diff --git a/404.html b/404.html
index 43e8591..0f19f17 100644
--- a/404.html
+++ b/404.html
@@ -49,7 +49,7 @@
   </a>
   <ul class="dropdown-menu" role="menu">
 <li>
-      <a href="https://sdgamboa.github.io/taxPPro/articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="https://sdgamboa.github.io/taxPPro/articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul>
 </li>
diff --git a/LICENSE-text.html b/LICENSE-text.html
index ffde16f..4c051e1 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/LICENSE.html b/LICENSE.html
index 73695aa..3f211c5 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/articles/index.html b/articles/index.html
index 60cdc1a..f83a82f 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
@@ -57,7 +57,7 @@ <h1>Articles</h1>
       <h3>All vignettes</h3>
       <p class="section-desc"></p>
 
-      <dl><dt><a href="phytools.html">A propagation workflow with phytools</a></dt>
+      <dl><dt><a href="phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a></dt>
         <dd>
       </dd></dl></div>
   </div>
diff --git a/articles/phytools.html b/articles/phytools.html
index c17254d..45291a5 100644
--- a/articles/phytools.html
+++ b/articles/phytools.html
@@ -5,13 +5,13 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>A propagation workflow with phytools • taxPPro</title>
+<title>A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance • taxPPro</title>
 <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
 <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script><meta property="og:title" content="A propagation workflow with phytools">
+<script src="../pkgdown.js"></script><meta property="og:title" content="A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance">
 <meta property="og:description" content="taxPPro">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -50,7 +50,7 @@
   </a>
   <ul class="dropdown-menu" role="menu">
 <li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul>
 </li>
@@ -75,7 +75,8 @@
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
-      <h1 data-toc-skip>A propagation workflow with phytools</h1>
+      <h1 data-toc-skip>A propagation workflow with taxonomic pooling,
+asr (phytools), and inhertiance</h1>
             
       
       <small class="dont-index">Source: <a href="https://github.com/sdgamboa/taxPPro/blob/HEAD/vignettes/articles/phytools.Rmd" class="external-link"><code>vignettes/articles/phytools.Rmd</code></a></small>
@@ -106,9 +107,10 @@ <h2 id="filter-data">Filter data<a class="anchor" aria-label="anchor" href="#fil
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">select_cols</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
 <span>    <span class="co">## Columns with information needed for propagation</span></span>
-<span>    <span class="st">'NCBI_ID'</span>, <span class="st">'Taxon_name'</span>, <span class="st">'Attribute'</span>, <span class="st">'Attribute_source'</span>,</span>
-<span>    <span class="st">'Frequency'</span>, <span class="st">'Score'</span>, <span class="st">'Parent_NCBI_ID'</span>, <span class="st">'Confidence_in_curation'</span>,</span>
-<span>    <span class="st">'Rank'</span>, <span class="st">'Evidence'</span>,</span>
+<span>    <span class="st">'NCBI_ID'</span>, <span class="st">'Taxon_name'</span>, <span class="st">'Attribute'</span>,</span>
+<span>    <span class="st">'Frequency'</span>, <span class="st">'Score'</span>, <span class="st">'Evidence'</span>, </span>
+<span>    <span class="st">'Attribute_source'</span>, <span class="st">'Confidence_in_curation'</span>,</span>
+<span>    <span class="st">'Parent_NCBI_ID'</span>,</span>
 <span>    </span>
 <span>    <span class="co">## Columns only used for controlling the behavior of the code</span></span>
 <span>    <span class="st">'Attribute_type'</span>, <span class="st">'Attribute_group'</span></span>
@@ -124,12 +126,10 @@ <h2 id="filter-data">Filter data<a class="anchor" aria-label="anchor" href="#fil
 <span>    <span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">phys_data</span> <span class="op">&lt;-</span> <span class="va">phys</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span> <span class="op">|&gt;</span> </span>
 <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="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="co"># filter(!is.na(Rank), Rank %in% valid_ranks) |&gt;</span></span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">Attribute_value</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="co"># only for discrete traits with multiple states </span></span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">Attribute</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">valid_attributes</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
-<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">Rank</span><span class="op">)</span>, <span class="va">Rank</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">valid_ranks</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span></span>
-<span>        <span class="co">## Filter rows with NCBI_ID.</span></span>
-<span>        <span class="co">## If NCBI_ID is missing, Parent_NCBI_ID must be present</span></span>
 <span>        <span class="op">!</span><span class="op">(</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">NCBI_ID</span><span class="op">)</span> <span class="op">|</span> <span class="va">NCBI_ID</span> <span class="op">==</span> <span class="st">'unknown'</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">Parent_NCBI_ID</span><span class="op">)</span><span class="op">)</span></span>
 <span>    <span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="st">'Attribute_source'</span><span class="op">)</span>, <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="st">'Frequency'</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span></span>
@@ -145,7 +145,7 @@ <h2 id="filter-data">Filter data<a class="anchor" aria-label="anchor" href="#fil
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/distinct.html" class="external-link">distinct</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="va">n_dropped_rows</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">phys</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">phys_data</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/message.html" class="external-link">message</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">n_dropped_rows</span>, big.mark <span class="op">=</span> <span class="st">','</span><span class="op">)</span>, <span class="st">' rows were dropped.'</span><span class="op">)</span></span>
-<span><span class="co">#&gt; 3,952 rows were dropped.</span></span></code></pre></div>
