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microbiome · Dec 17, 2024 · c92ba5c · c92ba5c
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diff --git a/docs/datacontainers.html b/docs/datacontainers.html
@@ -531,87 +531,6 @@ <h2>Task: load microbiome data</h2>
 </div>
 </div>
 </section>
-<section id="section-9" class="slide level2">
-<h2></h2>
-<p>We can then retrieve the abundance table.</p>
-<div class="cell">
-<div class="cell-output cell-output-stdout">
-<pre><code>                     C1 C2 C3 C4 C5
-GAYR01026362.62.2014  0  0  0  0  0
-CVJT01000011.50.2173  1  0  1  1  0</code></pre>
-</div>
-</div>
-</section>
-<section id="section-10" class="slide level2">
-<h2></h2>
-<p>And check sample metadata.</p>
-<div class="cell">
-<div class="cell-output cell-output-stdout">
-<pre><code>DataFrame with 40 rows and 0 columns</code></pre>
-</div>
-</div>
-</section>
-<section id="section-11" class="slide level2">
-<h2></h2>
-<p>And access the feature metadata, i.e., taxonomy table.</p>
-<div class="cell">
-<div class="cell-output cell-output-stdout">
-<pre><code>DataFrame with 12706 rows and 7 columns
-                                    Phylum                  Class
-                               &lt;character&gt;            &lt;character&gt;
-GAYR01026362.62.2014   D_1__Proteobacteria D_2__Alphaproteobact..
-CVJT01000011.50.2173       D_1__Firmicutes           D_2__Bacilli
-KF625183.1.1786        D_1__Proteobacteria D_2__Gammaproteobact..
-AYSG01000002.292.2076      D_1__Firmicutes           D_2__Bacilli
-CCPS01000022.154.1916  D_1__Proteobacteria D_2__Gammaproteobact..
-...                                    ...                    ...
-JRJTB:03786:02940     D_1__Verrucomicrobia  D_2__Verrucomicrobiae
-JRJTB:03786:03034          D_1__Firmicutes        D_2__Clostridia
-JRJTB:03787:02353          D_1__Firmicutes        D_2__Clostridia
-JRJTB:03787:02429       D_1__Bacteroidetes       D_2__Bacteroidia
-JRJTB:03787:02478       D_1__Bacteroidetes       D_2__Bacteroidia
-                                       Order                 Family
-                                 &lt;character&gt;            &lt;character&gt;
-GAYR01026362.62.2014      D_3__Rickettsiales      D_4__Mitochondria
-CVJT01000011.50.2173         D_3__Bacillales D_4__Staphylococcaceae
-KF625183.1.1786       D_3__Enterobacteriales D_4__Enterobacteriac..
-AYSG01000002.292.2076   D_3__Lactobacillales  D_4__Streptococcaceae
-CCPS01000022.154.1916 D_3__Enterobacteriales D_4__Enterobacteriac..
-...                                      ...                    ...
-JRJTB:03786:02940     D_3__Verrucomicrobia..   D_4__Akkermansiaceae
-JRJTB:03786:03034         D_3__Clostridiales   D_4__Ruminococcaceae
-JRJTB:03787:02353         D_3__Clostridiales       D_4__Family XIII
-JRJTB:03787:02429         D_3__Bacteroidales    D_4__Muribaculaceae
-JRJTB:03787:02478         D_3__Bacteroidales    D_4__Muribaculaceae
-                                       Genus                Species
-                                 &lt;character&gt;            &lt;character&gt;
-GAYR01026362.62.2014  D_5__Solanum melonge.. D_6__Solanum melonge..
-CVJT01000011.50.2173     D_5__Staphylococcus D_6__Staphylococcus ..
-KF625183.1.1786              D_5__Klebsiella D_6__Klebsiella oxyt..
-AYSG01000002.292.2076     D_5__Streptococcus D_6__Streptococcus t..
-CCPS01000022.154.1916 D_5__Escherichia-Shi..  D_6__Escherichia coli
-...                                      ...                    ...
-JRJTB:03786:02940           D_5__Akkermansia                     NA
-JRJTB:03786:03034     D_5__Ruminococcaceae.. D_6__uncultured bact..
-JRJTB:03787:02353     D_5__Family XIII AD3.. D_6__uncultured bact..
-JRJTB:03787:02429     D_5__uncultured bact.. D_6__uncultured bact..
-JRJTB:03787:02478     D_5__uncultured bact.. D_6__uncultured bact..
-                                        OTU
-                                &lt;character&gt;
-GAYR01026362.62.2014   GAYR01026362.62.2014
-CVJT01000011.50.2173   CVJT01000011.50.2173
-KF625183.1.1786             KF625183.1.1786
-AYSG01000002.292.2076 AYSG01000002.292.2076
-CCPS01000022.154.1916 CCPS01000022.154.1916
-...                                     ...
-JRJTB:03786:02940         JRJTB:03786:02940
-JRJTB:03786:03034         JRJTB:03786:03034
-JRJTB:03787:02353         JRJTB:03787:02353
-JRJTB:03787:02429         JRJTB:03787:02429
-JRJTB:03787:02478         JRJTB:03787:02478</code></pre>
-</div>
-</div>
-</section>
 <section id="open-microbiome-data-resources" class="slide level2">
 <h2>Open microbiome data resources</h2>
 <p>Open microbiome data resources supporting <em>TreeSummarizedExperiment</em>:</p>

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diff --git a/docs/index.html b/docs/index.html
@@ -147,7 +147,6 @@ <h3 class="anchored" data-anchor-id="microbiome-data-analysis">Microbiome data a
 <li><a href="https://microbiome.github.io/outreach/quarto.html" target="_blank">Introduction to Quarto</a></li>
 <li><a href="https://microbiome.github.io/outreach/alpha_diversity.html" target="_blank">Alpha Diversity</a></li>
 <li><a href="https://microbiome.github.io/outreach/ordination.html" target="_blank">Ordination</a></li>
-<li><a href="https://microbiome.github.io/outreach/dbrda.html" target="_blank">dbRDA</a></li>
 <li><a href="https://microbiome.github.io/outreach/compositional_heatmap.html" target="_blank">Compositional Heatmaps</a></li>
 <li><a href="https://microbiome.github.io/outreach/differential_abundance.html" target="_blank">Differential Abundance</a></li>
 <li><a href="https://microbiome.github.io/outreach/day2.html" target="_blank">Day 2</a></li>

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diff --git a/docs/oma_files/figure-revealjs/pages_and_book-1.png b/docs/oma_files/figure-revealjs/pages_and_book-1.png
diff --git a/docs/oma_files/figure-revealjs/se_field-1.png b/docs/oma_files/figure-revealjs/se_field-1.png