Binary files /tmp/tmphEnBrH/NqJhFZ_sZA/r-cran-rnexml-2.4.4+ds/build/vignette.rds and /tmp/tmphEnBrH/GDK9lWVYoP/r-cran-rnexml-2.4.5+ds/build/vignette.rds differ
diff -Nru r-cran-rnexml-2.4.4+ds/debian/changelog r-cran-rnexml-2.4.5+ds/debian/changelog
--- r-cran-rnexml-2.4.4+ds/debian/changelog	2020-05-31 06:23:54.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/debian/changelog	2020-09-04 08:56:03.000000000 +0000
@@ -1,8 +1,9 @@
-r-cran-rnexml (2.4.4+ds-2build1) groovy; urgency=medium
+r-cran-rnexml (2.4.5+ds-1) unstable; urgency=medium
 
-  * No-change rebuild against r-api-4.0
+  * New upstream version
+  * debhelper-compat 13 (routine-update)
 
- -- Steve Langasek <steve.langasek@ubuntu.com>  Sun, 31 May 2020 06:23:54 +0000
+ -- Andreas Tille <tille@debian.org>  Fri, 04 Sep 2020 10:56:03 +0200
 
 r-cran-rnexml (2.4.4+ds-2) unstable; urgency=medium
 
diff -Nru r-cran-rnexml-2.4.4+ds/debian/control r-cran-rnexml-2.4.5+ds/debian/control
--- r-cran-rnexml-2.4.4+ds/debian/control	2020-05-31 06:23:54.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/debian/control	2020-09-04 08:56:03.000000000 +0000
@@ -1,11 +1,10 @@
 Source: r-cran-rnexml
-Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
-XSBC-Original-Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
+Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Uploaders: Andreas Tille <tille@debian.org>
 Section: gnu-r
 Testsuite: autopkgtest-pkg-r
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                dh-r,
                r-base-dev,
                r-cran-ape,
diff -Nru r-cran-rnexml-2.4.4+ds/DESCRIPTION r-cran-rnexml-2.4.5+ds/DESCRIPTION
--- r-cran-rnexml-2.4.4+ds/DESCRIPTION	2020-05-10 07:20:06.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/DESCRIPTION	2020-06-18 18:40:03.000000000 +0000
@@ -1,7 +1,7 @@
 Package: RNeXML
 Type: Package
 Title: Semantically Rich I/O for the 'NeXML' Format
-Version: 2.4.4
+Version: 2.4.5
 Authors@R: c(person("Carl", "Boettiger", role = c("cre", "aut"),
     email="cboettig@gmail.com", comment = c(ORCID="0000-0002-1642-628X")), 
     person("Scott", "Chamberlain", role ="aut", comment = c(ORCID="0000-0003-1444-9135")), 
@@ -37,14 +37,14 @@
         'nexml_read.R' 'nexml_validate.R' 'nexml_write.R'
         'prefixed-uris.R' 'simmap.R' 'taxize_nexml.R' 'tbl_df.R'
         'utils.R'
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.0.9000
 X-schema.org-applicationCategory: Data Publication
 X-schema.org-keywords: metadata, nexml, phylogenetics, linked-data
 X-schema.org-isPartOf: https://ropensci.org
 Language: en-US
 Encoding: UTF-8
 NeedsCompilation: no
-Packaged: 2020-05-10 04:09:39 UTC; cboettig
+Packaged: 2020-06-18 17:34:14 UTC; root
 Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
   Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
   Hilmar Lapp [aut] (<https://orcid.org/0000-0001-9107-0714>),
@@ -52,4 +52,4 @@
   Rutger Vos [aut] (<https://orcid.org/0000-0001-9254-7318>)
 Maintainer: Carl Boettiger <cboettig@gmail.com>
 Repository: CRAN
-Date/Publication: 2020-05-10 07:20:06 UTC
+Date/Publication: 2020-06-18 18:40:02 UTC
diff -Nru r-cran-rnexml-2.4.4+ds/inst/doc/intro.html r-cran-rnexml-2.4.5+ds/inst/doc/intro.html
--- r-cran-rnexml-2.4.4+ds/inst/doc/intro.html	2020-05-10 04:09:38.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/inst/doc/intro.html	2020-06-18 17:34:12.000000000 +0000
@@ -22,9 +22,9 @@
 
 <style type="text/css">code{white-space: pre;}</style>
 <style type="text/css" data-origin="pandoc">
-a.sourceLine { display: inline-block; line-height: 1.25; }
-a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+code.sourceCode > span { display: inline-block; line-height: 1.25; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 div.sourceCode { margin: 1em 0; }
@@ -34,14 +34,16 @@
 }
 @media print {
 code.sourceCode { white-space: pre-wrap; }
-a.sourceLine { text-indent: -1em; padding-left: 1em; }
+code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
 }
-pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
-pre.numberSource a.sourceLine::before
-  { content: attr(data-line-number);
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
     position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    border: none; display: inline-block;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;
@@ -50,9 +52,9 @@
   }
 pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
 div.sourceCode
-  {  }
+  {   }
 @media screen {
-a.sourceLine::before { text-decoration: underline; }
+code.sourceCode > span > a:first-child::before { text-decoration: underline; }
 }
 code span.al { color: #ff0000; font-weight: bold; } /* Alert */
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
@@ -314,10 +316,10 @@
 %\VignetteIndexEntry{A Brief Introduction to RNeXMLL}
 -->
 <p>Read in a <code>nexml</code> file:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">f &lt;-<span class="st"> </span><span class="kw">system.file</span>(<span class="st">&quot;examples&quot;</span>, <span class="st">&quot;comp_analysis.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>)</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2">nexml &lt;-<span class="st"> </span><span class="kw">nexml_read</span>(f)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>f &lt;-<span class="st"> </span><span class="kw">system.file</span>(<span class="st">&quot;examples&quot;</span>, <span class="st">&quot;comp_analysis.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>)</span>
+<span id="cb1-2"><a href="#cb1-2"></a>nexml &lt;-<span class="st"> </span><span class="kw">nexml_read</span>(f)</span></code></pre></div>
 <p>Pretty-print an overview of the components and metadata that make up the nexml object:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">nexml  <span class="co"># this is the same as show(nexml)</span></a></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>nexml  <span class="co"># this is the same as show(nexml)</span></span></code></pre></div>
 <pre><code>## A nexml object representing:
 ##       1 phylogenetic tree block(s), where:
 ##     block 1 contains 1 phylogenetic tree(s) 
@@ -342,7 +344,7 @@
 ## NeXML generated by Bio::Phylo::Project v.0.56 using schema version: 0.9 
 ## Size: 289.3 Kb</code></pre>
 <p>Create a summary object of various component and metadata counts (the <code>show()</code> method uses this):</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw">summary</span>(nexml)</a></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="kw">summary</span>(nexml)</span></code></pre></div>
 <pre><code>## $nblocks
 ##      trees       otus characters 
 ##          1          1          2 
@@ -393,22 +395,22 @@
 ## block.1 block.2 
 ##       0       0</code></pre>
 <p>Extract trees from nexml into the <code>ape::phylo</code> format:</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">tr &lt;-<span class="st"> </span><span class="kw">get_trees</span>(nexml) <span class="co"># or: as(nexml, &quot;phylo&quot;)</span></a>
-<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw">plot</span>(tr)</a></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a>tr &lt;-<span class="st"> </span><span class="kw">get_trees</span>(nexml) <span class="co"># or: as(nexml, &quot;phylo&quot;)</span></span>
+<span id="cb6-2"><a href="#cb6-2"></a><span class="kw">plot</span>(tr)</span></code></pre></div>
 <div class="figure">
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+<img src="data:image/png;base64,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" alt />
 <p class="caption">plot of chunk unnamed-chunk-5</p>
 </div>
 <p>Write an <code>ape::phylo</code> tree into the <code>nexml</code> format:</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">data</span>(bird.orders)</a>
-<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="kw">nexml_write</span>(bird.orders, <span class="st">&quot;test.xml&quot;</span>, <span class="dt">creator =</span> <span class="st">&quot;Carl Boettiger&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="kw">data</span>(bird.orders)</span>
+<span id="cb7-2"><a href="#cb7-2"></a><span class="kw">nexml_write</span>(bird.orders, <span class="st">&quot;test.xml&quot;</span>, <span class="dt">creator =</span> <span class="st">&quot;Carl Boettiger&quot;</span>)</span></code></pre></div>
 <pre><code>## [1] &quot;test.xml&quot;</code></pre>
 <p>A key feature of NeXML is the ability to formally validate the construction of the data file against the standard (the lack of such a feature in nexus files had lead to inconsistencies across different software platforms, and some files that cannot be read at all). While it is difficult to make an invalid NeXML file from <code>RNeXML</code>, it never hurts to validate just to be sure:</p>
-<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw">nexml_validate</span>(<span class="st">&quot;test.xml&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a><span class="kw">nexml_validate</span>(<span class="st">&quot;test.xml&quot;</span>)</span></code></pre></div>
 <pre><code>## [1] TRUE</code></pre>
 <p>Extract metadata from the NeXML file:</p>
-<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">birds &lt;-<span class="st"> </span><span class="kw">nexml_read</span>(<span class="st">&quot;test.xml&quot;</span>)</a>
-<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="kw">get_taxa</span>(birds)</a></code></pre></div>
+<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a>birds &lt;-<span class="st"> </span><span class="kw">nexml_read</span>(<span class="st">&quot;test.xml&quot;</span>)</span>
+<span id="cb11-2"><a href="#cb11-2"></a><span class="kw">get_taxa</span>(birds)</span></code></pre></div>
 <pre><code>##     otu            label xsi.type otus
 ## 1  ou37 Struthioniformes       NA  os3
 ## 2  ou38     Tinamiformes       NA  os3
@@ -433,28 +435,28 @@
 ## 21 ou57       Gruiformes       NA  os3
 ## 22 ou58    Ciconiiformes       NA  os3
 ## 23 ou59    Passeriformes       NA  os3</code></pre>
-<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="kw">get_metadata</span>(birds) </a></code></pre></div>
+<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a><span class="kw">get_metadata</span>(birds) </span></code></pre></div>
 <pre><code>##           property   datatype                 content     xsi.type                                              href Meta
 ## 1       dc:creator xsd:string          Carl Boettiger  LiteralMeta                                              &lt;NA&gt; m278
 ## 2 dcterms:modified xsd:string 2020-01-28 23:24:19 GMT  LiteralMeta                                              &lt;NA&gt; m279
 ## 3       cc:license       &lt;NA&gt;                    &lt;NA&gt; ResourceMeta http://creativecommons.org/publicdomain/zero/1.0/ m280</code></pre>
 <hr />
 <p>Add basic additional metadata:</p>
-<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">  <span class="kw">nexml_write</span>(bird.orders, <span class="dt">file=</span><span class="st">&quot;meta_example.xml&quot;</span>,</a>
-<a class="sourceLine" id="cb15-2" data-line-number="2">              <span class="dt">title =</span> <span class="st">&quot;My test title&quot;</span>,</a>
-<a class="sourceLine" id="cb15-3" data-line-number="3">              <span class="dt">description =</span> <span class="st">&quot;A description of my test&quot;</span>,</a>
-<a class="sourceLine" id="cb15-4" data-line-number="4">              <span class="dt">creator =</span> <span class="st">&quot;Carl Boettiger &lt;cboettig@gmail.com&gt;&quot;</span>,</a>
-<a class="sourceLine" id="cb15-5" data-line-number="5">              <span class="dt">publisher =</span> <span class="st">&quot;unpublished data&quot;</span>,</a>
-<a class="sourceLine" id="cb15-6" data-line-number="6">              <span class="dt">pubdate =</span> <span class="st">&quot;2012-04-01&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1"></a>  <span class="kw">nexml_write</span>(bird.orders, <span class="dt">file=</span><span class="st">&quot;meta_example.xml&quot;</span>,</span>
+<span id="cb15-2"><a href="#cb15-2"></a>              <span class="dt">title =</span> <span class="st">&quot;My test title&quot;</span>,</span>
+<span id="cb15-3"><a href="#cb15-3"></a>              <span class="dt">description =</span> <span class="st">&quot;A description of my test&quot;</span>,</span>
+<span id="cb15-4"><a href="#cb15-4"></a>              <span class="dt">creator =</span> <span class="st">&quot;Carl Boettiger &lt;cboettig@gmail.com&gt;&quot;</span>,</span>
+<span id="cb15-5"><a href="#cb15-5"></a>              <span class="dt">publisher =</span> <span class="st">&quot;unpublished data&quot;</span>,</span>
+<span id="cb15-6"><a href="#cb15-6"></a>              <span class="dt">pubdate =</span> <span class="st">&quot;2012-04-01&quot;</span>)</span></code></pre></div>
 <pre><code>## [1] &quot;meta_example.xml&quot;</code></pre>
 <p>By default, <code>RNeXML</code> adds certain metadata, including the NCBI taxon id numbers for all named taxa. This acts a check on the spelling and definitions of the taxa as well as providing a link to additional metadata about each taxonomic unit described in the dataset.</p>
 <div id="advanced-annotation" class="section level3">
 <h3>Advanced annotation</h3>
 <p>We can also add arbitrary metadata to a NeXML tree by define <code>meta</code> objects:</p>
-<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">modified &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">property =</span> <span class="st">&quot;prism:modificationDate&quot;</span>,</a>
-<a class="sourceLine" id="cb17-2" data-line-number="2">                 <span class="dt">content =</span> <span class="st">&quot;2013-10-04&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1"></a>modified &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">property =</span> <span class="st">&quot;prism:modificationDate&quot;</span>,</span>
+<span id="cb17-2"><a href="#cb17-2"></a>                 <span class="dt">content =</span> <span class="st">&quot;2013-10-04&quot;</span>)</span></code></pre></div>
 <p>Advanced use requires specifying the namespace used. Metadata follows the RDFa conventions. Here we indicate the modification date using the prism vocabulary. This namespace is included by default, as it is used for some of the basic metadata shown in the previous example. We can see from this list:</p>
-<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">RNeXML<span class="op">:::</span>nexml_namespaces</a></code></pre></div>
+<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1"></a>RNeXML<span class="op">:::</span>nexml_namespaces</span></code></pre></div>
 <pre><code>##                                              nex                                              xsi 
 ##                      &quot;http://www.nexml.org/2009&quot;      &quot;http://www.w3.org/2001/XMLSchema-instance&quot; 
 ##                                              xml                                             cdao 
@@ -468,27 +470,27 @@
 ##                                               tc 
 ##  &quot;http://rs.tdwg.org/ontology/voc/TaxonConcept#&quot;</code></pre>
 <p>This next block defines a resource (link), described by the <code>rel</code> attribute as a homepage, a term in the <code>foaf</code> vocabulary. Because <code>foaf</code> is not a default namespace, we will have to provide its URL in the full definition below.</p>
-<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">website &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">href =</span> <span class="st">&quot;http://carlboettiger.info&quot;</span>, </a>
-<a class="sourceLine" id="cb20-2" data-line-number="2">                <span class="dt">rel =</span> <span class="st">&quot;foaf:homepage&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a>website &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">href =</span> <span class="st">&quot;http://carlboettiger.info&quot;</span>, </span>
+<span id="cb20-2"><a href="#cb20-2"></a>                <span class="dt">rel =</span> <span class="st">&quot;foaf:homepage&quot;</span>)</span></code></pre></div>
 <p>Here we create a history node using the <code>skos</code> namespace. We can also add id values to any metadata element to make the element easier to reference externally:</p>
-<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">  history &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">property =</span> <span class="st">&quot;skos:historyNote&quot;</span>, </a>
-<a class="sourceLine" id="cb21-2" data-line-number="2">                  <span class="dt">content =</span> <span class="st">&quot;Mapped from the bird.orders data in the ape package using RNeXML&quot;</span>,</a>
-<a class="sourceLine" id="cb21-3" data-line-number="3">                  <span class="dt">id =</span> <span class="st">&quot;meta123&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1"></a>  history &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">property =</span> <span class="st">&quot;skos:historyNote&quot;</span>, </span>
+<span id="cb21-2"><a href="#cb21-2"></a>                  <span class="dt">content =</span> <span class="st">&quot;Mapped from the bird.orders data in the ape package using RNeXML&quot;</span>,</span>
+<span id="cb21-3"><a href="#cb21-3"></a>                  <span class="dt">id =</span> <span class="st">&quot;meta123&quot;</span>)</span></code></pre></div>
 <p>For this kind of richer annotation, it is best to build up our NeXML object sequentially. First we will add <code>bird.orders</code> phylogeny to a new phylogenetic object, and then we will add the metadata elements created above to this object. Finally, we will write the object out as an XML file:</p>
-<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">  birds &lt;-<span class="st"> </span><span class="kw">add_trees</span>(bird.orders)</a>
-<a class="sourceLine" id="cb22-2" data-line-number="2">  birds &lt;-<span class="st"> </span><span class="kw">add_meta</span>(<span class="dt">meta =</span> <span class="kw">list</span>(history, modified, website),</a>
-<a class="sourceLine" id="cb22-3" data-line-number="3">                    <span class="dt">namespaces =</span> <span class="kw">c</span>(<span class="dt">skos =</span> <span class="st">&quot;http://www.w3.org/2004/02/skos/core#&quot;</span>,</a>
-<a class="sourceLine" id="cb22-4" data-line-number="4">                                   <span class="dt">foaf =</span> <span class="st">&quot;http://xmlns.com/foaf/0.1/&quot;</span>),</a>
-<a class="sourceLine" id="cb22-5" data-line-number="5">                    <span class="dt">nexml=</span>birds)</a>
-<a class="sourceLine" id="cb22-6" data-line-number="6">  <span class="kw">nexml_write</span>(birds, </a>
-<a class="sourceLine" id="cb22-7" data-line-number="7">              <span class="dt">file =</span> <span class="st">&quot;example.xml&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1"></a>  birds &lt;-<span class="st"> </span><span class="kw">add_trees</span>(bird.orders)</span>
+<span id="cb22-2"><a href="#cb22-2"></a>  birds &lt;-<span class="st"> </span><span class="kw">add_meta</span>(<span class="dt">meta =</span> <span class="kw">list</span>(history, modified, website),</span>
+<span id="cb22-3"><a href="#cb22-3"></a>                    <span class="dt">namespaces =</span> <span class="kw">c</span>(<span class="dt">skos =</span> <span class="st">&quot;http://www.w3.org/2004/02/skos/core#&quot;</span>,</span>
+<span id="cb22-4"><a href="#cb22-4"></a>                                   <span class="dt">foaf =</span> <span class="st">&quot;http://xmlns.com/foaf/0.1/&quot;</span>),</span>
+<span id="cb22-5"><a href="#cb22-5"></a>                    <span class="dt">nexml=</span>birds)</span>
+<span id="cb22-6"><a href="#cb22-6"></a>  <span class="kw">nexml_write</span>(birds, </span>
+<span id="cb22-7"><a href="#cb22-7"></a>              <span class="dt">file =</span> <span class="st">&quot;example.xml&quot;</span>)</span></code></pre></div>
 <pre><code>## [1] &quot;example.xml&quot;</code></pre>
 </div>
 <div id="taxonomic-identifiers" class="section level3">
 <h3>Taxonomic identifiers</h3>
 <p>Add taxonomic identifier metadata to the OTU elements: <!-- This block relies on a robust internet connection that can occassionally fail.  Also it's a bit slow, so don't run it. After all, this command is tested in the unit tests.--></p>
-<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">nex &lt;-<span class="st"> </span><span class="kw">add_trees</span>(bird.orders)</a>
-<a class="sourceLine" id="cb24-2" data-line-number="2">nex &lt;-<span class="st"> </span><span class="kw">taxize_nexml</span>(nex)</a></code></pre></div>
+<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1"></a>nex &lt;-<span class="st"> </span><span class="kw">add_trees</span>(bird.orders)</span>
+<span id="cb24-2"><a href="#cb24-2"></a>nex &lt;-<span class="st"> </span><span class="kw">taxize_nexml</span>(nex)</span></code></pre></div>
 </div>
 <div id="working-with-character-data" class="section level2">
 <h2>Working with character data</h2>
@@ -496,15 +498,15 @@
 <div id="extracting-character-data" class="section level3">
 <h3>Extracting character data</h3>
 <p>We can load the library, parse the NeXML file and extract both the characters and the phylogeny.</p>
-<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw">library</span>(RNeXML)</a>
-<a class="sourceLine" id="cb25-2" data-line-number="2">nexml &lt;-<span class="st"> </span><span class="kw">read.nexml</span>(<span class="kw">system.file</span>(<span class="st">&quot;examples&quot;</span>, <span class="st">&quot;comp_analysis.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>))</a>
-<a class="sourceLine" id="cb25-3" data-line-number="3">traits &lt;-<span class="st"> </span><span class="kw">get_characters</span>(nexml)</a>
-<a class="sourceLine" id="cb25-4" data-line-number="4">tree &lt;-<span class="st"> </span><span class="kw">get_trees</span>(nexml)</a></code></pre></div>
+<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a><span class="kw">library</span>(RNeXML)</span>
+<span id="cb25-2"><a href="#cb25-2"></a>nexml &lt;-<span class="st"> </span><span class="kw">read.nexml</span>(<span class="kw">system.file</span>(<span class="st">&quot;examples&quot;</span>, <span class="st">&quot;comp_analysis.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>))</span>
+<span id="cb25-3"><a href="#cb25-3"></a>traits &lt;-<span class="st"> </span><span class="kw">get_characters</span>(nexml)</span>
+<span id="cb25-4"><a href="#cb25-4"></a>tree &lt;-<span class="st"> </span><span class="kw">get_trees</span>(nexml)</span></code></pre></div>
 <p>(Note that <code>get_characters</code> would return both discrete and continuous characters together in the same data.frame, but we use <code>get_characters_list</code> to get separate data.frames for the continuous <code>characters</code> block and the discrete <code>characters</code> block).</p>
 <p>We can then fire up <code>geiger</code> and fit, say, a Brownian motion model the continuous data and a Markov transition matrix to the discrete states:</p>
-<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw">library</span>(geiger)</a>
-<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="kw">fitContinuous</span>(tree, traits[<span class="dv">1</span>], <span class="dt">ncores=</span><span class="dv">1</span>)</a>
-<a class="sourceLine" id="cb26-3" data-line-number="3"><span class="kw">fitDiscrete</span>(tree, traits[<span class="dv">2</span>], <span class="dt">ncores=</span><span class="dv">1</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1"></a><span class="kw">library</span>(geiger)</span>
+<span id="cb26-2"><a href="#cb26-2"></a><span class="kw">fitContinuous</span>(tree, traits[<span class="dv">1</span>], <span class="dt">ncores=</span><span class="dv">1</span>)</span>
+<span id="cb26-3"><a href="#cb26-3"></a><span class="kw">fitDiscrete</span>(tree, traits[<span class="dv">2</span>], <span class="dt">ncores=</span><span class="dv">1</span>)</span></code></pre></div>
 </div>
 </div>
 