+<span><span class="co">#&gt; 3,891 rows were dropped.</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="taxonomic-pooling-for-taxa-without-ncbi_id-taxid">Taxonomic pooling for taxa without NCBI_ID (taxid)<a class="anchor" aria-label="anchor" href="#taxonomic-pooling-for-taxa-without-ncbi_id-taxid"></a>
@@ -155,9 +155,11 @@ <h2 id="taxonomic-pooling-for-taxa-without-ncbi_id-taxid">Taxonomic pooling for
 <code class="sourceCode R"><span><span class="va">lgl_vct</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">phys_data</span><span class="op">$</span><span class="va">NCBI_ID</span><span class="op">)</span> <span class="op">|</span> <span class="va">phys_data</span><span class="op">$</span><span class="va">NCBI_ID</span> <span class="op">==</span> <span class="st">'unknown'</span></span>
 <span><span class="va">set_with_ids</span> <span class="op">&lt;-</span> <span class="va">phys_data</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="va">lgl_vct</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
-<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">NCBI_ID</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
-<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Taxon_name <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="va">Taxon_name</span><span class="op">)</span><span class="op">)</span>, collapse <span class="op">=</span> <span class="st">'|'</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
-<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
+<span>        Rank <span class="op">=</span> <span class="fu">taxizedb</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/taxizedb/reference/taxid2rank.html" class="external-link">taxid2rank</a></span><span class="op">(</span><span class="va">NCBI_ID</span>, db <span class="op">=</span> <span class="st">'ncbi'</span><span class="op">)</span></span>
+<span>    <span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">Rank</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">valid_ranks</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Taxon_name <span class="op">=</span> <span class="fu">taxizedb</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/taxizedb/reference/taxid2name.html" class="external-link">taxid2name</a></span><span class="op">(</span><span class="va">NCBI_ID</span>, db <span class="op">=</span> <span class="st">'ncbi'</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/distinct.html" class="external-link">distinct</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">NCBI_ID</span>, <span class="va">Attribute</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/slice.html" class="external-link">slice_head</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
@@ -168,84 +170,14 @@ <h2 id="taxonomic-pooling-for-taxa-without-ncbi_id-taxid">Taxonomic pooling for
 <span>        Score <span class="op">=</span> <span class="va">Score</span> <span class="op">/</span> <span class="va">Total_score</span></span>
 <span>    <span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">Parent_NCBI_ID</span>, <span class="op">-</span><span class="va">Total_score</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/distinct.html" class="external-link">distinct</a></span><span class="op">(</span><span class="op">)</span></span>
-<span><span class="va">w</span> <span class="op">&lt;-</span> <span class="cn">NULL</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/base/conditions.html" class="external-link">withCallingHandlers</a></span><span class="op">(</span></span>
-<span>    warning <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">cnd</span><span class="op">)</span> <span class="va">w</span> <span class="op">&lt;&lt;-</span> <span class="va">cnd</span>,</span>
-<span>    <span class="va">set_with_ids</span><span class="op">$</span><span class="va">Rank</span> <span class="op">&lt;-</span> <span class="fu">taxizedb</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/taxizedb/reference/taxid2rank.html" class="external-link">taxid2rank</a></span><span class="op">(</span><span class="va">set_with_ids</span><span class="op">$</span><span class="va">NCBI_ID</span>, db <span class="op">=</span> <span class="st">'ncbi'</span><span class="op">)</span></span>
-<span><span class="op">)</span></span>
-<span><span class="co">#&gt; Warning in taxizedb::taxid2rank(set_with_ids$NCBI_ID, db = "ncbi"): No rank</span></span>
-<span><span class="co">#&gt; found for 18 of 9767 taxon IDs. The followings are left unrankd: 1398560,</span></span>
-<span><span class="co">#&gt; 1400058, 1551, 1560, 168810, 1796653, 1830421, 220622, 263820, 307251, 342610,</span></span>
-<span><span class="co">#&gt; 355929, 440512, 513651, 65497, 68570, 84593, 93930</span></span>
-<span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">w</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
-<span>    <span class="va">taxids_with_missing_rank</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/unlist.html" class="external-link">unlist</a></span><span class="op">(</span></span>
-<span>        <span class="fu"><a href="https://rdrr.io/r/base/strsplit.html" class="external-link">strsplit</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">sub</a></span><span class="op">(</span><span class="st">'^.*: (.*$)'</span>, <span class="st">'\\1'</span>, <span class="va">w</span><span class="op">$</span><span class="va">message</span><span class="op">)</span>, <span class="st">', '</span><span class="op">)</span></span>
-<span>    <span class="op">)</span></span>
-<span>    <span class="va">no_longer_missing_ranks</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/unlist.html" class="external-link">unlist</a></span><span class="op">(</span></span>
-<span>        <span class="fu">taxize</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/taxize/reference/tax_rank.html" class="external-link">tax_rank</a></span><span class="op">(</span><span class="va">taxids_with_missing_rank</span>, db <span class="op">=</span> <span class="st">'ncbi'</span><span class="op">)</span></span>
-<span>    <span class="op">)</span></span>
-<span>    <span class="kw">for</span> <span class="op">(</span><span class="va">i</span> <span class="kw">in</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_along</a></span><span class="op">(</span><span class="va">no_longer_missing_ranks</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
-<span>        <span class="va">pos</span> <span class="op">&lt;-</span> <span class="va">set_with_ids</span><span class="op">$</span><span class="va">NCBI_ID</span> <span class="op">==</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">no_longer_missing_ranks</span><span class="op">)</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span>
