From d0c13065a84a5a222e57af35078a96a469c32b9b Mon Sep 17 00:00:00 2001
From: sdgamboa <53412049+sdgamboa@users.noreply.github.com>
Date: Thu, 21 Sep 2023 21:23:36 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20sdgamboa?=
 =?UTF-8?q?/taxPPro@cbb141b859537fb1c659834d27c8f42f984c1a32=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 articles/explore_taxids.html | 8 ++++----
 articles/phytools.html       | 4 ++--
 pkgdown.yml                  | 2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/articles/explore_taxids.html b/articles/explore_taxids.html
index 4c25cdf..72b5dc1 100644
--- a/articles/explore_taxids.html
+++ b/articles/explore_taxids.html
@@ -209,8 +209,8 @@ <h2 id="ncbi-sets">NCBI sets<a class="anchor" aria-label="anchor" href="#ncbi-se
 <span>  <span class="va">taxids_summary</span>, </span>
 <span>  caption <span class="op">=</span> <span class="st">'Table 1. Number of taxa per rank and NCBI set.'</span></span>
 <span><span class="op">)</span></span></code></pre></div>
-<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-19007ab1a288e288b894" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-19007ab1a288e288b894">{"x":{"filter":"none","vertical":false,"caption":"<caption>Table 1. Number of taxa per rank and NCBI set.<\/caption>","data":[["1","2","3","4","5","6","7","8"],["exclude_all","exclude_informal","exclude_unclassified_informal","exclude_uncultured_informal","exclude_unclassified_uncultured","exclude_unclassified","exclude_uncultured","include_all"],[5332,5332,5332,5332,5332,5332,5332,5332],[26150,26150,26150,26150,31788,80761,446685,497076],[0,0,0,0,42148,42273,42287,42412],[31482,31482,31482,31482,79268,128366,494304,544820]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>set<\/th>\n      <th>genus<\/th>\n      <th>species<\/th>\n      <th>strain<\/th>\n      <th>total<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[2,3,4,5]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-c66cc846e24c6992b269" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-c66cc846e24c6992b269">{"x":{"filter":"none","vertical":false,"caption":"<caption>Table 1. Number of taxa per rank and NCBI set.<\/caption>","data":[["1","2","3","4","5","6","7","8"],["exclude_all","exclude_informal","exclude_unclassified_informal","exclude_uncultured_informal","exclude_unclassified_uncultured","exclude_unclassified","exclude_uncultured","include_all"],[5332,5332,5332,5332,5332,5332,5332,5332],[26150,26150,26150,26150,31788,80761,446685,497076],[0,0,0,0,42148,42273,42287,42412],[31482,31482,31482,31482,79268,128366,494304,544820]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>set<\/th>\n      <th>genus<\/th>\n      <th>species<\/th>\n      <th>strain<\/th>\n      <th>total<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[2,3,4,5]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
 </div>
 <div class="section level2">
 <h2 id="percentage-of-bugphyzz-taxids-annotated-in-the-ncbi">Percentage of bugphyzz taxids annotated in the NCBI:<a class="anchor" aria-label="anchor" href="#percentage-of-bugphyzz-taxids-annotated-in-the-ncbi"></a>
@@ -328,8 +328,8 @@ <h2 id="percentage-of-bugphyzz-taxids-annotated-in-the-ncbi">Percentage of bugph
 <span>  <span class="va">bp_ids_summary</span>,</span>
 <span>  caption <span class="op">=</span> <span class="st">'Table 2. Percentage of bugphyzz taxa also annotated in the NCBI sets per rank.'</span></span>
 <span><span class="op">)</span></span></code></pre></div>