diff -Nru r-cran-rnexml-2.4.4+ds/inst/doc/metadata.html r-cran-rnexml-2.4.5+ds/inst/doc/metadata.html
--- r-cran-rnexml-2.4.4+ds/inst/doc/metadata.html	2020-05-10 04:09:39.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/inst/doc/metadata.html	2020-06-18 17:34:13.000000000 +0000
@@ -22,9 +22,9 @@
 
 <style type="text/css">code{white-space: pre;}</style>
 <style type="text/css" data-origin="pandoc">
-a.sourceLine { display: inline-block; line-height: 1.25; }
-a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+code.sourceCode > span { display: inline-block; line-height: 1.25; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 div.sourceCode { margin: 1em 0; }
@@ -34,14 +34,16 @@
 }
 @media print {
 code.sourceCode { white-space: pre-wrap; }
-a.sourceLine { text-indent: -1em; padding-left: 1em; }
+code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
 }
-pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
-pre.numberSource a.sourceLine::before
-  { content: attr(data-line-number);
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
     position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    border: none; display: inline-block;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;
@@ -50,9 +52,9 @@
   }
 pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
 div.sourceCode
-  {  }
+  {   }
 @media screen {
-a.sourceLine::before { text-decoration: underline; }
+code.sourceCode > span > a:first-child::before { text-decoration: underline; }
 }
 code span.al { color: #ff0000; font-weight: bold; } /* Alert */
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
@@ -317,65 +319,65 @@
 <h2>Writing NeXML metadata</h2>
 <p>The <code>add_basic_meta()</code> function takes as input an existing <code>nexml</code> object (like the other <code>add_</code> functions, if none is provided it will create one), and at the time of this writing any of the following parameters: <code>title</code>, <code>description</code>, <code>creator</code>, <code>pubdate</code>, <code>rights</code>, <code>publisher</code>, <code>citation</code>. Other metadata elements and corresponding parameters may be added in the future.</p>
 <p>Load the packages and data:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(<span class="st">'RNeXML'</span>)</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw">data</span>(bird.orders)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw">library</span>(<span class="st">&#39;RNeXML&#39;</span>)</span>
+<span id="cb1-2"><a href="#cb1-2"></a><span class="kw">data</span>(bird.orders)</span></code></pre></div>
 <p>Create an <code>nexml</code> object for the phylogeny <code>bird.orders</code> and add appropriate metadata:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">birds &lt;-<span class="st"> </span><span class="kw">add_trees</span>(bird.orders)</a>
-<a class="sourceLine" id="cb2-2" data-line-number="2">birds &lt;-<span class="st"> </span><span class="kw">add_basic_meta</span>(</a>
-<a class="sourceLine" id="cb2-3" data-line-number="3">  <span class="dt">title =</span> <span class="st">&quot;Phylogeny of the Orders of Birds From Sibley and Ahlquist&quot;</span>,</a>
-<a class="sourceLine" id="cb2-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb2-5" data-line-number="5">  <span class="dt">description =</span> <span class="st">&quot;This data set describes the phylogenetic relationships of the</span></a>
-<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="st">     orders of birds as reported by Sibley and Ahlquist (1990). Sibley</span></a>
-<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="st">     and Ahlquist inferred this phylogeny from an extensive number of</span></a>
-<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="st">     DNA/DNA hybridization experiments. The ``tapestry'' reported by</span></a>
-<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="st">     these two authors (more than 1000 species out of the ca. 9000</span></a>
-<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="st">     extant bird species) generated a lot of debates.</span></a>
-<a class="sourceLine" id="cb2-11" data-line-number="11"></a>
-<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="st">     The present tree is based on the relationships among orders. The</span></a>
-<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="st">     branch lengths were calculated from the values of Delta T50H as</span></a>
-<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="st">     found in Sibley and Ahlquist (1990, fig. 353).&quot;</span>,</a>
-<a class="sourceLine" id="cb2-15" data-line-number="15"></a>
-<a class="sourceLine" id="cb2-16" data-line-number="16">  <span class="dt">citation =</span> <span class="st">&quot;Sibley, C. G. and Ahlquist, J. E. (1990) Phylogeny and</span></a>
-<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="st">     classification of birds: a study in molecular evolution. New</span></a>
-<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="st">     Haven: Yale University Press.&quot;</span>,</a>
-<a class="sourceLine" id="cb2-19" data-line-number="19"></a>
-<a class="sourceLine" id="cb2-20" data-line-number="20">  <span class="dt">creator =</span> <span class="st">&quot;Sibley, C. G. and Ahlquist, J. E.&quot;</span>,</a>
-<a class="sourceLine" id="cb2-21" data-line-number="21">    <span class="dt">nexml=</span>birds)</a></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>birds &lt;-<span class="st"> </span><span class="kw">add_trees</span>(bird.orders)</span>
+<span id="cb2-2"><a href="#cb2-2"></a>birds &lt;-<span class="st"> </span><span class="kw">add_basic_meta</span>(</span>
+<span id="cb2-3"><a href="#cb2-3"></a>  <span class="dt">title =</span> <span class="st">&quot;Phylogeny of the Orders of Birds From Sibley and Ahlquist&quot;</span>,</span>
+<span id="cb2-4"><a href="#cb2-4"></a></span>
+<span id="cb2-5"><a href="#cb2-5"></a>  <span class="dt">description =</span> <span class="st">&quot;This data set describes the phylogenetic relationships of the</span></span>
+<span id="cb2-6"><a href="#cb2-6"></a><span class="st">     orders of birds as reported by Sibley and Ahlquist (1990). Sibley</span></span>
+<span id="cb2-7"><a href="#cb2-7"></a><span class="st">     and Ahlquist inferred this phylogeny from an extensive number of</span></span>
+<span id="cb2-8"><a href="#cb2-8"></a><span class="st">     DNA/DNA hybridization experiments. The ``tapestry&#39;&#39; reported by</span></span>
+<span id="cb2-9"><a href="#cb2-9"></a><span class="st">     these two authors (more than 1000 species out of the ca. 9000</span></span>
+<span id="cb2-10"><a href="#cb2-10"></a><span class="st">     extant bird species) generated a lot of debates.</span></span>
+<span id="cb2-11"><a href="#cb2-11"></a></span>
+<span id="cb2-12"><a href="#cb2-12"></a><span class="st">     The present tree is based on the relationships among orders. The</span></span>
+<span id="cb2-13"><a href="#cb2-13"></a><span class="st">     branch lengths were calculated from the values of Delta T50H as</span></span>
+<span id="cb2-14"><a href="#cb2-14"></a><span class="st">     found in Sibley and Ahlquist (1990, fig. 353).&quot;</span>,</span>
+<span id="cb2-15"><a href="#cb2-15"></a></span>
+<span id="cb2-16"><a href="#cb2-16"></a>  <span class="dt">citation =</span> <span class="st">&quot;Sibley, C. G. and Ahlquist, J. E. (1990) Phylogeny and</span></span>
+<span id="cb2-17"><a href="#cb2-17"></a><span class="st">     classification of birds: a study in molecular evolution. New</span></span>
+<span id="cb2-18"><a href="#cb2-18"></a><span class="st">     Haven: Yale University Press.&quot;</span>,</span>
+<span id="cb2-19"><a href="#cb2-19"></a></span>
+<span id="cb2-20"><a href="#cb2-20"></a>  <span class="dt">creator =</span> <span class="st">&quot;Sibley, C. G. and Ahlquist, J. E.&quot;</span>,</span>
+<span id="cb2-21"><a href="#cb2-21"></a>    <span class="dt">nexml=</span>birds)</span></code></pre></div>
 <p>Instead of a literal string, citations can also be provided in R’s <code>bibentry</code> type, which is the one in which R package citations are obtained:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">birds &lt;-<span class="st"> </span><span class="kw">add_basic_meta</span>(<span class="dt">citation =</span> <span class="kw">citation</span>(<span class="st">&quot;ape&quot;</span>), <span class="dt">nexml =</span> birds)</a></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>birds &lt;-<span class="st"> </span><span class="kw">add_basic_meta</span>(<span class="dt">citation =</span> <span class="kw">citation</span>(<span class="st">&quot;ape&quot;</span>), <span class="dt">nexml =</span> birds)</span></code></pre></div>
 </div>
 <div id="taxonomic-identifiers" class="section level2">
 <h2>Taxonomic identifiers</h2>
 <p>RNeXML now uses <code>taxald</code> for fast look-up of taxonomic information. If a unique match is found, a metadata annotation is added to the taxon providing the unique URI to the taxonomic unit.</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">birds &lt;-<span class="st"> </span><span class="kw">taxize_nexml</span>(birds, <span class="st">&quot;NCBI&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>birds &lt;-<span class="st"> </span><span class="kw">taxize_nexml</span>(birds, <span class="st">&quot;NCBI&quot;</span>)</span></code></pre></div>
 <p>If no perfect match is found, the user is warned to check for possible typographic errors in the taxonomic labels provided.</p>
 </div>
 <div id="custom-metadata-extensions" class="section level2">
 <h2>Custom metadata extensions</h2>
 <p>We can get a list of namespaces along with their prefixes from the <code>nexml</code> object:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">prefixes &lt;-<span class="st"> </span><span class="kw">get_namespaces</span>(birds)</a>
-<a class="sourceLine" id="cb5-2" data-line-number="2">prefixes[<span class="st">&quot;dc&quot;</span>]</a></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a>prefixes &lt;-<span class="st"> </span><span class="kw">get_namespaces</span>(birds)</span>
+<span id="cb5-2"><a href="#cb5-2"></a>prefixes[<span class="st">&quot;dc&quot;</span>]</span></code></pre></div>
 <pre><code>                                dc 
 &quot;http://purl.org/dc/elements/1.1/&quot; </code></pre>
 <p>We create a <code>meta</code> element containing this annotation using the <code>meta</code> function:</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">modified &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">property =</span> <span class="st">&quot;prism:modificationDate&quot;</span>, <span class="dt">content =</span> <span class="st">&quot;2013-10-04&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>modified &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">property =</span> <span class="st">&quot;prism:modificationDate&quot;</span>, <span class="dt">content =</span> <span class="st">&quot;2013-10-04&quot;</span>)</span></code></pre></div>
 <p>We can add this annotation to our existing <code>birds</code> NeXML file using the <code>add_meta()</code> function. Because we do not specify a level, it is added to the root node, referring to the NeXML file as a whole.</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">birds &lt;-<span class="st"> </span><span class="kw">add_meta</span>(modified, birds) </a></code></pre></div>
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>birds &lt;-<span class="st"> </span><span class="kw">add_meta</span>(modified, birds) </span></code></pre></div>
 <p>The built-in vocabularies are just the tip of the iceberg of established vocabularies. Here we add an annotation from the <code>skos</code> namespace which describes the history of where the data comes from:</p>
-<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">history &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">property =</span> <span class="st">&quot;skos:historyNote&quot;</span>,</a>
-<a class="sourceLine" id="cb9-2" data-line-number="2">  <span class="dt">content =</span> <span class="st">&quot;Mapped from the bird.orders data in the ape package using RNeXML&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a>history &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="dt">property =</span> <span class="st">&quot;skos:historyNote&quot;</span>,</span>
+<span id="cb9-2"><a href="#cb9-2"></a>  <span class="dt">content =</span> <span class="st">&quot;Mapped from the bird.orders data in the ape package using RNeXML&quot;</span>)</span></code></pre></div>
 <p>Because <code>skos</code> is not in the current namespace list, we add it with a url when adding this meta element. We also specify that this annotation be placed at the level of the <code>trees</code> sub-node in the NeXML file.</p>
-<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">birds &lt;-<span class="st"> </span><span class="kw">add_meta</span>(history, </a>
-<a class="sourceLine" id="cb10-2" data-line-number="2">                birds, </a>
-<a class="sourceLine" id="cb10-3" data-line-number="3">                <span class="dt">level =</span> <span class="st">&quot;trees&quot;</span>,</a>
-<a class="sourceLine" id="cb10-4" data-line-number="4">                <span class="dt">namespaces =</span> <span class="kw">c</span>(<span class="dt">skos =</span> <span class="st">&quot;http://www.w3.org/2004/02/skos/core#&quot;</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1"></a>birds &lt;-<span class="st"> </span><span class="kw">add_meta</span>(history, </span>
+<span id="cb10-2"><a href="#cb10-2"></a>                birds, </span>
+<span id="cb10-3"><a href="#cb10-3"></a>                <span class="dt">level =</span> <span class="st">&quot;trees&quot;</span>,</span>
+<span id="cb10-4"><a href="#cb10-4"></a>                <span class="dt">namespaces =</span> <span class="kw">c</span>(<span class="dt">skos =</span> <span class="st">&quot;http://www.w3.org/2004/02/skos/core#&quot;</span>))</span></code></pre></div>
 <p>For finer control of the level at which a <code>meta</code> element is added, we will manipulate the <code>nexml</code> R object directly using S4 sub-setting, as shown in the supplement.</p>
 <p>Much richer metadata annotation is possible. Later we illustrate how metadata annotation can be used to extend the base NeXML format to represent new forms of data while maintaining compatibility with any NeXML parser. The <code>RNeXML</code> package can be easily extended to support helper functions such as <code>taxize_nexml</code> to add additional metadata without imposing a large burden on the user.</p>
 </div>
 <div id="reading-nexml-metadata" class="section level2">
 <h2>Reading NeXML metadata</h2>
 <p>A call to the <code>nexml</code> object prints some metadata summarizing the data structure:</p>
-<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">birds</a></code></pre></div>
+<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a>birds</span></code></pre></div>
 <pre><code>A nexml object representing:
      1 phylogenetic tree block(s), where:
        block 1 contains 1 phylogenetic tree(s) 
@@ -389,7 +391,7 @@
 This data set describes the phylogenetic relationships of the
      orders of birds as reported by Sibley and Ahlquist (1990). Sibley
      and Ahlquist inferred this phylogeny from an extensive number of
-     DNA/DNA hybridization experiments. The ``tapestry'' reported by
+     DNA/DNA hybridization experiments. The ``tapestry&#39;&#39; reported by
      these two authors (more than 1000 species out of the ca. 9000
      extant bird species) generated a lot of debates.
 
@@ -404,9 +406,9 @@
 NeXML generated by RNeXML using schema version: 0.9 
 Size: 358.3 Kb </code></pre>
 <p>We can extract all metadata pertaining to the NeXML document as a whole (annotations of the XML root node, <code>&lt;nexml&gt;</code>) with the command</p>
-<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">meta &lt;-<span class="st"> </span><span class="kw">get_metadata</span>(birds) </a></code></pre></div>
+<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a>meta &lt;-<span class="st"> </span><span class="kw">get_metadata</span>(birds) </span></code></pre></div>
 <p>This returns a data.frame of available metadata. We can see the kinds of metadata recorded from the names:</p>
-<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">meta</a></code></pre></div>
+<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1"></a>meta</span></code></pre></div>
 <pre><code>                        property   datatype
 1                       dc:title xsd:string
 2                     dc:creator xsd:string
@@ -429,7 +431,7 @@
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              content
 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Phylogeny of the Orders of Birds From Sibley and Ahlquist
 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Sibley, C. G. and Ahlquist, J. E.
-3  This data set describes the phylogenetic relationships of the\n     orders of birds as reported by Sibley and Ahlquist (1990). Sibley\n     and Ahlquist inferred this phylogeny from an extensive number of\n     DNA/DNA hybridization experiments. The ``tapestry'' reported by\n     these two authors (more than 1000 species out of the ca. 9000\n     extant bird species) generated a lot of debates.\n\n     The present tree is based on the relationships among orders. The\n     branch lengths were calculated from the values of Delta T50H as\n     found in Sibley and Ahlquist (1990, fig. 353).
+3  This data set describes the phylogenetic relationships of the\n     orders of birds as reported by Sibley and Ahlquist (1990). Sibley\n     and Ahlquist inferred this phylogeny from an extensive number of\n     DNA/DNA hybridization experiments. The ``tapestry&#39;&#39; reported by\n     these two authors (more than 1000 species out of the ca. 9000\n     extant bird species) generated a lot of debates.\n\n     The present tree is based on the relationships among orders. The\n     branch lengths were calculated from the values of Delta T50H as\n     found in Sibley and Ahlquist (1990, fig. 353).
 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               &lt;NA&gt;
 5                                                                                                                                                                                                                                                                                                                                                                                                                                                      Sibley, C. G. and Ahlquist, J. E. (1990) Phylogeny and\n     classification of birds: a study in molecular evolution. New\n     Haven: Yale University Press.
 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           cboettig
@@ -465,7 +467,7 @@
 17  LiteralMeta                                              &lt;NA&gt; &lt;NA&gt; m560
 18  LiteralMeta                                              &lt;NA&gt; &lt;NA&gt; m560</code></pre>
 <p>We can also access a table of taxonomic metadata:</p>
-<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="kw">get_taxa</span>(birds)</a></code></pre></div>
+<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1"></a><span class="kw">get_taxa</span>(birds)</span></code></pre></div>
 <pre><code>     otu            label xsi.type otus
 1  ou362 Struthioniformes       NA  os8
 2  ou363     Tinamiformes       NA  os8
@@ -492,29 +494,29 @@
 23 ou384    Passeriformes       NA  os8</code></pre>
 <p>Which returns text from the otu element labels, typically used to define taxonomic names, rather than text from explicit meta elements.</p>
 <p>We can also access metadata at a specific level (or use <code>level=all</code> to extract all meta elements in a list). Here we show only the first few results:</p>
-<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">otu_meta &lt;-<span class="st"> </span><span class="kw">get_metadata</span>(birds, <span class="dt">level=</span><span class="st">&quot;otus/otu&quot;</span>)</a>
-<a class="sourceLine" id="cb18-2" data-line-number="2">otu_meta</a></code></pre></div>
+<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1"></a>otu_meta &lt;-<span class="st"> </span><span class="kw">get_metadata</span>(birds, <span class="dt">level=</span><span class="st">&quot;otus/otu&quot;</span>)</span>
+<span id="cb18-2"><a href="#cb18-2"></a>otu_meta</span></code></pre></div>
 <pre><code># A tibble: 0 x 3
 # … with 3 variables: otu &lt;chr&gt;, otus &lt;chr&gt;, Meta &lt;chr&gt;</code></pre>
 </div>
 <div id="merging-metadata-tables" class="section level2">
 <h2>Merging metadata tables</h2>
 <p>We often want to combine metadata from multiple tables. For instance, in this exercise we want to include the taxonomic identifier and id value for each species returned in the character table. This helps us more precisely identify the species whose traits are described by the table.</p>
-<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="kw">library</span>(<span class="st">&quot;RNeXML&quot;</span>)</a>
-<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="kw">library</span>(<span class="st">&quot;dplyr&quot;</span>)</a>
-<a class="sourceLine" id="cb20-3" data-line-number="3"><span class="kw">library</span>(<span class="st">&quot;geiger&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a><span class="kw">library</span>(<span class="st">&quot;RNeXML&quot;</span>)</span>
+<span id="cb20-2"><a href="#cb20-2"></a><span class="kw">library</span>(<span class="st">&quot;dplyr&quot;</span>)</span>
+<span id="cb20-3"><a href="#cb20-3"></a><span class="kw">library</span>(<span class="st">&quot;geiger&quot;</span>)</span></code></pre></div>
 <p>To begin, let’s generate a <code>NeXML</code> file using the tree and trait data from the <code>geiger</code> package’s “primates” data:</p>
-<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">data</span>(<span class="st">&quot;primates&quot;</span>)</a>
-<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="kw">add_trees</span>(primates<span class="op">$</span>phy) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st">  </span><span class="kw">add_characters</span>(primates<span class="op">$</span>dat, ., <span class="dt">append=</span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb21-4" data-line-number="4"><span class="st">  </span><span class="kw">taxize_nexml</span>(<span class="st">&quot;itis&quot;</span>) -&gt;<span class="st"> </span>nex </a></code></pre></div>
+<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1"></a><span class="kw">data</span>(<span class="st">&quot;primates&quot;</span>)</span>
+<span id="cb21-2"><a href="#cb21-2"></a><span class="kw">add_trees</span>(primates<span class="op">$</span>phy) <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb21-3"><a href="#cb21-3"></a><span class="st">  </span><span class="kw">add_characters</span>(primates<span class="op">$</span>dat, ., <span class="dt">append=</span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb21-4"><a href="#cb21-4"></a><span class="st">  </span><span class="kw">taxize_nexml</span>(<span class="st">&quot;itis&quot;</span>) -&gt;<span class="st"> </span>nex </span></code></pre></div>
 <p>(Note that we’ve used <code>dplyr</code>’s cute pipe syntax, but unfortunately our <code>add_</code> methods take the <code>nexml</code> object as the <em>second</em> argument instead of the first, so this isn’t as elegant since we need the stupid <code>.</code> to show where the piped output should go…)</p>
 <p>We now read in the three tables of interest. Note that we tell <code>get_characters</code> to give us species labels as there own column, rather than as rownames. The latter is the default only because this plays more nicely with the default format for character matrices that is expected by <code>geiger</code> and other phylogenetics packages, but is in general a silly choice for data manipulation.</p>
-<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">otu_meta &lt;-<span class="st"> </span><span class="kw">get_metadata</span>(nex, <span class="st">&quot;otus/otu&quot;</span>)</a>
-<a class="sourceLine" id="cb22-2" data-line-number="2">taxa &lt;-<span class="st"> </span><span class="kw">get_taxa</span>(nex)</a>
-<a class="sourceLine" id="cb22-3" data-line-number="3">char &lt;-<span class="st"> </span><span class="kw">get_characters</span>(nex, <span class="dt">rownames_as_col =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1"></a>otu_meta &lt;-<span class="st"> </span><span class="kw">get_metadata</span>(nex, <span class="st">&quot;otus/otu&quot;</span>)</span>
+<span id="cb22-2"><a href="#cb22-2"></a>taxa &lt;-<span class="st"> </span><span class="kw">get_taxa</span>(nex)</span>
+<span id="cb22-3"><a href="#cb22-3"></a>char &lt;-<span class="st"> </span><span class="kw">get_characters</span>(nex, <span class="dt">rownames_as_col =</span> <span class="ot">TRUE</span>)</span></code></pre></div>
 <p>We can take a peek at what the tables look like, just to orient ourselves:</p>
-<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1">otu_meta</a></code></pre></div>
+<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1"></a>otu_meta</span></code></pre></div>
 <pre><code>      property                                                                                  href     xsi.type   otu otus
 1   tc:toTaxon  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&amp;search_value=572992 ResourceMeta ou385  os9
 2   tc:toTaxon  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&amp;search_value=572857 ResourceMeta ou386  os9
@@ -849,8 +851,8 @@
 164 m726
 165 m727
 166 m728
- [ reached 'max' / getOption(&quot;max.print&quot;) -- omitted 66 rows ]</code></pre>
-<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">taxa</a></code></pre></div>
+ [ reached &#39;max&#39; / getOption(&quot;max.print&quot;) -- omitted 66 rows ]</code></pre>
+<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a>taxa</span></code></pre></div>
 <pre><code>      otu                        label xsi.type otus
 1   ou385  Allenopithecus_nigroviridis       NA  os9
 2   ou386          Allocebus_trichotis       NA  os9
@@ -1085,7 +1087,7 @@
 231 ou615      Trachypithecus_pileatus       NA  os9
 232 ou616       Trachypithecus_vetulus       NA  os9
 233 ou617            Varecia_variegata       NA  os9</code></pre>
-<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1"><span class="kw">head</span>(char)</a></code></pre></div>
+<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1"></a><span class="kw">head</span>(char)</span></code></pre></div>
 <pre><code>                         taxa        x
 1 Allenopithecus_nigroviridis 8.465900
 2         Allocebus_trichotis 4.368181
@@ -1094,10 +1096,10 @@
 5          Alouatta_coibensis 8.764053
 6              Alouatta_fusca 8.554489</code></pre>
 <p>Now that we have nice <code>data.frame</code> objects for all our data, it’s easy to join them into the desired table with a few obvious <code>dplyr</code> commands:</p>
-<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">taxa <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="st">  </span><span class="kw">left_join</span>(char, <span class="dt">by =</span> <span class="kw">c</span>(<span class="st">&quot;label&quot;</span> =<span class="st"> &quot;taxa&quot;</span>)) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb29-3" data-line-number="3"><span class="st">  </span><span class="kw">left_join</span>(otu_meta, <span class="dt">by =</span> <span class="st">&quot;otu&quot;</span>) <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb29-4" data-line-number="4"><span class="st">  </span><span class="kw">select</span>(otu, label, x, href)</a></code></pre></div>
+<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb29-1"><a href="#cb29-1"></a>taxa <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb29-2"><a href="#cb29-2"></a><span class="st">  </span><span class="kw">left_join</span>(char, <span class="dt">by =</span> <span class="kw">c</span>(<span class="st">&quot;label&quot;</span> =<span class="st"> &quot;taxa&quot;</span>)) <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb29-3"><a href="#cb29-3"></a><span class="st">  </span><span class="kw">left_join</span>(otu_meta, <span class="dt">by =</span> <span class="st">&quot;otu&quot;</span>) <span class="op">%&gt;%</span></span>
+<span id="cb29-4"><a href="#cb29-4"></a><span class="st">  </span><span class="kw">select</span>(otu, label, x, href)</span></code></pre></div>
 <pre><code>      otu                        label         x
 1   ou385  Allenopithecus_nigroviridis  8.465900
 2   ou386          Allocebus_trichotis  4.368181
diff -Nru r-cran-rnexml-2.4.4+ds/inst/doc/S4.html r-cran-rnexml-2.4.5+ds/inst/doc/S4.html
--- r-cran-rnexml-2.4.4+ds/inst/doc/S4.html	2020-05-10 04:09:38.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/inst/doc/S4.html	2020-06-18 17:34:13.000000000 +0000
@@ -22,9 +22,9 @@
 