-<span>        <span class="va">set_with_ids</span><span class="op">$</span><span class="va">Rank</span><span class="op">[</span><span class="va">pos</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="va">no_longer_missing_ranks</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span>
-<span>    <span class="op">}</span></span>
-<span><span class="op">}</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
+<span><span class="co">#&gt; Warning: There was 1 warning in `mutate()`.</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> In argument: `Rank = taxizedb::taxid2rank(NCBI_ID, db = "ncbi")`.</span></span>
+<span><span class="co">#&gt; Caused by warning in `taxizedb::taxid2rank()`:</span></span>
+<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> No rank found for 79 of 10425 taxon IDs. The followings are left unrankd: 65497, 287094, 196083, 136160, 513651, 1606016, 1646339, 126790, 1830421, 1400058, 165807, 134962, 48937, 263820, 1311788, 342610, 166934, 1398496, 307251, 262776, 45461, 211759, 244407, 332057, 332056, 46170, 46170, 68202, 84593, 62153, 109214, 1398560, 355929, 1551, 1560, 86662, 168810, 495036, 1345697, 1166016, 741091, 195041, 140100, 62153, 675810, 65497, 861208, 340044, 335659, 546899, 656024, 440512, 147710, 931223, 420233, 332056, 68570, 68202, 563191, 665937, 469586, 469587, 665938, 469594, 52765, 52766, 699245, 97139, 327817, 644968, 228748, 477693, 652712, 796939, 796940, 36876, 93930, 220622, 1796653</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">set_with_ids</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 9767   13</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 9668   11</span></span></code></pre></div>
 <p>Get attribute annotations and scores for taxa without NCBI_ID from
 sources:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
@@ -253,44 +185,12 @@ <h2 id="taxonomic-pooling-for-taxa-without-ncbi_id-taxid">Taxonomic pooling for
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">lgl_vct</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">NCBI_ID</span>, <span class="op">-</span><span class="va">Taxon_name</span>, <span class="op">-</span><span class="va">Frequency</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/relocate.html" class="external-link">relocate</a></span><span class="op">(</span>NCBI_ID <span class="op">=</span> <span class="va">Parent_NCBI_ID</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
-<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/distinct.html" class="external-link">distinct</a></span><span class="op">(</span><span class="op">)</span></span>
-<span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">set_with_ids</span><span class="op">)</span> <span class="op">&gt;</span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span></span>
-<span>    <span class="va">set_without_ids</span> <span class="op">&lt;-</span> <span class="va">set_without_ids</span> <span class="op">|&gt;</span> </span>
-<span>        <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="va">NCBI_ID</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="va">set_with_ids</span><span class="op">$</span><span class="va">NCBI_ID</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="op">}</span></span>
-<span><span class="va">w2</span> <span class="op">&lt;-</span> <span class="cn">NULL</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/base/conditions.html" class="external-link">withCallingHandlers</a></span><span class="op">(</span></span>
-<span>    warning <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">cnd</span><span class="op">)</span> <span class="va">w2</span> <span class="op">&lt;&lt;-</span> <span class="va">cnd</span>,</span>
-<span>    <span class="va">set_without_ids</span><span class="op">$</span><span class="va">Rank</span> <span class="op">&lt;-</span> <span class="fu">taxizedb</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/taxizedb/reference/taxid2rank.html" class="external-link">taxid2rank</a></span><span class="op">(</span><span class="va">set_without_ids</span><span class="op">$</span><span class="va">NCBI_ID</span>, db <span class="op">=</span> <span class="st">'ncbi'</span><span class="op">)</span></span>
-<span><span class="op">)</span></span>
-<span><span class="co">#&gt; Warning in taxizedb::taxid2rank(set_without_ids$NCBI_ID, db = "ncbi"): No rank</span></span>
-<span><span class="co">#&gt; found for 4 of 6631 taxon IDs. The followings are left unrankd: 2751472,</span></span>
-<span><span class="co">#&gt; 2679994, 1704088, 648567</span></span>
-<span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">w2</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
-<span>    <span class="va">taxids_with_missing_rank2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/unlist.html" class="external-link">unlist</a></span><span class="op">(</span></span>
-<span>        <span class="fu"><a href="https://rdrr.io/r/base/strsplit.html" class="external-link">strsplit</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">sub</a></span><span class="op">(</span><span class="st">'^.*: (.*$)'</span>, <span class="st">'\\1'</span>, <span class="va">w2</span><span class="op">$</span><span class="va">message</span><span class="op">)</span>, <span class="st">', '</span><span class="op">)</span></span>
-<span>    <span class="op">)</span></span>
-<span>    <span class="va">no_longer_missing_ranks2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/unlist.html" class="external-link">unlist</a></span><span class="op">(</span></span>
-<span>        <span class="fu">taxize</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/taxize/reference/tax_rank.html" class="external-link">tax_rank</a></span><span class="op">(</span><span class="va">taxids_with_missing_rank2</span>, db <span class="op">=</span> <span class="st">'ncbi'</span><span class="op">)</span></span>
-<span>    <span class="op">)</span></span>
-<span>    <span class="kw">for</span> <span class="op">(</span><span class="va">i</span> <span class="kw">in</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_along</a></span><span class="op">(</span><span class="va">no_longer_missing_ranks2</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
-<span>        <span class="va">pos2</span> <span class="op">&lt;-</span> <span class="va">set_without_ids</span><span class="op">$</span><span class="va">NCBI_ID</span> <span class="op">==</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">no_longer_missing_ranks2</span><span class="op">)</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span>
