06      </span></span>
 <span><span class="co">##                                          </span></span>
-<span><span class="co">##                    Kappa : 0.287         </span></span>
+<span><span class="co">##                    Kappa : 0.33          </span></span>
 <span><span class="co">##                                          </span></span>
-<span><span class="co">##   Mcnemar's Test P-Value : 0.693         </span></span>
+<span><span class="co">##   Mcnemar's Test P-Value : 0.839         </span></span>
 <span><span class="co">##                                          </span></span>
-<span><span class="co">##              Sensitivity : 0.603         </span></span>
-<span><span class="co">##              Specificity : 0.684         </span></span>
-<span><span class="co">##           Pos Pred Value : 0.626         </span></span>
-<span><span class="co">##           Neg Pred Value : 0.662         </span></span>
+<span><span class="co">##              Sensitivity : 0.632         </span></span>
+<span><span class="co">##              Specificity : 0.697         </span></span>
+<span><span class="co">##           Pos Pred Value : 0.647         </span></span>
+<span><span class="co">##           Neg Pred Value : 0.684         </span></span>
 <span><span class="co">##               Prevalence : 0.467         </span></span>
-<span><span class="co">##           Detection Rate : 0.282         </span></span>
-<span><span class="co">##     Detection Prevalence : 0.450         </span></span>
-<span><span class="co">##        Balanced Accuracy : 0.643         </span></span>
+<span><span class="co">##           Detection Rate : 0.296         </span></span>
+<span><span class="co">##     Detection Prevalence : 0.457         </span></span>
+<span><span class="co">##        Balanced Accuracy : 0.665         </span></span>
 <span><span class="co">##                                          </span></span>
 <span><span class="co">##         'Positive' Class : T2D           </span></span>
 <span><span class="co">##  </span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>