 <style type="text/css">code{white-space: pre;}</style>
 <style type="text/css" data-origin="pandoc">
-a.sourceLine { display: inline-block; line-height: 1.25; }
-a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+code.sourceCode > span { display: inline-block; line-height: 1.25; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 div.sourceCode { margin: 1em 0; }
@@ -34,14 +34,16 @@
 }
 @media print {
 code.sourceCode { white-space: pre-wrap; }
-a.sourceLine { text-indent: -1em; padding-left: 1em; }
+code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
 }
-pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
-pre.numberSource a.sourceLine::before
-  { content: attr(data-line-number);
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
     position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    border: none; display: inline-block;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;
@@ -50,9 +52,9 @@
   }
 pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
 div.sourceCode
-  {  }
+  {   }
 @media screen {
-a.sourceLine::before { text-decoration: underline; }
+code.sourceCode > span > a:first-child::before { text-decoration: underline; }
 }
 code span.al { color: #ff0000; font-weight: bold; } /* Alert */
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
@@ -318,15 +320,15 @@
 <p>The <code>RNeXML</code> package provides many convenient functions to add and extract information from <code>nexml</code> objects in the R environment without requiring the reader to understand the details of the NeXML data structure and making it less likely that a user will generate invalid NeXML syntax that could not be read by other parsers. The <code>nexml</code> object we have been using in all of the examples is built on R’s S4 mechanism. Advanced users may sometimes prefer to interact with the data structure more directly using R’s S4 class mechanism and subsetting methods. Many R users are more familiar with the S3 class mechanism (such as in the <code>ape</code> package phylo objects) rather than the S4 class mechanism used in phylogenetics packages such as <code>ouch</code> and <code>phylobase</code>. The <code>phylobase</code> vignette provides an excellent introduction to these data structures. Users already familiar with subsetting lists and other S3 objects in R are likely familiar with the use of the <code>$</code> operator, such as <code>phy$edge</code>. S4 objects simply use an <code>@</code> operator instead (but cannot be subset using numeric arguments such as <code>phy[[1]]</code> or named arguments such as phy[[“edge”]]).</p>
 <p>The <code>nexml</code> object is an S4 object, as are all of its components (slots). Its hierarchical structure corresponds exactly with the XML tree of a NeXML file, with the single exception that both XML attributes and children are represented as slots.<br />
 S4 objects have constructor functions to initialize them. We create a new <code>nexml</code> object with the command:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">nex &lt;-<span class="st"> </span><span class="kw">new</span>(<span class="st">&quot;nexml&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>nex &lt;-<span class="st"> </span><span class="kw">new</span>(<span class="st">&quot;nexml&quot;</span>)</span></code></pre></div>
 <p>We can see a list of slots contained in this object with</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw">slotNames</span>(nex)</a></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="kw">slotNames</span>(nex)</span></code></pre></div>
 <pre><code> [1] &quot;version&quot;            &quot;generator&quot;          &quot;xsi:schemaLocation&quot; &quot;namespaces&quot;         &quot;otus&quot;              
  [6] &quot;trees&quot;              &quot;characters&quot;         &quot;meta&quot;               &quot;about&quot;              &quot;xsi:type&quot;          </code></pre>
 <p>Some of these slots have already been populated for us, for instance, the schema version and default namespaces:</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">nex<span class="op">@</span>version</a></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>nex<span class="op">@</span>version</span></code></pre></div>
 <pre><code>[1] &quot;0.9&quot;</code></pre>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">nex<span class="op">@</span>namespaces</a></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a>nex<span class="op">@</span>namespaces</span></code></pre></div>
 <pre><code>                                             nex                                              xsi 
                      &quot;http://www.nexml.org/2009&quot;      &quot;http://www.w3.org/2001/XMLSchema-instance&quot; 
                                              xml                                             cdao 
@@ -341,35 +343,35 @@
  &quot;http://rs.tdwg.org/ontology/voc/TaxonConcept#&quot;                      &quot;http://www.nexml.org/2009&quot; </code></pre>
 <p>Recognize that <code>nex@namespaces</code> serves the same role as <code>get_namespaces</code> function, but provides direct access to the slot data. For instance, with this syntax we could also overwrite the existing namespaces with <code>nex@namespaces &lt;- NULL</code>. Changing the namespace in this way is not advised.</p>
 <p>Some slots can contain multiple elements of the same type, such as <code>trees</code>, <code>characters</code>, and <code>otus</code>. For instance, we see that</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw">class</span>(nex<span class="op">@</span>characters)</a></code></pre></div>
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a><span class="kw">class</span>(nex<span class="op">@</span>characters)</span></code></pre></div>
 <pre><code>[1] &quot;ListOfcharacters&quot;
 attr(,&quot;package&quot;)
 [1] &quot;RNeXML&quot;</code></pre>
 <p>is an object of class <code>ListOfcharacters</code>, and is currently empty,</p>
-<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw">length</span>(nex<span class="op">@</span>characters)</a></code></pre></div>
+<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1"></a><span class="kw">length</span>(nex<span class="op">@</span>characters)</span></code></pre></div>
 <pre><code>[1] 0</code></pre>
 <p>In order to assign an object to a slot, it must match the class definition of the slot. We can create a new element of any given class with the <code>new</code> function,</p>
-<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">nex<span class="op">@</span>characters &lt;-<span class="st"> </span><span class="kw">new</span>(<span class="st">&quot;ListOfcharacters&quot;</span>, <span class="kw">list</span>(<span class="kw">new</span>(<span class="st">&quot;characters&quot;</span>)))</a></code></pre></div>
+<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1"></a>nex<span class="op">@</span>characters &lt;-<span class="st"> </span><span class="kw">new</span>(<span class="st">&quot;ListOfcharacters&quot;</span>, <span class="kw">list</span>(<span class="kw">new</span>(<span class="st">&quot;characters&quot;</span>)))</span></code></pre></div>
 <p>and now we have a length-1 list of character matrices,</p>
-<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="kw">length</span>(nex<span class="op">@</span>characters)</a></code></pre></div>
+<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a><span class="kw">length</span>(nex<span class="op">@</span>characters)</span></code></pre></div>
 <pre><code>[1] 1</code></pre>
 <p>and we access the first character matrix using the list notation, <code>[[1]]</code>. Here we check the class is a <code>characters</code> object.</p>
-<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">class</span>(nex<span class="op">@</span>characters[[<span class="dv">1</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1"></a><span class="kw">class</span>(nex<span class="op">@</span>characters[[<span class="dv">1</span>]])</span></code></pre></div>
 <pre><code>[1] &quot;characters&quot;
 attr(,&quot;package&quot;)
 [1] &quot;RNeXML&quot;</code></pre>
 <p>Direct subsetting has two primary use cases: (a) useful in looking up (and possibly editing) a specific value of an element, or (b) when adding metadata annotations to specific elements. Consider the example file</p>
-<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">f &lt;-<span class="st"> </span><span class="kw">system.file</span>(<span class="st">&quot;examples&quot;</span>, <span class="st">&quot;trees.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>)</a>
-<a class="sourceLine" id="cb17-2" data-line-number="2">nex &lt;-<span class="st"> </span><span class="kw">nexml_read</span>(f)</a></code></pre></div>
+<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1"></a>f &lt;-<span class="st"> </span><span class="kw">system.file</span>(<span class="st">&quot;examples&quot;</span>, <span class="st">&quot;trees.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>)</span>
+<span id="cb17-2"><a href="#cb17-2"></a>nex &lt;-<span class="st"> </span><span class="kw">nexml_read</span>(f)</span></code></pre></div>
 <p>We can look up the species label of the first <code>otu</code> in the first <code>otus</code> block:</p>
-<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">nex<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[<span class="dv">1</span>]]<span class="op">@</span>label</a></code></pre></div>
+<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1"></a>nex<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[<span class="dv">1</span>]]<span class="op">@</span>label</span></code></pre></div>
 <pre><code>      label 
 &quot;species 1&quot; </code></pre>
 <p>We can add metadata to this particular OTU using this subsetting format</p>
-<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">nex<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[<span class="dv">1</span>]]<span class="op">@</span>meta &lt;-<span class="st"> </span></a>
-<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="st">  </span><span class="kw">c</span>(<span class="kw">meta</span>(<span class="st">&quot;skos:note&quot;</span>, </a>
-<a class="sourceLine" id="cb20-3" data-line-number="3">          <span class="st">&quot;This species was incorrectly identified&quot;</span>),</a>
-<a class="sourceLine" id="cb20-4" data-line-number="4">         nex<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[<span class="dv">1</span>]]<span class="op">@</span>meta)</a></code></pre></div>
+<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a>nex<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[<span class="dv">1</span>]]<span class="op">@</span>meta &lt;-<span class="st"> </span></span>
+<span id="cb20-2"><a href="#cb20-2"></a><span class="st">  </span><span class="kw">c</span>(<span class="kw">meta</span>(<span class="st">&quot;skos:note&quot;</span>, </span>
+<span id="cb20-3"><a href="#cb20-3"></a>          <span class="st">&quot;This species was incorrectly identified&quot;</span>),</span>
+<span id="cb20-4"><a href="#cb20-4"></a>         nex<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[<span class="dv">1</span>]]<span class="op">@</span>meta)</span></code></pre></div>
 <p>Here we use the <code>c</code> operator to append this element to any existing meta annotations to this otu.</p>
 </div>
 
diff -Nru r-cran-rnexml-2.4.4+ds/inst/doc/simmap.html r-cran-rnexml-2.4.5+ds/inst/doc/simmap.html
--- r-cran-rnexml-2.4.4+ds/inst/doc/simmap.html	2020-05-10 04:09:39.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/inst/doc/simmap.html	2020-06-18 17:34:14.000000000 +0000
@@ -22,9 +22,9 @@
 