-<span>        <span class="va">set_without_ids</span><span class="op">$</span><span class="va">Rank</span><span class="op">[</span><span class="va">pos2</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="va">no_longer_missing_ranks2</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span>
-<span>    <span class="op">}</span></span>
-<span><span class="op">}</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="co">#&gt; No ENTREZ API key provided</span></span>
-<span><span class="co">#&gt;  Get one via taxize::use_entrez()</span></span>
-<span><span class="co">#&gt; See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/</span></span>
-<span><span class="va">set_without_ids</span> <span class="op">&lt;-</span> <span class="va">set_without_ids</span> <span class="op">|&gt;</span>    </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
+<span>        Rank <span class="op">=</span> <span class="fu">taxizedb</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/taxizedb/reference/taxid2rank.html" class="external-link">taxid2rank</a></span><span class="op">(</span><span class="va">NCBI_ID</span>, db <span class="op">=</span> <span class="st">'ncbi'</span><span class="op">)</span></span>
+<span>    <span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">Rank</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">valid_ranks</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Taxon_name <span class="op">=</span> <span class="fu">taxizedb</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/taxizedb/reference/taxid2name.html" class="external-link">taxid2name</a></span><span class="op">(</span><span class="va">NCBI_ID</span>, db <span class="op">=</span> <span class="st">'ncbi'</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/distinct.html" class="external-link">distinct</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">NCBI_ID</span>, <span class="va">Attribute</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/slice.html" class="external-link">slice_head</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
@@ -301,12 +201,17 @@ <h2 id="taxonomic-pooling-for-taxa-without-ncbi_id-taxid">Taxonomic pooling for
 <span>    <span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>Evidence <span class="op">=</span> <span class="st">'tax'</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">Total_score</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="va">NCBI_ID</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="va">set_with_ids</span><span class="op">$</span><span class="va">NCBI_ID</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/distinct.html" class="external-link">distinct</a></span><span class="op">(</span><span class="op">)</span></span>
+<span><span class="co">#&gt; Warning: There was 1 warning in `mutate()`.</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> In argument: `Rank = taxizedb::taxid2rank(NCBI_ID, db = "ncbi")`.</span></span>
+<span><span class="co">#&gt; Caused by warning in `taxizedb::taxid2rank()`:</span></span>
+<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> No rank found for 4 of 15276 taxon IDs. The followings are left unrankd: 2751472, 2679994, 1704088, 648567</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">set_without_ids</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 6631   10</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 6503   10</span></span></code></pre></div>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">phys_data_ready</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows</a></span><span class="op">(</span><span class="va">set_with_ids</span>, <span class="va">set_without_ids</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
-<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">Total_score</span>, <span class="op">-</span><span class="va">Parent_NCBI_ID</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span>
 <span>        NCBI_ID <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when</a></span><span class="op">(</span></span>
 <span>            <span class="va">Rank</span> <span class="op">==</span> <span class="st">'strain'</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">'t__'</span>, <span class="va">NCBI_ID</span><span class="op">)</span>,</span>
@@ -315,16 +220,12 @@ <h2 id="taxonomic-pooling-for-taxa-without-ncbi_id-taxid">Taxonomic pooling for
 <span>            <span class="cn">TRUE</span> <span class="op">~</span> <span class="cn">NA</span></span>
 <span>        <span class="op">)</span></span>
 <span>    <span class="op">)</span> <span class="op">|&gt;</span> </span>
-<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">NCBI_ID</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
+<span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">NCBI_ID</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="co"># NAs migth be added because of the mutate call above</span></span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>taxid <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">sub</a></span><span class="op">(</span><span class="st">'^\\w__'</span>, <span class="st">''</span>, <span class="va">NCBI_ID</span><span class="op">)</span><span class="op">)</span></span>
-<span>    <span class="co"># complete(</span></span>
-<span>    <span class="co">#     NCBI_ID, Taxon_name, Rank, Attribute, Attribute_type, Attribute_group,</span></span>
-<span>    <span class="co">#     fill = list(Score = 0, Frequency = 'neve')</span></span>
-<span>    <span class="co"># ) </span></span>
 <span><span class="co">## Split in lists to use with the NCBI taxonomic tree</span></span>
 <span><span class="va">phys_data_list</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/split.html" class="external-link">split</a></span><span class="op">(</span><span class="va">phys_data_ready</span>, <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">phys_data_ready</span><span class="op">$</span><span class="va">NCBI_ID</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">phys_data_list</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 15893</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 15872</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="tree-data">Tree data<a class="anchor" aria-label="anchor" href="#tree-data"></a>
@@ -336,24 +237,8 @@ <h3 id="taxonomic-tree">Taxonomic tree<a class="anchor" aria-label="anchor" href
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">'tree_list'</span><span class="op">)</span></span>
