included pca into toc

MPI-EVA-Archaeogenetics · Mar 11, 2024 · 80bbe5f · 80bbe5f
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Showing 14 changed files with 1,093 additions and 1 deletion.
diff --git a/_quarto.yml b/_quarto.yml
@@ -13,6 +13,7 @@ book:
     - fstats.qmd
     - eager.qmd
     - fst.qmd
+    - pca_mds.qmd
     - pmrread.qmd
     - references.qmd
 

diff --git a/docs/fstats.html b/docs/fstats.html
@@ -191,11 +191,17 @@
   <a href="./fst.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Measuring population structure using Fst</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./pca_mds.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Dimensionality reduction using PCA and MDS</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./pmrread.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Pairwise mismatch rate (PMR) and READ relatedness inference</span></span></a>
+ <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Pairwise mismatch rate (PMR) and READ relatedness inference</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">

diff --git a/docs/fstats_files/figure-html/unnamed-chunk-9-1.png b/docs/fstats_files/figure-html/unnamed-chunk-9-1.png
diff --git a/docs/img/pca_mds/MDS_poplist1.png b/docs/img/pca_mds/MDS_poplist1.png
diff --git a/docs/img/pca_mds/PCA_plot_1.png b/docs/img/pca_mds/PCA_plot_1.png
diff --git a/docs/img/pca_mds/PCA_plot_2.png b/docs/img/pca_mds/PCA_plot_2.png
diff --git a/docs/img/pca_mds/PCA_plot_ap.png b/docs/img/pca_mds/PCA_plot_ap.png
diff --git a/docs/img/pca_mds/missingness_in_PCA.png b/docs/img/pca_mds/missingness_in_PCA.png
diff --git a/docs/img/pca_mds/pca.gif b/docs/img/pca_mds/pca.gif
diff --git a/docs/img/pca_mds/projection_comparison.png b/docs/img/pca_mds/projection_comparison.png
diff --git a/docs/img/pca_mds/shrinkage.png b/docs/img/pca_mds/shrinkage.png
diff --git a/docs/img/pca_mds/shrinkmode.png b/docs/img/pca_mds/shrinkmode.png
diff --git a/docs/pca_mds.html b/docs/pca_mds.html
diff --git a/docs/search.json b/docs/search.json