 <style type="text/css">code{white-space: pre;}</style>
 <style type="text/css" data-origin="pandoc">
-a.sourceLine { display: inline-block; line-height: 1.25; }
-a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+code.sourceCode > span { display: inline-block; line-height: 1.25; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 div.sourceCode { margin: 1em 0; }
@@ -34,14 +34,16 @@
 }
 @media print {
 code.sourceCode { white-space: pre-wrap; }
-a.sourceLine { text-indent: -1em; padding-left: 1em; }
+code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
 }
-pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
-pre.numberSource a.sourceLine::before
-  { content: attr(data-line-number);
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
     position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    border: none; display: inline-block;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;
@@ -50,9 +52,9 @@
   }
 pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
 div.sourceCode
-  {  }
+  {   }
 @media screen {
-a.sourceLine::before { text-decoration: underline; }
+code.sourceCode > span > a:first-child::before { text-decoration: underline; }
 }
 code span.al { color: #ff0000; font-weight: bold; } /* Alert */
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
@@ -333,52 +335,52 @@
 </ul></li>
 </ul>
 <p>Thus the annotation for an edge that switches from state <code>s2</code> to state <code>s1</code> of character <code>cr1</code> would be constructed like this:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"> m &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="st">&quot;simmap:reconstructions&quot;</span>, <span class="dt">children =</span> <span class="kw">c</span>(</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2">        <span class="kw">meta</span>(<span class="st">&quot;simmap:reconstruction&quot;</span>, <span class="dt">children =</span> <span class="kw">c</span>(</a>
-<a class="sourceLine" id="cb1-3" data-line-number="3"></a>
-<a class="sourceLine" id="cb1-4" data-line-number="4">          <span class="kw">meta</span>(<span class="st">&quot;simmap:char&quot;</span>, <span class="st">&quot;cr1&quot;</span>),</a>
-<a class="sourceLine" id="cb1-5" data-line-number="5">          <span class="kw">meta</span>(<span class="st">&quot;simmap:stateChange&quot;</span>, <span class="dt">children =</span> <span class="kw">c</span>(</a>
-<a class="sourceLine" id="cb1-6" data-line-number="6">            <span class="kw">meta</span>(<span class="st">&quot;simmap:order&quot;</span>, <span class="dv">1</span>),</a>
-<a class="sourceLine" id="cb1-7" data-line-number="7">            <span class="kw">meta</span>(<span class="st">&quot;simmap:length&quot;</span>, <span class="st">&quot;0.2030&quot;</span>),</a>
-<a class="sourceLine" id="cb1-8" data-line-number="8">            <span class="kw">meta</span>(<span class="st">&quot;simmap:state&quot;</span>, <span class="st">&quot;s2&quot;</span>))),</a>
-<a class="sourceLine" id="cb1-9" data-line-number="9">          </a>
-<a class="sourceLine" id="cb1-10" data-line-number="10">          <span class="kw">meta</span>(<span class="st">&quot;simmap:char&quot;</span>, <span class="st">&quot;cr1&quot;</span>),</a>
-<a class="sourceLine" id="cb1-11" data-line-number="11">          <span class="kw">meta</span>(<span class="st">&quot;simmap:stateChange&quot;</span>, <span class="dt">children =</span> <span class="kw">c</span>(</a>
-<a class="sourceLine" id="cb1-12" data-line-number="12">            <span class="kw">meta</span>(<span class="st">&quot;simmap:order&quot;</span>, <span class="dv">2</span>),</a>
-<a class="sourceLine" id="cb1-13" data-line-number="13">            <span class="kw">meta</span>(<span class="st">&quot;simmap:length&quot;</span>, <span class="st">&quot;0.0022&quot;</span>),</a>
-<a class="sourceLine" id="cb1-14" data-line-number="14">            <span class="kw">meta</span>(<span class="st">&quot;simmap:state&quot;</span>, <span class="st">&quot;s1&quot;</span>)))</a>
-<a class="sourceLine" id="cb1-15" data-line-number="15">          ))))</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a> m &lt;-<span class="st"> </span><span class="kw">meta</span>(<span class="st">&quot;simmap:reconstructions&quot;</span>, <span class="dt">children =</span> <span class="kw">c</span>(</span>
+<span id="cb1-2"><a href="#cb1-2"></a>        <span class="kw">meta</span>(<span class="st">&quot;simmap:reconstruction&quot;</span>, <span class="dt">children =</span> <span class="kw">c</span>(</span>
+<span id="cb1-3"><a href="#cb1-3"></a></span>
+<span id="cb1-4"><a href="#cb1-4"></a>          <span class="kw">meta</span>(<span class="st">&quot;simmap:char&quot;</span>, <span class="st">&quot;cr1&quot;</span>),</span>
+<span id="cb1-5"><a href="#cb1-5"></a>          <span class="kw">meta</span>(<span class="st">&quot;simmap:stateChange&quot;</span>, <span class="dt">children =</span> <span class="kw">c</span>(</span>
+<span id="cb1-6"><a href="#cb1-6"></a>            <span class="kw">meta</span>(<span class="st">&quot;simmap:order&quot;</span>, <span class="dv">1</span>),</span>
+<span id="cb1-7"><a href="#cb1-7"></a>            <span class="kw">meta</span>(<span class="st">&quot;simmap:length&quot;</span>, <span class="st">&quot;0.2030&quot;</span>),</span>
+<span id="cb1-8"><a href="#cb1-8"></a>            <span class="kw">meta</span>(<span class="st">&quot;simmap:state&quot;</span>, <span class="st">&quot;s2&quot;</span>))),</span>
+<span id="cb1-9"><a href="#cb1-9"></a>          </span>
+<span id="cb1-10"><a href="#cb1-10"></a>          <span class="kw">meta</span>(<span class="st">&quot;simmap:char&quot;</span>, <span class="st">&quot;cr1&quot;</span>),</span>
+<span id="cb1-11"><a href="#cb1-11"></a>          <span class="kw">meta</span>(<span class="st">&quot;simmap:stateChange&quot;</span>, <span class="dt">children =</span> <span class="kw">c</span>(</span>
+<span id="cb1-12"><a href="#cb1-12"></a>            <span class="kw">meta</span>(<span class="st">&quot;simmap:order&quot;</span>, <span class="dv">2</span>),</span>
+<span id="cb1-13"><a href="#cb1-13"></a>            <span class="kw">meta</span>(<span class="st">&quot;simmap:length&quot;</span>, <span class="st">&quot;0.0022&quot;</span>),</span>
+<span id="cb1-14"><a href="#cb1-14"></a>            <span class="kw">meta</span>(<span class="st">&quot;simmap:state&quot;</span>, <span class="st">&quot;s1&quot;</span>)))</span>
+<span id="cb1-15"><a href="#cb1-15"></a>          ))))</span></code></pre></div>
 <p>Of course writing out such a definition manually becomes tedious quickly. Because these are just R commands, we can easily define a function that can loop over an assignment like this for each edge, extracting the appropriate order, length and state from an existing R object such as that provided in the <code>phytools</code> package.<br />
 Likewise, it is straightforward to define a function that reads this data using the <code>RNeXML</code> utilities and converts it back to the <code>phytools</code> package. The full implementation of this mapping can be seen in the <code>simmap_to_nexml()</code> and the <code>nexml_to_simmap()</code> functions provided in the <code>RNeXML</code> package.</p>
 <p>As the code indicates, the key step is simply to define the data in meta elements. In so doing, we have defined a custom namespace, <code>simmap</code>, to hold our variables. This allows us to provide a URL with more detailed descriptions of what each of these elements mean:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">nex &lt;-<span class="st"> </span><span class="kw">add_namespaces</span>(<span class="kw">c</span>(<span class="dt">simmap =</span> <span class="st">&quot;https://github.com/ropensci/RNeXML/tree/master/inst/simmap.md&quot;</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>nex &lt;-<span class="st"> </span><span class="kw">add_namespaces</span>(<span class="kw">c</span>(<span class="dt">simmap =</span> <span class="st">&quot;https://github.com/ropensci/RNeXML/tree/master/inst/simmap.md&quot;</span>))</span></code></pre></div>
 <p>At that URL we have posted a simple description of each term.</p>
 <p>Using this convention we can generate NeXML files containing <code>simmap</code> data, read those files into R, and convert them back into the <code>phytools</code> package format. These simple functions serve as further illustration of how <code>RNeXML</code> can be used to extend the NeXML standard. We illustrate their use briefly here, starting with loading a <code>nexml</code> object containing a <code>simmap</code> reconstruction into R:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">f &lt;-<span class="st"> </span><span class="kw">system.file</span>(<span class="st">&quot;examples&quot;</span>, <span class="st">&quot;simmap_ex.xml&quot;</span>, <span class="dt">package =</span> <span class="st">&quot;RNeXML&quot;</span>)</a>
-<a class="sourceLine" id="cb3-2" data-line-number="2">simmap_ex &lt;-<span class="st"> </span><span class="kw">read.nexml</span>(f)</a></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>f &lt;-<span class="st"> </span><span class="kw">system.file</span>(<span class="st">&quot;examples&quot;</span>, <span class="st">&quot;simmap_ex.xml&quot;</span>, <span class="dt">package =</span> <span class="st">&quot;RNeXML&quot;</span>)</span>
+<span id="cb3-2"><a href="#cb3-2"></a>simmap_ex &lt;-<span class="st"> </span><span class="kw">read.nexml</span>(f)</span></code></pre></div>
 <p>The <code>get_trees()</code> function can be used to return an <code>ape::phylo</code> tree as usual. <code>RNeXML</code> automatically detects the <code>simmap</code> reconstruction data and returns includes this in a <code>maps</code> element of the <code>ape::phylo</code> object, for use with other <code>phytools</code> functions.</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">phy &lt;-<span class="st"> </span><span class="kw">nexml_to_simmap</span>(simmap_ex)</a></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>phy &lt;-<span class="st"> </span><span class="kw">nexml_to_simmap</span>(simmap_ex)</span></code></pre></div>
 <p>We can then use various functions from <code>phytools</code> designed for <code>simmap</code> objects <span class="citation">(Revell 2012)</span>, such as the plotting function:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw">library</span>(<span class="st">&quot;phytools&quot;</span>)</a>
-<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="kw">plotSimmap</span>(phy)</a></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw">library</span>(<span class="st">&quot;phytools&quot;</span>)</span>
+<span id="cb5-2"><a href="#cb5-2"></a><span class="kw">plotSimmap</span>(phy)</span></code></pre></div>
 <pre><code>no colors provided. using the following legend:
        A        B        C 
  &quot;black&quot;    &quot;red&quot; &quot;green3&quot; </code></pre>
 <div class="figure">
-<img 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" alt="Stochastic character mapping on a phylogeny, as generated by the phytools package after parsing the simmap-extended NeXML." />
+<img 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alt />
 <p class="caption">Stochastic character mapping on a phylogeny, as generated by the phytools package after parsing the simmap-extended NeXML.</p>
 </div>
 <p>Likewise, we can convert the object back in the NeXML format and write it out to file to be read by other users.</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">nex &lt;-<span class="st"> </span><span class="kw">simmap_to_nexml</span>(phy) </a>
-<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="kw">nexml_write</span>(nex, <span class="st">&quot;simmap.xml&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>nex &lt;-<span class="st"> </span><span class="kw">simmap_to_nexml</span>(phy) </span>
+<span id="cb7-2"><a href="#cb7-2"></a><span class="kw">nexml_write</span>(nex, <span class="st">&quot;simmap.xml&quot;</span>)</span></code></pre></div>
 <pre><code>[1] &quot;simmap.xml&quot;</code></pre>
 <p>Though other NeXML parsers (for instance, for Perl or Python) have not been written explicitly to express <code>simmap</code> data, those parsers will nonetheless be able to successfully parse this file and expose the <code>simmap</code> data to the user.</p>
 <div id="refs" class="references">
 <div id="ref-Bollback_2006">
-<p>Bollback, JonathanP. 2006. <em>BMC Bioinformatics</em> 7 (1). Springer Science + Business Media: 88. <a href="https://doi.org/10.1186/1471-2105-7-88">https://doi.org/10.1186/1471-2105-7-88</a>.</p>
+<p>Bollback, JonathanP. 2006. <em>BMC Bioinformatics</em> 7 (1): 88. <a href="https://doi.org/10.1186/1471-2105-7-88">https://doi.org/10.1186/1471-2105-7-88</a>.</p>
 </div>
 <div id="ref-Huelsenbeck_2003">
-<p>Huelsenbeck, John P., Rasmus Nielsen, and Jonathan P. Bollback. 2003. “Stochastic Mapping of Morphological Characters.” <em>Systematic Biology</em> 52 (2). Oxford University Press (OUP): 131–58. <a href="https://doi.org/10.1080/10635150390192780">https://doi.org/10.1080/10635150390192780</a>.</p>
+<p>Huelsenbeck, John P., Rasmus Nielsen, and Jonathan P. Bollback. 2003. “Stochastic Mapping of Morphological Characters.” <em>Systematic Biology</em> 52 (2): 131–58. <a href="https://doi.org/10.1080/10635150390192780">https://doi.org/10.1080/10635150390192780</a>.</p>
 </div>
 <div id="ref-Revell_2012">
 <p>Revell, Liam J. 2012. “Phytools: An R Package for Phylogenetic Comparative Biology (and Other Things).” <em>Methods in Ecology and Evolution</em> 3: 217–23.</p>
diff -Nru r-cran-rnexml-2.4.4+ds/inst/doc/sparql.html r-cran-rnexml-2.4.5+ds/inst/doc/sparql.html
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 <h2>SPARQL Queries</h2>
 <p>Rich, semantically meaningful metadata lies at the heart of the NeXML standard. R provides a rich environment to unlock this information. While our previous examples have relied on the user knowing exactly what metadata they intend to extract (title, publication date, citation information, and so forth), <em>semantic</em> metadata has meaning that a computer can make use of, allowing us to make much more conceptually rich queries than those simple examples. The SPARQL query language is a powerful way to make use of such semantic information in making complex queries.</p>
 <p>While users should consult a formal introduction to SPARQL for further background, here we illustrate how SPARQL can be used in combination with R functions in ways that would be much more tedious to assemble with only traditional/non-semantic queries. The SPARQL query language is provided for the R environment through the <code>rrdf</code> package <span class="citation">[@Willighagen_2014]</span>, so we start by loading that package. We will also make use of functions from <code>phytools</code> and <code>RNeXML</code>.</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(<span class="st">&quot;rdflib&quot;</span>)</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw">library</span>(<span class="st">&quot;xml2&quot;</span>)</a>
-<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw">library</span>(<span class="st">&quot;phytools&quot;</span>)</a>
-<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="kw">library</span>(<span class="st">&quot;RNeXML&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw">library</span>(<span class="st">&quot;rdflib&quot;</span>)</span>
+<span id="cb1-2"><a href="#cb1-2"></a><span class="kw">library</span>(<span class="st">&quot;xml2&quot;</span>)</span>
+<span id="cb1-3"><a href="#cb1-3"></a><span class="kw">library</span>(<span class="st">&quot;phytools&quot;</span>)</span>
+<span id="cb1-4"><a href="#cb1-4"></a><span class="kw">library</span>(<span class="st">&quot;RNeXML&quot;</span>)</span></code></pre></div>
 <p>We read in an example file that contains semantic metadata annotations describing the taxonomic units (OTUs) used in the tree.</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">nexml &lt;-<span class="st"> </span><span class="kw">nexml_read</span>(<span class="kw">system.file</span>(<span class="st">&quot;examples/primates.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>nexml &lt;-<span class="st"> </span><span class="kw">nexml_read</span>(<span class="kw">system.file</span>(<span class="st">&quot;examples/primates.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>))</span></code></pre></div>
 <p>In particular, this example declares the taxon rank, NCBI identifier and parent taxon for each OTU, such as:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode xml"><code class="sourceCode xml"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">&lt;otu</span><span class="ot"> about=</span><span class="st">&quot;#ou541&quot;</span><span class="ot"> id=</span><span class="st">&quot;ou541&quot;</span><span class="ot"> label=</span><span class="st">&quot;Alouatta guariba&quot;</span><span class="kw">&gt;</span></a>
-<a class="sourceLine" id="cb3-2" data-line-number="2">      <span class="kw">&lt;meta</span><span class="ot"> href=</span><span class="st">&quot;http://ncbi.nlm.nih.gov/taxonomy/182256&quot;</span> </a>
-<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="ot">            id=</span><span class="st">&quot;ma20&quot;</span> </a>
-<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="ot">            rel=</span><span class="st">&quot;concept:toTaxon&quot;</span> </a>
-<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="ot">            xsi:type=</span><span class="st">&quot;nex:ResourceMeta&quot;</span><span class="kw">/&gt;</span></a>
-<a class="sourceLine" id="cb3-6" data-line-number="6">      <span class="kw">&lt;meta</span><span class="ot"> href=</span><span class="st">&quot;http://rs.tdwg.org/ontology/voc/TaxonRank#Species&quot;</span> </a>
-<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="ot">            id=</span><span class="st">&quot;ma21&quot;</span> </a>
-<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="ot">            rel=</span><span class="st">&quot;concept:rank&quot;</span> </a>
-<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="ot">            xsi:type=</span><span class="st">&quot;nex:ResourceMeta&quot;</span><span class="kw">/&gt;</span></a>
-<a class="sourceLine" id="cb3-10" data-line-number="10">      <span class="kw">&lt;meta</span><span class="ot"> href=</span><span class="st">&quot;http://ncbi.nlm.nih.gov/taxonomy/9499&quot;</span> </a>
-<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="ot">            id=</span><span class="st">&quot;ma22&quot;</span> </a>
-<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="ot">            rel=</span><span class="st">&quot;rdfs:subClassOf&quot;</span> </a>
-<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="ot">            xsi:type=</span><span class="st">&quot;nex:ResourceMeta&quot;</span><span class="kw">/&gt;</span></a>
-<a class="sourceLine" id="cb3-14" data-line-number="14">    <span class="kw">&lt;/otu&gt;</span></a></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode xml"><code class="sourceCode xml"><span id="cb3-1"><a href="#cb3-1"></a><span class="kw">&lt;otu</span><span class="ot"> about=</span><span class="st">&quot;#ou541&quot;</span><span class="ot"> id=</span><span class="st">&quot;ou541&quot;</span><span class="ot"> label=</span><span class="st">&quot;Alouatta guariba&quot;</span><span class="kw">&gt;</span></span>
+<span id="cb3-2"><a href="#cb3-2"></a>      <span class="kw">&lt;meta</span><span class="ot"> href=</span><span class="st">&quot;http://ncbi.nlm.nih.gov/taxonomy/182256&quot;</span> </span>
+<span id="cb3-3"><a href="#cb3-3"></a><span class="ot">            id=</span><span class="st">&quot;ma20&quot;</span> </span>
+<span id="cb3-4"><a href="#cb3-4"></a><span class="ot">            rel=</span><span class="st">&quot;concept:toTaxon&quot;</span> </span>
+<span id="cb3-5"><a href="#cb3-5"></a><span class="ot">            xsi:type=</span><span class="st">&quot;nex:ResourceMeta&quot;</span><span class="kw">/&gt;</span></span>
+<span id="cb3-6"><a href="#cb3-6"></a>      <span class="kw">&lt;meta</span><span class="ot"> href=</span><span class="st">&quot;http://rs.tdwg.org/ontology/voc/TaxonRank#Species&quot;</span> </span>
+<span id="cb3-7"><a href="#cb3-7"></a><span class="ot">            id=</span><span class="st">&quot;ma21&quot;</span> </span>
+<span id="cb3-8"><a href="#cb3-8"></a><span class="ot">            rel=</span><span class="st">&quot;concept:rank&quot;</span> </span>
+<span id="cb3-9"><a href="#cb3-9"></a><span class="ot">            xsi:type=</span><span class="st">&quot;nex:ResourceMeta&quot;</span><span class="kw">/&gt;</span></span>
+<span id="cb3-10"><a href="#cb3-10"></a>      <span class="kw">&lt;meta</span><span class="ot"> href=</span><span class="st">&quot;http://ncbi.nlm.nih.gov/taxonomy/9499&quot;</span> </span>
+<span id="cb3-11"><a href="#cb3-11"></a><span class="ot">            id=</span><span class="st">&quot;ma22&quot;</span> </span>
+<span id="cb3-12"><a href="#cb3-12"></a><span class="ot">            rel=</span><span class="st">&quot;rdfs:subClassOf&quot;</span> </span>