 <span><span class="va">ncbi_tree</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/data.tree/man/as.Node.html" class="external-link">as.Node</a></span><span class="op">(</span><span class="va">tree_list</span><span class="op">)</span></span>
 <span><span class="va">ncbi_tree_nodes</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/unname.html" class="external-link">unname</a></span><span class="op">(</span><span class="va">ncbi_tree</span><span class="op">$</span><span class="fu">Get</span><span class="op">(</span><span class="st">'name'</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">ncbi_tree</span>, limit <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span>
-<span><span class="co">#&gt;                                            levelName</span></span>
-<span><span class="co">#&gt; 1  ArcBac                                           </span></span>
-<span><span class="co">#&gt; 2   ¦--d__2                                         </span></span>
-<span><span class="co">#&gt; 3   ¦   ¦--p__1224                                  </span></span>
-<span><span class="co">#&gt; 4   ¦   ¦   ¦--c__28211                             </span></span>
-<span><span class="co">#&gt; 5   ¦   ¦   ¦   ¦--o__356                           </span></span>
-<span><span class="co">#&gt; 6   ¦   ¦   ¦   ¦   ¦--f__335928                    </span></span>
-<span><span class="co">#&gt; 7   ¦   ¦   ¦   ¦   ¦   ¦--g__99                    </span></span>
-<span><span class="co">#&gt; 8   ¦   ¦   ¦   ¦   ¦   ¦   ¦--s__100               </span></span>
-<span><span class="co">#&gt; 9   ¦   ¦   ¦   ¦   ¦   ¦   ¦--s__1282440           </span></span>
-<span><span class="co">#&gt; 10  ¦   ¦   ¦   ¦   ¦   ¦   °--... 15 nodes w/ 0 sub</span></span>
-<span><span class="co">#&gt; 11  ¦   ¦   ¦   ¦   ¦   °--... 6 nodes w/ 49 sub    </span></span>
-<span><span class="co">#&gt; 12  ¦   ¦   ¦   ¦   °--... 41 nodes w/ 2405 sub     </span></span>
-<span><span class="co">#&gt; 13  ¦   ¦   ¦   °--... 20 nodes w/ 5970 sub         </span></span>
-<span><span class="co">#&gt; 14  ¦   ¦   °--... 5 nodes w/ 24398 sub             </span></span>
-<span><span class="co">#&gt; 15  ¦   °--... 58 nodes w/ 73761 sub                </span></span>
-<span><span class="co">#&gt; 16  °--... 1 nodes w/ 75454 sub</span></span></code></pre></div>
+<span><span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">ncbi_tree</span><span class="op">)</span></span>
+<span><span class="co">#&gt; [1] "Node" "R6"</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="phylogenectic-tree">Phylogenectic tree<a class="anchor" aria-label="anchor" href="#phylogenectic-tree"></a>
@@ -391,16 +276,16 @@ <h3 id="some-completeness-stats">Some completeness stats<a class="anchor" aria-l
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">ncbi_tree_nodes_gst</span> <span class="op">&lt;-</span> <span class="va">ncbi_tree_nodes</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">'^[wst]__'</span>, <span class="va">ncbi_tree_nodes</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">phys_data_ready</span><span class="op">$</span><span class="va">NCBI_ID</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">ncbi_tree_nodes_gst</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 0.8963068</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 0.8973471</span></span></code></pre></div>
 <p>Proportion of NCBI tree nodes (gst) with annotations:</p>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">ncbi_tree_nodes_gst</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">phys_data_ready</span><span class="op">$</span><span class="va">NCBI_ID</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 0.2057614</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 0.2057325</span></span></code></pre></div>
 <p>Annotations from sources than can me mapped to the phylogenetic tree
 tips:</p>
 <div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">phys_data_ready</span><span class="op">$</span><span class="va">taxid</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">tip_data</span><span class="op">$</span><span class="va">taxid</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 0.6353137</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 0.6361388</span></span></code></pre></div>
 <p>Proportion of tips in the phylogenetic tree with annotations:</p>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">tip_data</span><span class="op">$</span><span class="va">taxid</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">phys_data_ready</span><span class="op">$</span><span class="va">taxid</span><span class="op">)</span></span>
@@ -413,8 +298,6 @@ <h2 id="increase-number-of-tips-with-annotations">Increase number of tips with a
 <div class="section level3">
 <h3 id="map-ncbi-ids-to-the-ncbi-taxonomic-tree">Map NCBI IDs to the NCBI taxonomic tree<a class="anchor" aria-label="anchor" href="#map-ncbi-ids-to-the-ncbi-taxonomic-tree"></a>
 </h3>
-<p>At this point only genus, species, and strain annotations are
-present.</p>
 <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">ncbi_tree</span><span class="op">$</span><span class="fu">Do</span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">node</span><span class="op">)</span> <span class="op">{</span></span>
 <span>    <span class="kw">if</span> <span class="op">(</span><span class="va">node</span><span class="op">$</span><span class="va">name</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">phys_data_list</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
@@ -426,18 +309,18 @@ <h3 id="map-ncbi-ids-to-the-ncbi-taxonomic-tree">Map NCBI IDs to the NCBI taxono
 <span><span class="co">## An example (E. coli):</span></span>
 <span><span class="va">ncbi_tree</span><span class="op">$</span><span class="va">d__2</span><span class="op">$</span><span class="va">p__1224</span><span class="op">$</span><span class="va">c__1236</span><span class="op">$</span><span class="va">o__91347</span><span class="op">$</span><span class="va">f__543</span><span class="op">$</span><span class="va">g__561</span><span class="op">$</span><span class="va">s__562</span><span class="op">$</span><span class="va">attribute_tbl</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2 × 12</span></span></span>
-<span><span class="co">#&gt;   NCBI_ID Taxon_name       Attribute            Attribute_source Frequency Score</span></span>
-<span><span class="co">#&gt;   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>            <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>            <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> s__562  Escherichia coli aerobic              Madin_2020       always      0.5</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> s__562  Escherichia coli facultatively anaer… ProTraits        always      0.5</span></span>