-<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-1e3ef2fb07c56c90004a" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-1e3ef2fb07c56c90004a">{"x":{"filter":"none","vertical":false,"caption":"<caption>Table 2. Percentage of bugphyzz taxa also annotated in the NCBI sets per rank.<\/caption>","data":[["1","2","3","4","5","6","7","8"],["exclude_all","exclude_informal","exclude_unclassified_informal","exclude_uncultured_informal","exclude_unclassified_uncultured","exclude_unclassified","exclude_uncultured","include_all"],[100,100,100,100,100,100,100,100],[70,70,70,70,70,71,99,99],[0,0,0,0,100,100,100,100],[31482,31482,31482,31482,79268,128366,494304,544820]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>set<\/th>\n      <th>genus<\/th>\n      <th>species<\/th>\n      <th>strain<\/th>\n      <th>total<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[2,3,4,5]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-2565f8e6530cb78de39e" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-2565f8e6530cb78de39e">{"x":{"filter":"none","vertical":false,"caption":"<caption>Table 2. Percentage of bugphyzz taxa also annotated in the NCBI sets per rank.<\/caption>","data":[["1","2","3","4","5","6","7","8"],["exclude_all","exclude_informal","exclude_unclassified_informal","exclude_uncultured_informal","exclude_unclassified_uncultured","exclude_unclassified","exclude_uncultured","include_all"],[100,100,100,100,100,100,100,100],[70,70,70,70,70,71,99,99],[0,0,0,0,100,100,100,100],[31482,31482,31482,31482,79268,128366,494304,544820]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>set<\/th>\n      <th>genus<\/th>\n      <th>species<\/th>\n      <th>strain<\/th>\n      <th>total<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[2,3,4,5]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
 </div>
 <div class="section level2">
 <h2 id="creating-a-data-tree-stucture-based-on-strains-using-the-exclude-unclassified-and-uncultured-set">Creating a data.tree stucture based on strains using the exclude
diff --git a/articles/phytools.html b/articles/phytools.html
index 64525b4..e1c8e8b 100644
--- a/articles/phytools.html
+++ b/articles/phytools.html
@@ -426,7 +426,7 @@ <h2 id="first-part-of-asrinh">First part of ASR/INH<a class="anchor" aria-label=
 <span><span class="op">)</span></span>
 <span><span class="co">#&gt; Warning in log(pp): NaNs produced</span></span>
 <span><span class="co">#&gt;    user  system elapsed </span></span>
-<span><span class="co">#&gt;  73.381  24.076 412.266</span></span>
+<span><span class="co">#&gt;  59.197  18.834 322.338</span></span>
 <span><span class="co">## A few seconds or minutes with fitMK.parellel</span></span></code></pre></div>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span></span>
@@ -434,7 +434,7 @@ <h2 id="first-part-of-asrinh">First part of ASR/INH<a class="anchor" aria-label=
 <span>    <span class="va">ace</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/phytools/man/ancr.html" class="external-link">ancr</a></span><span class="op">(</span><span class="va">fit</span>, type <span class="op">=</span> <span class="st">'marginal'</span><span class="op">)</span> <span class="co"># don't include tips</span></span>
 <span><span class="op">)</span></span>
 <span><span class="co">#&gt;    user  system elapsed </span></span>
-<span><span class="co">#&gt;  39.838  12.755  27.624</span></span></code></pre></div>
+<span><span class="co">#&gt;  30.312   9.489  20.816</span></span></code></pre></div>
 <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">node_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html" class="external-link">as_tibble</a></span><span class="op">(</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/modify.html" class="external-link">modify</a></span><span class="op">(</span><span class="fu"><a href="../reference/mpa.html">mpa</a></span><span class="op">(</span><span class="st">'nodes'</span><span class="op">)</span>, <span class="va">as.character</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="va">res</span> <span class="op">&lt;-</span> <span class="va">ace</span><span class="op">$</span><span class="va">ace</span></span>
diff --git a/pkgdown.yml b/pkgdown.yml
index bdbcb98..0c2f49f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,7 +6,7 @@ articles:
   phylogenetic_trees: phylogenetic_trees.html
   phytools: phytools.html
   taxPPro: taxPPro.html
-last_built: 2023-09-21T19:14Z
+last_built: 2023-09-21T20:55Z
 urls:
   reference: https://sdgamboa.github.io/taxPPro/reference
   article: https://sdgamboa.github.io/taxPPro/articles