+<span id="cb3-13"><a href="#cb3-13"></a><span class="ot">            xsi:type=</span><span class="st">&quot;nex:ResourceMeta&quot;</span><span class="kw">/&gt;</span></span>
+<span id="cb3-14"><a href="#cb3-14"></a>    <span class="kw">&lt;/otu&gt;</span></span></code></pre></div>
 <p>In this example, we will construct a cladogram by using this information to identify the taxonomic rank of each OTU, and its shared parent taxonomic rank. (If this example looks complex, try writing down the steps to do this without the aid of the SPARQL queries). These examples show the manipulation of semantic triples, Unique Resource Identifiers (URIs) and use of the SPARQL “Join” operator.</p>
 <p>Note that this example can be run using <code>demo(&quot;sparql&quot;, &quot;RNeXML&quot;)</code> to see the code displayed in the R terminal and to avoid character errors that can occur in having to copy and paste from PDF files.</p>
 <p>We begin by extracting the RDF graph from the NeXML,</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">rdf &lt;-<span class="st"> </span><span class="kw">get_rdf</span>(<span class="kw">system.file</span>(<span class="st">&quot;examples/primates.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>))</a>
-<a class="sourceLine" id="cb4-2" data-line-number="2">tmp &lt;-<span class="st"> </span><span class="kw">tempfile</span>()  <span class="co"># so we must write the XML out first</span></a>
-<a class="sourceLine" id="cb4-3" data-line-number="3">xml2<span class="op">::</span><span class="kw">write_xml</span>(rdf, tmp) </a>
-<a class="sourceLine" id="cb4-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb4-5" data-line-number="5">graph &lt;-<span class="st"> </span><span class="kw">rdf_parse</span>(tmp)</a></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>rdf &lt;-<span class="st"> </span><span class="kw">get_rdf</span>(<span class="kw">system.file</span>(<span class="st">&quot;examples/primates.xml&quot;</span>, <span class="dt">package=</span><span class="st">&quot;RNeXML&quot;</span>))</span>
+<span id="cb4-2"><a href="#cb4-2"></a>tmp &lt;-<span class="st"> </span><span class="kw">tempfile</span>()  <span class="co"># so we must write the XML out first</span></span>
+<span id="cb4-3"><a href="#cb4-3"></a>xml2<span class="op">::</span><span class="kw">write_xml</span>(rdf, tmp) </span>
+<span id="cb4-4"><a href="#cb4-4"></a></span>
+<span id="cb4-5"><a href="#cb4-5"></a>graph &lt;-<span class="st"> </span><span class="kw">rdf_parse</span>(tmp)</span></code></pre></div>
 <p>We then fetch the NCBI URI for the taxon that has rank ‘Order’, i.e. the root of the primates phylogeny. The dot operator <code>.</code> between clauses implies a join, in this case</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">root &lt;-<span class="st"> </span><span class="kw">rdf_query</span>(graph, </a>
-<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="st">&quot;SELECT ?uri WHERE { </span></a>
-<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="st">    ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#rank&gt; &lt;http://rs.tdwg.org/ontology/voc/TaxonRank#Order&gt; . </span></a>
-<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="st">    ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#toTaxon&gt; ?uri    </span></a>
-<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="st">}&quot;</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a>root &lt;-<span class="st"> </span><span class="kw">rdf_query</span>(graph, </span>
+<span id="cb5-2"><a href="#cb5-2"></a><span class="st">&quot;SELECT ?uri WHERE { </span></span>
+<span id="cb5-3"><a href="#cb5-3"></a><span class="st">    ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#rank&gt; &lt;http://rs.tdwg.org/ontology/voc/TaxonRank#Order&gt; . </span></span>
+<span id="cb5-4"><a href="#cb5-4"></a><span class="st">    ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#toTaxon&gt; ?uri    </span></span>
+<span id="cb5-5"><a href="#cb5-5"></a><span class="st">}&quot;</span>)</span></code></pre></div>
 <p>This makes use of the SPARQL query language provided by the <code>rrdf</code> package. We will also define some helper functions that use SPARQL queries. Here we define a function to get the name</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">get_name &lt;-<span class="st"> </span><span class="cf">function</span>(id) {</a>
-<a class="sourceLine" id="cb6-2" data-line-number="2">  max &lt;-<span class="st"> </span><span class="kw">length</span>(nexml<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu)</a>
-<a class="sourceLine" id="cb6-3" data-line-number="3">  <span class="cf">for</span>(i <span class="cf">in</span> <span class="dv">1</span><span class="op">:</span>max) {</a>
-<a class="sourceLine" id="cb6-4" data-line-number="4">    <span class="cf">if</span> ( nexml<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[i]]<span class="op">@</span>id <span class="op">==</span><span class="st"> </span>id ) {</a>
-<a class="sourceLine" id="cb6-5" data-line-number="5">      label &lt;-<span class="st"> </span>nexml<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[i]]<span class="op">@</span>label</a>
-<a class="sourceLine" id="cb6-6" data-line-number="6">      label &lt;-<span class="st"> </span><span class="kw">gsub</span>(<span class="st">&quot; &quot;</span>,<span class="st">&quot;_&quot;</span>,label)</a>
-<a class="sourceLine" id="cb6-7" data-line-number="7">      <span class="kw">return</span>(label)</a>
-<a class="sourceLine" id="cb6-8" data-line-number="8">    }</a>
-<a class="sourceLine" id="cb6-9" data-line-number="9">  }</a>
-<a class="sourceLine" id="cb6-10" data-line-number="10">}</a></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a>get_name &lt;-<span class="st"> </span><span class="cf">function</span>(id) {</span>
+<span id="cb6-2"><a href="#cb6-2"></a>  max &lt;-<span class="st"> </span><span class="kw">length</span>(nexml<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu)</span>
+<span id="cb6-3"><a href="#cb6-3"></a>  <span class="cf">for</span>(i <span class="cf">in</span> <span class="dv">1</span><span class="op">:</span>max) {</span>
+<span id="cb6-4"><a href="#cb6-4"></a>    <span class="cf">if</span> ( nexml<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[i]]<span class="op">@</span>id <span class="op">==</span><span class="st"> </span>id ) {</span>
+<span id="cb6-5"><a href="#cb6-5"></a>      label &lt;-<span class="st"> </span>nexml<span class="op">@</span>otus[[<span class="dv">1</span>]]<span class="op">@</span>otu[[i]]<span class="op">@</span>label</span>
+<span id="cb6-6"><a href="#cb6-6"></a>      label &lt;-<span class="st"> </span><span class="kw">gsub</span>(<span class="st">&quot; &quot;</span>,<span class="st">&quot;_&quot;</span>,label)</span>
+<span id="cb6-7"><a href="#cb6-7"></a>      <span class="kw">return</span>(label)</span>
+<span id="cb6-8"><a href="#cb6-8"></a>    }</span>
+<span id="cb6-9"><a href="#cb6-9"></a>  }</span>
+<span id="cb6-10"><a href="#cb6-10"></a>}</span></code></pre></div>
 <p>Next, we define a recursive function to build a newick tree from the taxonomic rank information.</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">recurse &lt;-<span class="st"> </span><span class="cf">function</span>(node){</a>
-<a class="sourceLine" id="cb7-2" data-line-number="2">  </a>
-<a class="sourceLine" id="cb7-3" data-line-number="3">    <span class="co"># fetch the taxonomic rank and id string</span></a>
-<a class="sourceLine" id="cb7-4" data-line-number="4">    rank_query &lt;-<span class="st"> </span><span class="kw">paste0</span>(</a>
-<a class="sourceLine" id="cb7-5" data-line-number="5">        <span class="st">&quot;SELECT ?rank ?id WHERE {</span></a>
-<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="st">            ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#toTaxon&gt; &lt;&quot;</span>,node,<span class="st">&quot;&gt; .</span></a>
-<a class="sourceLine" id="cb7-7" data-line-number="7"><span class="st">            ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#rank&gt; ?rank</span></a>
-<a class="sourceLine" id="cb7-8" data-line-number="8"><span class="st">          }&quot;</span>)</a>
-<a class="sourceLine" id="cb7-9" data-line-number="9">    result &lt;-<span class="st"> </span><span class="kw">rdf_query</span>(graph, rank_query)</a>
-<a class="sourceLine" id="cb7-10" data-line-number="10">    </a>
-<a class="sourceLine" id="cb7-11" data-line-number="11">    <span class="co"># get the local ID, strip URI part</span></a>
-<a class="sourceLine" id="cb7-12" data-line-number="12">    id &lt;-<span class="st"> </span>result<span class="op">$</span>id</a>
-<a class="sourceLine" id="cb7-13" data-line-number="13">    id &lt;-<span class="st"> </span><span class="kw">gsub</span>(<span class="st">&quot;^.+#&quot;</span>, <span class="st">&quot;&quot;</span>, id, <span class="dt">perl =</span> <span class="ot">TRUE</span>)</a>
-<a class="sourceLine" id="cb7-14" data-line-number="14">    </a>
-<a class="sourceLine" id="cb7-15" data-line-number="15">    <span class="co"># if rank is terminal, return the name</span></a>
-<a class="sourceLine" id="cb7-16" data-line-number="16">    <span class="cf">if</span> (result<span class="op">$</span>rank <span class="op">==</span><span class="st"> &quot;http://rs.tdwg.org/ontology/voc/TaxonRank#Species&quot;</span>) {</a>
-<a class="sourceLine" id="cb7-17" data-line-number="17">        <span class="kw">return</span>(<span class="kw">get_name</span>(id))</a>
-<a class="sourceLine" id="cb7-18" data-line-number="18">    }</a>
-<a class="sourceLine" id="cb7-19" data-line-number="19">    </a>
-<a class="sourceLine" id="cb7-20" data-line-number="20">    <span class="co"># recurse deeper</span></a>
-<a class="sourceLine" id="cb7-21" data-line-number="21">    <span class="cf">else</span> {</a>
-<a class="sourceLine" id="cb7-22" data-line-number="22">        child_query &lt;-<span class="st"> </span><span class="kw">paste0</span>(</a>
-<a class="sourceLine" id="cb7-23" data-line-number="23">            <span class="st">&quot;SELECT ?uri WHERE {</span></a>
-<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="st">                ?id &lt;http://www.w3.org/2000/01/rdf-schema#subClassOf&gt; &lt;&quot;</span>,node,<span class="st">&quot;&gt; .</span></a>
-<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="st">                ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#toTaxon&gt; ?uri</span></a>
-<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="st">            }&quot;</span>)</a>
-<a class="sourceLine" id="cb7-27" data-line-number="27">        children &lt;-<span class="st"> </span><span class="kw">rdf_query</span>(graph, child_query)</a>
-<a class="sourceLine" id="cb7-28" data-line-number="28">        </a>
-<a class="sourceLine" id="cb7-29" data-line-number="29">        <span class="kw">return</span>(<span class="kw">paste</span>(<span class="st">&quot;(&quot;</span>, </a>
-<a class="sourceLine" id="cb7-30" data-line-number="30">                     <span class="kw">paste</span>(<span class="kw">sapply</span>(children<span class="op">$</span>uri, recurse), </a>
-<a class="sourceLine" id="cb7-31" data-line-number="31">                           <span class="dt">sep =</span> <span class="st">&quot;,&quot;</span>, <span class="dt">collapse =</span> <span class="st">&quot;,&quot;</span> ), </a>
-<a class="sourceLine" id="cb7-32" data-line-number="32">                     <span class="st">&quot;)&quot;</span>,  </a>
-<a class="sourceLine" id="cb7-33" data-line-number="33">                     <span class="kw">get_name</span>(id), <span class="co"># label interior nodes</span></a>
-<a class="sourceLine" id="cb7-34" data-line-number="34">                     <span class="dt">sep =</span> <span class="st">&quot;&quot;</span>, <span class="dt">collapse =</span> <span class="st">&quot;&quot;</span>))</a>
-<a class="sourceLine" id="cb7-35" data-line-number="35">    }</a>
-<a class="sourceLine" id="cb7-36" data-line-number="36">}</a></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>recurse &lt;-<span class="st"> </span><span class="cf">function</span>(node){</span>
+<span id="cb7-2"><a href="#cb7-2"></a>  </span>
+<span id="cb7-3"><a href="#cb7-3"></a>    <span class="co"># fetch the taxonomic rank and id string</span></span>
+<span id="cb7-4"><a href="#cb7-4"></a>    rank_query &lt;-<span class="st"> </span><span class="kw">paste0</span>(</span>
+<span id="cb7-5"><a href="#cb7-5"></a>        <span class="st">&quot;SELECT ?rank ?id WHERE {</span></span>
+<span id="cb7-6"><a href="#cb7-6"></a><span class="st">            ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#toTaxon&gt; &lt;&quot;</span>,node,<span class="st">&quot;&gt; .</span></span>
+<span id="cb7-7"><a href="#cb7-7"></a><span class="st">            ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#rank&gt; ?rank</span></span>
+<span id="cb7-8"><a href="#cb7-8"></a><span class="st">          }&quot;</span>)</span>
+<span id="cb7-9"><a href="#cb7-9"></a>    result &lt;-<span class="st"> </span><span class="kw">rdf_query</span>(graph, rank_query)</span>
+<span id="cb7-10"><a href="#cb7-10"></a>    </span>
+<span id="cb7-11"><a href="#cb7-11"></a>    <span class="co"># get the local ID, strip URI part</span></span>
+<span id="cb7-12"><a href="#cb7-12"></a>    id &lt;-<span class="st"> </span>result<span class="op">$</span>id</span>
+<span id="cb7-13"><a href="#cb7-13"></a>    id &lt;-<span class="st"> </span><span class="kw">gsub</span>(<span class="st">&quot;^.+#&quot;</span>, <span class="st">&quot;&quot;</span>, id, <span class="dt">perl =</span> <span class="ot">TRUE</span>)</span>
+<span id="cb7-14"><a href="#cb7-14"></a>    </span>
+<span id="cb7-15"><a href="#cb7-15"></a>    <span class="co"># if rank is terminal, return the name</span></span>
+<span id="cb7-16"><a href="#cb7-16"></a>    <span class="cf">if</span> (result<span class="op">$</span>rank <span class="op">==</span><span class="st"> &quot;http://rs.tdwg.org/ontology/voc/TaxonRank#Species&quot;</span>) {</span>
+<span id="cb7-17"><a href="#cb7-17"></a>        <span class="kw">return</span>(<span class="kw">get_name</span>(id))</span>
+<span id="cb7-18"><a href="#cb7-18"></a>    }</span>
+<span id="cb7-19"><a href="#cb7-19"></a>    </span>
+<span id="cb7-20"><a href="#cb7-20"></a>    <span class="co"># recurse deeper</span></span>
+<span id="cb7-21"><a href="#cb7-21"></a>    <span class="cf">else</span> {</span>
+<span id="cb7-22"><a href="#cb7-22"></a>        child_query &lt;-<span class="st"> </span><span class="kw">paste0</span>(</span>
+<span id="cb7-23"><a href="#cb7-23"></a>            <span class="st">&quot;SELECT ?uri WHERE {</span></span>
+<span id="cb7-24"><a href="#cb7-24"></a><span class="st">                ?id &lt;http://www.w3.org/2000/01/rdf-schema#subClassOf&gt; &lt;&quot;</span>,node,<span class="st">&quot;&gt; .</span></span>
+<span id="cb7-25"><a href="#cb7-25"></a><span class="st">                ?id &lt;http://rs.tdwg.org/ontology/voc/TaxonConcept#toTaxon&gt; ?uri</span></span>
+<span id="cb7-26"><a href="#cb7-26"></a><span class="st">            }&quot;</span>)</span>
+<span id="cb7-27"><a href="#cb7-27"></a>        children &lt;-<span class="st"> </span><span class="kw">rdf_query</span>(graph, child_query)</span>
+<span id="cb7-28"><a href="#cb7-28"></a>        </span>
+<span id="cb7-29"><a href="#cb7-29"></a>        <span class="kw">return</span>(<span class="kw">paste</span>(<span class="st">&quot;(&quot;</span>, </span>
+<span id="cb7-30"><a href="#cb7-30"></a>                     <span class="kw">paste</span>(<span class="kw">sapply</span>(children<span class="op">$</span>uri, recurse), </span>
+<span id="cb7-31"><a href="#cb7-31"></a>                           <span class="dt">sep =</span> <span class="st">&quot;,&quot;</span>, <span class="dt">collapse =</span> <span class="st">&quot;,&quot;</span> ), </span>
+<span id="cb7-32"><a href="#cb7-32"></a>                     <span class="st">&quot;)&quot;</span>,  </span>
+<span id="cb7-33"><a href="#cb7-33"></a>                     <span class="kw">get_name</span>(id), <span class="co"># label interior nodes</span></span>
+<span id="cb7-34"><a href="#cb7-34"></a>                     <span class="dt">sep =</span> <span class="st">&quot;&quot;</span>, <span class="dt">collapse =</span> <span class="st">&quot;&quot;</span>))</span>
+<span id="cb7-35"><a href="#cb7-35"></a>    }</span>
+<span id="cb7-36"><a href="#cb7-36"></a>}</span></code></pre></div>
 <p>With these functions in place, it is straight forward to build the tree from the semantic RDFa data and then visualize it</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">newick &lt;-<span class="st"> </span><span class="kw">paste</span>(<span class="kw">recurse</span>(root), <span class="st">&quot;;&quot;</span>, <span class="dt">sep =</span> <span class="st">&quot;&quot;</span>, <span class="dt">collapse =</span> <span class="st">&quot;&quot;</span>)</a>
-<a class="sourceLine" id="cb8-2" data-line-number="2">tree &lt;-<span class="st"> </span><span class="kw">read.newick</span>(<span class="dt">text =</span> newick)</a>
-<a class="sourceLine" id="cb8-3" data-line-number="3">collapsed &lt;-<span class="st"> </span><span class="kw">collapse.singles</span>(tree)</a>
-<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="kw">plot</span>(collapsed, </a>
-<a class="sourceLine" id="cb8-5" data-line-number="5">     <span class="dt">type=</span><span class="st">'cladogram'</span>, </a>
-<a class="sourceLine" id="cb8-6" data-line-number="6">     <span class="dt">show.tip.label=</span><span class="ot">FALSE</span>, </a>
-<a class="sourceLine" id="cb8-7" data-line-number="7">     <span class="dt">show.node.label=</span><span class="ot">TRUE</span>, </a>
-<a class="sourceLine" id="cb8-8" data-line-number="8">     <span class="dt">cex=</span><span class="fl">0.75</span>, </a>
-<a class="sourceLine" id="cb8-9" data-line-number="9">     <span class="dt">edge.color=</span><span class="st">'grey60'</span>, </a>
-<a class="sourceLine" id="cb8-10" data-line-number="10">     <span class="dt">label.offset=</span><span class="op">-</span><span class="dv">9</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>newick &lt;-<span class="st"> </span><span class="kw">paste</span>(<span class="kw">recurse</span>(root), <span class="st">&quot;;&quot;</span>, <span class="dt">sep =</span> <span class="st">&quot;&quot;</span>, <span class="dt">collapse =</span> <span class="st">&quot;&quot;</span>)</span>
+<span id="cb8-2"><a href="#cb8-2"></a>tree &lt;-<span class="st"> </span><span class="kw">read.newick</span>(<span class="dt">text =</span> newick)</span>
+<span id="cb8-3"><a href="#cb8-3"></a>collapsed &lt;-<span class="st"> </span><span class="kw">collapse.singles</span>(tree)</span>
+<span id="cb8-4"><a href="#cb8-4"></a><span class="kw">plot</span>(collapsed, </span>
+<span id="cb8-5"><a href="#cb8-5"></a>     <span class="dt">type=</span><span class="st">&#39;cladogram&#39;</span>, </span>
+<span id="cb8-6"><a href="#cb8-6"></a>     <span class="dt">show.tip.label=</span><span class="ot">FALSE</span>, </span>
+<span id="cb8-7"><a href="#cb8-7"></a>     <span class="dt">show.node.label=</span><span class="ot">TRUE</span>, </span>
+<span id="cb8-8"><a href="#cb8-8"></a>     <span class="dt">cex=</span><span class="fl">0.75</span>, </span>
+<span id="cb8-9"><a href="#cb8-9"></a>     <span class="dt">edge.color=</span><span class="st">&#39;grey60&#39;</span>, </span>
+<span id="cb8-10"><a href="#cb8-10"></a>     <span class="dt">label.offset=</span><span class="op">-</span><span class="dv">9</span>)</span></code></pre></div>
 <div class="figure">
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" 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" alt />
 <p class="caption">plot of chunk unnamed-chunk-8</p>
 </div>
 </div>
diff -Nru r-cran-rnexml-2.4.4+ds/inst/WORDLIST r-cran-rnexml-2.4.5+ds/inst/WORDLIST
--- r-cran-rnexml-2.4.4+ds/inst/WORDLIST	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/inst/WORDLIST	2020-06-18 17:32:34.000000000 +0000
@@ -4,6 +4,7 @@
 Bugfixes
 BugReports
 callNextMethod
+CDAO
 cladogram
 codecov
 datatypes
@@ -22,19 +23,15 @@
 ListOfmeta
 LiteralMeta
 MEE
-MethodDefinition
-MethodWithNext
 multiphylo
 multiPhylo
 namespaced
 newick
 Newick
-nex
 nexml
 NeXML
 NeXML's
 OmegaHat
-os
 otu
 OTU
 otus
@@ -60,8 +57,7 @@
 simmap
 solaris
 SPARQL
-standardGeneric
-taxadb
+taxald
 taxize
 testthat
 tidyr
diff -Nru r-cran-rnexml-2.4.4+ds/man/dot-callGeneric.Rd r-cran-rnexml-2.4.5+ds/man/dot-callGeneric.Rd
--- r-cran-rnexml-2.4.4+ds/man/dot-callGeneric.Rd	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/man/dot-callGeneric.Rd	2020-06-18 17:16:46.000000000 +0000
@@ -7,7 +7,7 @@
 .callGeneric(f, ..., .package = NULL)
 }
 \arguments{
-\item{f}{the generic, as a character string or a \link[methods:standardGeneric-class]{standardGeneric}
+\item{f}{the generic, as a character string or a \code{standardGeneric}
 object}
 