-<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 6 more variables: Confidence_in_curation &lt;chr&gt;, Rank &lt;chr&gt;, Evidence &lt;chr&gt;,</span></span></span>
-<span><span class="co">#&gt; <span style="color: #949494;">#   Attribute_type &lt;chr&gt;, Attribute_group &lt;chr&gt;, taxid &lt;chr&gt;</span></span></span></code></pre></div>
+<span><span class="co">#&gt;   NCBI_ID Taxon_name       Attribute   Frequency Score Evidence Attribute_source</span></span>
+<span><span class="co">#&gt;   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>            <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> s__562  Escherichia coli aerobic     always      0.5 tas      Madin_2020      </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> s__562  Escherichia coli facultativ… always      0.5 igc      ProTraits       </span></span>
+<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 5 more variables: Confidence_in_curation &lt;chr&gt;, Attribute_type &lt;chr&gt;,</span></span></span>
+<span><span class="co">#&gt; <span style="color: #949494;">#   Attribute_group &lt;chr&gt;, Rank &lt;chr&gt;, taxid &lt;chr&gt;</span></span></span></code></pre></div>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">ncbi_attr_gst</span> <span class="op">&lt;-</span> <span class="va">ncbi_tree</span><span class="op">$</span><span class="fu">Get</span><span class="op">(</span></span>
 <span>    <span class="st">'attribute_tbl'</span>, filterFun <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">node</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">'^[gst]__'</span>, <span class="va">node</span><span class="op">$</span><span class="va">name</span><span class="op">)</span></span>
 <span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map_lgl</a></span><span class="op">(</span><span class="va">ncbi_attr_gst</span>, <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">.x</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 0.208442</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 0.2084015</span></span></code></pre></div>
 <p>Removing annotations just to compare with result after
 propagation</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
@@ -509,7 +392,7 @@ <h3 id="map-ncbi-ids-to-the-ncbi-taxonomic-tree">Map NCBI IDs to the NCBI taxono
 zero)</p>
 <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">ncbi_attr_kpcof</span> <span class="op">&lt;-</span> <span class="va">ncbi_tree</span><span class="op">$</span><span class="fu">Get</span><span class="op">(</span></span>
-<span>    <span class="st">'attribute_tbl'</span>, filterFun <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">node</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">'^[kpcor]__'</span>, <span class="va">node</span><span class="op">$</span><span class="va">name</span><span class="op">)</span></span>
+<span>    <span class="st">'attribute_tbl'</span>, filterFun <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">node</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">'^[dpcor]__'</span>, <span class="va">node</span><span class="op">$</span><span class="va">name</span><span class="op">)</span></span>
 <span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map_lgl</a></span><span class="op">(</span><span class="va">ncbi_attr_kpcof</span>, <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">.x</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] 0</span></span></code></pre></div>
@@ -520,7 +403,7 @@ <h3 id="map-ncbi-ids-to-the-ncbi-taxonomic-tree">Map NCBI IDs to the NCBI taxono
 <span><span class="op">)</span></span>
 <span><span class="co">## A slight increase 12 to 15%</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map_lgl</a></span><span class="op">(</span><span class="va">ncbi_attr_gst</span>, <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">.x</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 0.2457337</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 0.2457067</span></span></code></pre></div>
 <p>Child taxa of E. coli with unobserved annotations can inherit these
 values with a slight penalty:</p>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
@@ -545,8 +428,8 @@ <h3 id="map-ncbi-ids-to-the-ncbi-taxonomic-tree">Map NCBI IDs to the NCBI taxono
 <span>    <span class="op">}</span></span>
 <span><span class="op">}</span></span>
 <span><span class="va">ncbi_tree</span><span class="op">$</span><span class="fu">Do</span><span class="op">(</span><span class="va">inh1</span>, traversal <span class="op">=</span> <span class="st">'pre-order'</span><span class="op">)</span></span></code></pre></div>
-<p>Proportion of nodes at the family level and above with
-attributes:</p>
+<p>Proportion of nodes at the family level and above with attributes (it
+should be zero):</p>
 <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">ncbi_attr_kpcof</span> <span class="op">&lt;-</span> <span class="va">ncbi_tree</span><span class="op">$</span><span class="fu">Get</span><span class="op">(</span></span>
 <span>    <span class="st">'attribute_tbl'</span>, filterFun <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">node</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">'^[kpcor]__'</span>, <span class="va">node</span><span class="op">$</span><span class="va">name</span><span class="op">)</span></span>
@@ -578,7 +461,7 @@ <h3 id="map-ncbi-ids-to-the-ncbi-taxonomic-tree">Map NCBI IDs to the NCBI taxono
 <span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">new_attributes</span><span class="op">$</span><span class="va">Evidence</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt;   exp   igc   inh   nas   tas   tax </span></span>
-<span><span class="co">#&gt;  3568  1106 65314  1284  3727  9511</span></span></code></pre></div>
+<span><span class="co">#&gt;  3562  1102 65321  1282  3722  9508</span></span></code></pre></div>
 <p>Now almost 90% of the tips have annotations:</p>
 <div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">tip_data</span><span class="op">$</span><span class="va">taxid</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="va">new_attributes</span><span class="op">$</span><span class="va">taxid</span><span class="op">)</span></span>
@@ -659,12 +542,12 @@ <h2 id="asr-with-phytools">ASR with phytools<a class="anchor" aria-label="anchor
 <span>    <span class="va">asr</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/phytools/man/ancr.html" class="external-link">ancr</a></span><span class="op">(</span>object <span class="op">=</span> <span class="va">fit</span>, tips <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span><span class="op">}</span><span class="op">)</span></span>
 <span><span class="co">#&gt;    user  system elapsed </span></span>
-<span><span class="co">#&gt; 585.378 201.048 413.176</span></span></code></pre></div>
+<span><span class="co">#&gt; 559.238 212.146 402.743</span></span></code></pre></div>
 <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">res</span> <span class="op">&lt;-</span> <span class="va">asr</span><span class="op">$</span><span class="va">ace</span></span>
 <span><span class="va">node_rows</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">tree</span><span class="op">$</span><span class="va">tip.label</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span><span class="op">:</span><span class="va">tree</span><span class="op">$</span><span class="va">Nnode</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">res</span><span class="op">)</span><span class="op">[</span><span class="va">node_rows</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="va">tree</span><span class="op">$</span><span class="va">node.label</span></span></code></pre></div>
-<p>Probabiliites of internal nodes</p>
+<p>Probabilities of internal nodes</p>
 <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>prob <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="va">res</span><span class="op">[</span><span class="va">tree</span><span class="op">$</span><span class="va">node.label</span>,<span class="op">]</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">prob</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
@@ -885,7 +768,7 @@ <h2 id="asr-with-phytools">ASR with phytools<a class="anchor" aria-label="anchor
 <span><span class="va">final_output</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">output</span>, <span class="va">addTaxa1</span>, <span class="va">addTaxa2</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">Score</span> <span class="op">&gt;</span> <span class="va">min_thr</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">final_output</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 89382    14</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 89365    14</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="session-information">Session information<a class="anchor" aria-label="anchor" href="#session-information"></a>
@@ -999,9 +882,7 @@ <h2 id="session-information">Session information<a class="anchor" aria-label="an
 <span><span class="co">#&gt;  tibble              3.2.1      <span style="color: #555555;">2023-03-20</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
 <span><span class="co">#&gt;  tidyr             * 1.3.0      <span style="color: #555555;">2023-01-24</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
 <span><span class="co">#&gt;  tidyselect          1.2.0      <span style="color: #555555;">2022-10-10</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  triebeard           0.4.1      <span style="color: #555555;">2023-03-04</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
 <span><span class="co">#&gt;  tzdb                0.4.0      <span style="color: #555555;">2023-05-12</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
-<span><span class="co">#&gt;  urltools            1.7.3      <span style="color: #555555;">2019-04-14</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
 <span><span class="co">#&gt;  utf8                1.2.3      <span style="color: #555555;">2023-01-31</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
 <span><span class="co">#&gt;  uuid                1.1-1      <span style="color: #555555;">2023-08-17</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
 <span><span class="co">#&gt;  vctrs               0.6.3      <span style="color: #555555;">2023-06-14</span> <span style="color: #555555;">[1]</span> <span style="color: #555555;">CRAN (R 4.3.1)</span></span></span>
diff --git a/articles/phytools_files/figure-html/unnamed-chunk-25-1.png b/articles/phytools_files/figure-html/unnamed-chunk-25-1.png
index ec64835..e3fded7 100644
Binary files a/articles/phytools_files/figure-html/unnamed-chunk-25-1.png and b/articles/phytools_files/figure-html/unnamed-chunk-25-1.png differ
diff --git a/articles/phytools_files/figure-html/unnamed-chunk-27-1.png b/articles/phytools_files/figure-html/unnamed-chunk-27-1.png
index 994599a..bf60284 100644
Binary files a/articles/phytools_files/figure-html/unnamed-chunk-27-1.png and b/articles/phytools_files/figure-html/unnamed-chunk-27-1.png differ
diff --git a/authors.html b/authors.html
index ca18436..d83de89 100644
--- a/authors.html
+++ b/authors.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/index.html b/index.html
index 98d6167..8e878dd 100644
--- a/index.html
+++ b/index.html
@@ -50,7 +50,7 @@
   </a>
   <ul class="dropdown-menu" role="menu">
 <li>
-      <a href="articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul>
 </li>
diff --git a/pkgdown.yml b/pkgdown.yml
index 78f98c4..7fbb0ad 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   phytools: phytools.html
-last_built: 2023-09-27T00:34Z
+last_built: 2023-09-27T03:13Z
 urls:
   reference: https://sdgamboa.github.io/taxPPro/reference
   article: https://sdgamboa.github.io/taxPPro/articles
diff --git a/reference/addAttributes.html b/reference/addAttributes.html
index 8143dbd..4de0704 100644
--- a/reference/addAttributes.html
+++ b/reference/addAttributes.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/addAttributesLogical.html b/reference/addAttributesLogical.html
index e8b4c6d..89f3e05 100644
--- a/reference/addAttributesLogical.html
+++ b/reference/addAttributesLogical.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/addAttributesNumeric.html b/reference/addAttributesNumeric.html
index 80fc914..7eada42 100644
--- a/reference/addAttributesNumeric.html
+++ b/reference/addAttributesNumeric.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/addAttributesRange.html b/reference/addAttributesRange.html
index 8355182..8dc87ce 100644
--- a/reference/addAttributesRange.html
+++ b/reference/addAttributesRange.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/addStrains.html b/reference/addStrains.html
index 7ed084f..3a5537e 100644
--- a/reference/addStrains.html
+++ b/reference/addStrains.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/asr.html b/reference/asr.html
index a1d8d6a..5e6c1c5 100644
--- a/reference/asr.html
+++ b/reference/asr.html
@@ -34,7 +34,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/asrUpstreamLogical.html b/reference/asrUpstreamLogical.html