 \item{...}{the arguments (named and/or unnamed) with which to call the
@@ -24,12 +24,12 @@
 whose signature matches the arguments.
 }
 \details{
-Uses \code{\link[methods:selectMethod]{methods::selectMethod()}} to find the matching method. In theory,
+Uses \code{methods::selectMethod()} to find the matching method. In theory,
 this is at best wholly redundant with what standard S4 generics already
 do by themselves. However, the generics dispatch for S4 seems (at least
 currently) broken at least if the first argument in the signature is
 a class that name-clashes with a class defined in another package. In
 that case, whether the standard dispatch works correctly or not can depend
-on \link[base:search]{search order}, and can change within a session
+on \code{search()} order, and can change within a session
 depending on the order in which packages are loaded.
 }
diff -Nru r-cran-rnexml-2.4.4+ds/man/dot-methodWithNext.Rd r-cran-rnexml-2.4.5+ds/man/dot-methodWithNext.Rd
--- r-cran-rnexml-2.4.4+ds/man/dot-methodWithNext.Rd	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/man/dot-methodWithNext.Rd	2020-06-18 17:16:46.000000000 +0000
@@ -7,25 +7,25 @@
 .methodWithNext(method, nextMethod, .cache = FALSE)
 }
 \arguments{
-\item{method}{the \link[methods:MethodDefinition-class]{MethodDefinition} object to promote}
+\item{method}{the \code{MethodDefinition} object to promote}
 