index 8a4a21d..4e159f3 100644
--- a/reference/asrUpstreamLogical.html
+++ b/reference/asrUpstreamLogical.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/asrUpstreamNumeric.html b/reference/asrUpstreamNumeric.html
index 503236c..92f59ea 100644
--- a/reference/asrUpstreamNumeric.html
+++ b/reference/asrUpstreamNumeric.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/asrUpstreamRange.html b/reference/asrUpstreamRange.html
index 32134fb..9e2e64d 100644
--- a/reference/asrUpstreamRange.html
+++ b/reference/asrUpstreamRange.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/calcParentScore.html b/reference/calcParentScore.html
index 5c9e166..e3f58e2 100644
--- a/reference/calcParentScore.html
+++ b/reference/calcParentScore.html
@@ -34,7 +34,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/calcParentScores.html b/reference/calcParentScores.html
index 92051db..8923844 100644
--- a/reference/calcParentScores.html
+++ b/reference/calcParentScores.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/chooseColVal.html b/reference/chooseColVal.html
index 6f551f9..25dd04e 100644
--- a/reference/chooseColVal.html
+++ b/reference/chooseColVal.html
@@ -33,7 +33,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/classif2Table.html b/reference/classif2Table.html
index b28bd3b..a9ac80b 100644
--- a/reference/classif2Table.html
+++ b/reference/classif2Table.html
@@ -33,7 +33,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/fillNAs.html b/reference/fillNAs.html
index 940f64e..be53229 100644
--- a/reference/fillNAs.html
+++ b/reference/fillNAs.html
@@ -32,7 +32,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/freq2Scores.html b/reference/freq2Scores.html
index 2f5ffa7..34cfeed 100644
--- a/reference/freq2Scores.html
+++ b/reference/freq2Scores.html
@@ -34,7 +34,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/getAgreements.html b/reference/getAgreements.html
index 202b1a1..5921d60 100644
--- a/reference/getAgreements.html
+++ b/reference/getAgreements.html
@@ -33,7 +33,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/getConflicts.html b/reference/getConflicts.html
index 411a423..9e8fc75 100644
--- a/reference/getConflicts.html
+++ b/reference/getConflicts.html
@@ -33,7 +33,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
     </li>
   </ul></li>
       </ul><ul class="nav navbar-nav navbar-right"><li>
diff --git a/reference/getDoubleAnnotations.html b/reference/getDoubleAnnotations.html
index 521884c..af24199 100644
--- a/reference/getDoubleAnnotations.html
+++ b/reference/getDoubleAnnotations.html
@@ -33,7 +33,7 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu"><li>
-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/getDuplicates.html b/reference/getDuplicates.html
index 815adb7..b0f455a 100644
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+++ b/reference/getDuplicates.html
@@ -35,7 +35,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/getMpaTable.html b/reference/getMpaTable.html
index 57ed53f..b9486f8 100644
--- a/reference/getMpaTable.html
+++ b/reference/getMpaTable.html
@@ -32,7 +32,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/getMpaTree.html b/reference/getMpaTree.html
index 138d824..2818473 100644
--- a/reference/getMpaTree.html
+++ b/reference/getMpaTree.html
@@ -32,7 +32,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/getNCBI.html b/reference/getNCBI.html
index d123c73..2ecec71 100644
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@@ -34,7 +34,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/index.html b/reference/index.html
index 18e48e8..3d952ab 100644
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@@ -32,7 +32,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/inh.html b/reference/inh.html
index 0533c9e..7a7cbf8 100644
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/inhDownstreamLogical.html b/reference/inhDownstreamLogical.html
index 2ff3f43..88e7021 100644
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/inhDownstreamNumeric.html b/reference/inhDownstreamNumeric.html
index 2f05f6e..7f5540d 100644
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/inhDownstreamRange.html b/reference/inhDownstreamRange.html
index 6a378bc..68899f5 100644
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/ltp.html b/reference/ltp.html
index 23a317f..f78bdd7 100644
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@@ -32,7 +32,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/mergeOriginalAndEarlyASR.html b/reference/mergeOriginalAndEarlyASR.html
index c17394d..cbb1dba 100644
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/mpa.html b/reference/mpa.html
index 40c4b14..86eac00 100644
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@@ -32,7 +32,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/prepareDataForPropagation.html b/reference/prepareDataForPropagation.html
index 3f4858c..e2e44ca 100644
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@@ -32,7 +32,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/propagate.html b/reference/propagate.html
index ee9ba3b..cefb218 100644
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@@ -32,7 +32,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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index 073d024..b42ac24 100644
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/removeDuplicates.html b/reference/removeDuplicates.html
index a4796dd..9eafbd6 100644
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@@ -38,7 +38,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/resolveAgreements.html b/reference/resolveAgreements.html
index badf2e6..a720675 100644
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@@ -34,7 +34,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/resolveConflicts.html b/reference/resolveConflicts.html
index 7d6d87b..69d99f4 100644
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@@ -34,7 +34,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/scores2Freq.html b/reference/scores2Freq.html
index 87c2a1e..dfc85e1 100644
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@@ -32,7 +32,7 @@
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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diff --git a/reference/taxname2taxid.html b/reference/taxname2taxid.html
index c11df0b..fe593af 100644
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-      <a href="../articles/phytools.html">A propagation workflow with phytools</a>
+      <a href="../articles/phytools.html">A propagation workflow with taxonomic pooling, asr (phytools), and inhertiance</a>
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