-\item{nextMethod}{the \link[methods:MethodDefinition-class]{MethodDefinition}
+\item{nextMethod}{the \code{MethodDefinition}
 object to record as the next method}
 
 \item{.cache}{whether to cache the promoted method definition object
-(using \code{\link[methods:cacheMethod]{methods::cacheMethod()}})}
+(using \code{methods::cacheMethod()})}
 }
 \value{
-an instance of \link[methods:MethodWithNext-class]{MethodWithNext},
+an instance of \code{MethodWithNext},
 which has the next method in the \code{nextMethod} slot
 }
 \description{
 Promotes the given method definition to an instance of
-\link[methods:MethodWithNext-class]{MethodWithNext}, thereby recording the next
+\code{MethodWithNext}, thereby recording the next
 method in the \code{nextMethod} slot.
 }
 \note{
 \code{MethodWithNext} objects are normally returned by
-\code{\link[methods:addNextMethod]{methods::addNextMethod()}}, but a constructor function for the class
+\code{methods::addNextMethod()}, but a constructor function for the class
 seems missing (or is undocumented?). This provides one.
 }
diff -Nru r-cran-rnexml-2.4.4+ds/man/dot-sigLabel.Rd r-cran-rnexml-2.4.5+ds/man/dot-sigLabel.Rd
--- r-cran-rnexml-2.4.4+ds/man/dot-sigLabel.Rd	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/man/dot-sigLabel.Rd	2020-06-18 17:16:46.000000000 +0000
@@ -8,7 +8,7 @@
 }
 \arguments{
 \item{signature}{the signature for which to create a label, as a vector
-or list of strings, or as an instance of \link[methods:signature-class]{signature}.}
+or list of strings, or as an instance of \code{signature}.}
 }
 \value{
 a character string
@@ -17,5 +17,5 @@
 Creates a label for a signature mirroring the result of \code{.sigLabel()}
 in the \code{methods} package, which unfortunately does not export the function.
 This is needed, for example, for the \code{excluded} slot in the
-\link[methods:MethodWithNext-class]{MethodWithNext} class.
+\code{MethodWithNext} class.
 }
diff -Nru r-cran-rnexml-2.4.4+ds/man/findNextMethod.Rd r-cran-rnexml-2.4.5+ds/man/findNextMethod.Rd
--- r-cran-rnexml-2.4.4+ds/man/findNextMethod.Rd	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/man/findNextMethod.Rd	2020-06-18 17:16:46.000000000 +0000
@@ -7,23 +7,23 @@
 findNextMethod(method, f = NULL, envir = topenv())
 }
 \arguments{
-\item{method}{\link[methods:MethodDefinition-class]{MethodDefinition}), the method for which to find
+\item{method}{\code{MethodDefinition}, the method for which to find
 the next method}
 
-\item{f}{\link[methods:standardGeneric-class]{standardGeneric}, the standard generic for which to find
+\item{f}{\code{standardGeneric}, the standard generic for which to find
 the next method. By default this will be obtained from \code{method}.}
 
 \item{envir}{the environment in which to find the method}
 }
 \value{
-a \link[methods:MethodDefinition-class]{MethodDefinition} object that is the next method in the
+a \code{MethodDefinition} object that is the next method in the
 chain by inheritance
 }
 \description{
 Attempts to find the "next" method in the inheritance chain. This would
-(ideally) be the method that \code{\link[methods:callNextMethod]{methods::callNextMethod()}} would chain to,
-as a result of the method \code{\link[methods:addNextMethod]{methods::addNextMethod()}} would find (and return
-in the \code{nextMethod} slot of the \link[methods:MethodWithNext-class]{MethodWithNext}
+(ideally) be the method that \code{methods::callNextMethod()} would chain to,
+as a result of the method \code{methods::addNextMethod()} would find (and return
+in the \code{nextMethod} slot of the \code{MethodWithNext}
 object). Hence, in theory one shouldn't ever need this, but unfortunately
 \code{addNextMethod()} is broken (and errors out) if one of the classes in the
 signature name-clashes with an S4 class defined in another package that is
@@ -35,11 +35,11 @@
 the signature that are defined in the package of the generic method from
 which this function was invoked (directly or indirectly). If there are
 no such parameters in the signature, or if there is more than one,
-finding the next method is handed off to \code{\link[methods:addNextMethod]{methods::addNextMethod()}}.
+finding the next method is handed off to \code{methods::addNextMethod()}.
 }
 \note{
 In theory a class name clash between packages shouldn't be a problem
-because class names can be namespaced, and the \link[methods:MethodDefinition-class]{MethodDefinition}
+because class names can be namespaced, and the \code{MethodDefinition}
 object passed to \code{addNextMethod()} has all the necessary namespace
 information. Hopefully, at some point this gets fixed in R, and then we
 don't need this anymore.
diff -Nru r-cran-rnexml-2.4.4+ds/man/New.Rd r-cran-rnexml-2.4.5+ds/man/New.Rd
--- r-cran-rnexml-2.4.4+ds/man/New.Rd	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/man/New.Rd	2020-06-18 17:23:21.000000000 +0000
@@ -9,7 +9,7 @@
 \arguments{
 \item{Class}{the name of the S4 class to be instantiated}
 
-\item{...}{additional parameters for \code{\link[methods:new]{methods::new()}}}
+\item{...}{additional parameters for \code{methods::new()}}
 }
 \description{
 Convenience function for \code{\link[methods:new]{methods::new()}} that ensures that the provided
@@ -17,7 +17,7 @@
 }
 \details{
 If the provided class name is not already namespaced (see
-\code{\link[methods:packageSlot]{methods::packageSlot()}}), it will be namespaced with this package. This
+\code{methods::packageSlot()}), it will be namespaced with this package. This
 mechanism is used by \code{new()} to disambiguate if the class name clashes
 with a class defined in another package.
 }
@@ -25,5 +25,5 @@
 This may not completely eliminate messages on standard error about
 classes with the same name having been found in different packages. If
 they appear, they will most likely have come from the call to the
-\code{\link[methods:initialize]{methods::initialize()}} generic that \code{new()} issues at the end.
+\code{methods::initialize()} generic that \code{new()} issues at the end.
 }
diff -Nru r-cran-rnexml-2.4.4+ds/man/nexml_read.Rd r-cran-rnexml-2.4.5+ds/man/nexml_read.Rd
--- r-cran-rnexml-2.4.4+ds/man/nexml_read.Rd	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/man/nexml_read.Rd	2020-06-18 17:23:21.000000000 +0000
@@ -17,10 +17,10 @@
 \method{nexml_read}{XMLInternalNode}(x, ...)
 }
 \arguments{
-\item{x}{Path to the file to be read in. Or an \code{\link[XML]{XMLInternalDocument-class}}
-or \code{\link[XML]{XMLInternalNode-class}}}
+\item{x}{Path to the file to be read in. An \code{XML::XMLDocument-class}
+or \code{\link[XML]{XMLNode-class}}}
 
-\item{...}{Further arguments passed on to \code{\link[XML]{xmlParse}}}
+\item{...}{Further arguments passed on to \code{\link[XML]{xmlTreeParse}}}
 }
 \description{
 Read NeXML files into various R formats
diff -Nru r-cran-rnexml-2.4.4+ds/MD5 r-cran-rnexml-2.4.5+ds/MD5
--- r-cran-rnexml-2.4.4+ds/MD5	2020-05-10 07:20:06.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/MD5	2020-06-18 18:40:03.000000000 +0000
@@ -1,8 +1,8 @@
-5873214b38c6b263d661241008dbcd28 *DESCRIPTION
+bf4a60f68b8b88f01b01d05c285fbfd6 *DESCRIPTION
 15d87f8d4ecfd954c8dd3fc2b69a0cbb *LICENSE
 d3ca4a4a30db107bf214546993da18b0 *NAMESPACE
-e3ed91e89baa4ffcc562c865f6d5bf96 *NEWS.md
-fc64572d16aa8abed873a2d06d5f9202 *R/S4-utils.R
+d6d546910a9a609b9d1cf45385c93d56 *NEWS.md
+3b26266a79aa7be66ca089052978cda7 *R/S4-utils.R
 617ee40ffc60e9773ab6cb577795d5a3 *R/add_basic_meta.R
 60cae3f3a6b6937333174e993c62dc1e *R/add_characters.R
 d45bee5d6216eb5a58ace2ac03a01605 *R/add_meta.R
@@ -11,7 +11,7 @@
 203cc0d072014189f2d58bbd98f2c04b *R/character_classes.R
 dd365556d442022b36d9a35d3575c711 *R/classes.R
 3e199e16f9eb274d90a57f5a8d0ba60d *R/concatenate_nexml.R
-503aa392f7d16d171dd19675c15ab885 *R/constructors.R
+5bf67394fed601e4e3727ee7e23583c3 *R/constructors.R
 7bd3c9c98ffe79c342f9c367137050f5 *R/deprecated.R
 37f947cba89f7ff4fe149812311d314c *R/get_basic_metadata.R
 5bfd7fb03547cc2498c2a833a7f42fe2 *R/get_characters.R
@@ -32,7 +32,7 @@
 ea22b74789949c0aee569e7723171457 *R/nexml_get.R
 d615f93e38824b4b99547f9980201e7f *R/nexml_methods.R
 fb4f7834f086d1463b4b2ea12b895d5e *R/nexml_publish.R
-e55ca62202b4a3ea46b584fc3e8f2a6b *R/nexml_read.R
+1efeb260bd2678453c2e86ada5c9d0f0 *R/nexml_read.R
 226d8c580a9651bbf87fd6a87e4f8862 *R/nexml_validate.R
 2b511d5e0fd3f0a3e84b3d87dd589dbb *R/nexml_write.R
 3320451ddd2d28c9103af5791aedd8df *R/prefixed-uris.R
@@ -41,19 +41,19 @@
 78ad6d9378c8d09f85d70b4f62b176b6 *R/tbl_df.R
 f4b6cb1ca6b9aa652acfa20fd45c64bf *R/utils.R
 26bdb592ba52c26c5c72e2b7fa0103cc *README.md
-19c3e6244936634c32ab26cc7ca40474 *build/vignette.rds
+8b9bdce1678e392f58f88d8c8751ea89 *build/vignette.rds
 84b45265f4efcfb698335957ec44d7ba *inst/CITATION
-5b93ca7d234652c67049c98c84a77f1b *inst/WORDLIST
+df6222da66512d8ea0229e854a04c45a *inst/WORDLIST
 53d9a35d9cd319712e03e7fbb708fa4e *inst/doc/S4.Rmd
-97ac6eddb6197d775ee8cc808a39c9d4 *inst/doc/S4.html
+2cfe0746a8d164f76073f254dcd94785 *inst/doc/S4.html
 a45d97dd85139a23e964a1e1de851a1b *inst/doc/intro.Rmd
-2409b231751f0902780b1089d0a17862 *inst/doc/intro.html
+4ed9e538a789260750a3d85d93907af7 *inst/doc/intro.html
 45a7fb53f35659f31c048687f98b3c1f *inst/doc/metadata.Rmd
-985d4bb923a8c2eab7b84943b7415a02 *inst/doc/metadata.html
+33eb58084113eb3ab21e69b8c86622d1 *inst/doc/metadata.html
 056d24b223b46fc0684d0700ef60b898 *inst/doc/simmap.Rmd
-14192c0ede197123307d3630e31266b7 *inst/doc/simmap.html
+341e227f229a2ddf00c4feb1c01139e5 *inst/doc/simmap.html
 a30cf610a0caaa9c55570375365a50cf *inst/doc/sparql.Rmd
-83961633992319ff8eb593f18788f792 *inst/doc/sparql.html
+c2b06389ed5a0dd7339575fdfd2a5ba1 *inst/doc/sparql.html
 2de44d2898c22479b8a449767f1ab627 *inst/examples/RDFa2RDFXML.xsl
 64a60bc7b825e88ba931e1da5fd08e28 *inst/examples/biophylo.xml
 41cf6116441773694f8f32b88900d346 *inst/examples/characters.xml
@@ -88,7 +88,7 @@
 74361320b5d4bc935ea9d09a35463708 *inst/examples/trees.xml
 797825bdfed94f7c25aff9b96cbe7c09 *inst/simmap.md
 0a5770e137c21faf757227701e64ce44 *man/Annotated-class.Rd
-fe625e9a1df46abc18a8a6c828da8ea7 *man/New.Rd
+f93bfc6c6a7ebf7d67be1fafb0e51af1 *man/New.Rd
 075b4e06a9f9870eb384905adc088b69 *man/add_basic_meta.Rd
 d8dce73bf43efc048b5b58784ef2a344 *man/add_characters.Rd
 ae1683091ec897a6081b1c3544454693 *man/add_meta.Rd
@@ -99,15 +99,15 @@
 073c5a4efa3439f9d5f97f33907a662a *man/charzero_as_empty.Rd
 a077e4820b3c1fc2acc8140f76816986 *man/coalesce_.Rd
 5e89d73d8f6f29f11b30e7407393c8a5 *man/constructors.Rd
-d9fb8add43d81022f3e3bac75a6d1e99 *man/dot-callGeneric.Rd
-e1210d83531da37a56eef78191adfbd5 *man/dot-methodWithNext.Rd
-0610d2bef9e1ba3bb6ccf950086e903e *man/dot-sigLabel.Rd
+9a63c1626bfce5ef2f73f48be1123165 *man/dot-callGeneric.Rd
+73cb59252c5763ccf945d60b754390b2 *man/dot-methodWithNext.Rd
+31f6dad68afd80100630973f0fec6168 *man/dot-sigLabel.Rd
 5933d8fbe23bf032e4f1f5833a9a1bfc *man/expand_prefix.Rd
 a208c0e85e8f757aa4874a46605399c2 *man/figures/Figure1-1.png
 137d3ca84d14b53bd115dc20fc543e32 *man/figures/logo.svg
 1094ac0f795bcfad18b3a471460394e1 *man/figures/unnamed-chunk-5-1.png
 c6c9401b08aed0ae9428fe3942744a29 *man/figures/unnamed-chunk-8-1.png
-3f0a5106de00eddd401a7ab97addde7f *man/findNextMethod.Rd
+622df1d39255824c0f9377b1b1b71606 *man/findNextMethod.Rd
 46141ac49e495797b726d46e7a3047ff *man/flatten_multiphylo.Rd
 0b14b4b9bed1b3a5a7fd8c596da679c3 *man/get_all_meta.Rd
 6e9da9c9841c59d476b5ff5b015dc31c *man/get_characters.Rd
@@ -134,7 +134,7 @@
 e31ce2ecf494fb019749f5fbae9bc0bf *man/nexml_figshare.Rd
 8870b15dc364067f1d46389e8abf312c *man/nexml_get.Rd
 047f7282c78133f948b4c507316bf040 *man/nexml_publish.Rd
-dfb35fa6a865cef5f5903c13134e1833 *man/nexml_read.Rd
+4b05c4f7535aa8c62bc618650aab7012 *man/nexml_read.Rd
 006dec7bb0b1700d3f93f23c3f029667 *man/nexml_validate.Rd
 744fdbd499c02480061d87d9f1b84d2c *man/nexml_write.Rd
 24a6d3057367c0a59b27575ee62d765e *man/reset_id_counter.Rd
@@ -145,12 +145,11 @@
 48237ccd63c622e45f6ce13edbd3d9b3 *man/toPhylo.Rd
 78a7f421feb7208c58c9197ba4eb5edb *tests/spelling.R
 bbde9fbfa538d3160fff44967d1fb0dd *tests/test-all.R
-853b41159e31e64a801403e3142ec108 *tests/testthat/Rplots.pdf
 c64d6a3a0af9b631471c129a0957e626 *tests/testthat/conversions.R
 6f68db3a881fdbb5e0dfd5a68c165f8d *tests/testthat/geiger_test.R
 47bde26b1620dc77e8309d4246102c8e *tests/testthat/helper-RNeXML.R
 0a11f0ca45c7d531e3e3631ee8a9ca1a *tests/testthat/test_01_exported_util.R
-ca733e6e0b5034244edf7c65eb359658 *tests/testthat/test_01_utils.R
+93e4a7c1e64144d6f7e4fcbfabd2b3c5 *tests/testthat/test_01_utils.R
 831365b04f052e195e869edb3dd4e9bf *tests/testthat/test_02_summary.R
 d2a1f07f597acaf42f5d159747bd6175 *tests/testthat/test_ape.R
 11363dfa842ebea09a74ad972a8b6e12 *tests/testthat/test_characters.R
diff -Nru r-cran-rnexml-2.4.4+ds/NEWS.md r-cran-rnexml-2.4.5+ds/NEWS.md
--- r-cran-rnexml-2.4.4+ds/NEWS.md	2020-05-09 05:40:35.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/NEWS.md	2020-06-18 17:32:09.000000000 +0000
@@ -14,7 +14,7 @@
 v2.4.3
 ------
 
-- This update fixes a minor bug in a unit test for compatibilty 
+- This update fixes a minor bug in a unit test for compatibility 
   with R-devel (4.0.0) as requested by CRAN (#245)
 
 v2.4.2
diff -Nru r-cran-rnexml-2.4.4+ds/R/constructors.R r-cran-rnexml-2.4.5+ds/R/constructors.R
--- r-cran-rnexml-2.4.4+ds/R/constructors.R	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/R/constructors.R	2020-06-18 17:23:21.000000000 +0000
@@ -4,15 +4,15 @@
 #' class name is namespaced with a package name.
 #'
 #' If the provided class name is not already namespaced (see
-#' [methods::packageSlot()]), it will be namespaced with this package. This
+#' `methods::packageSlot()`), it will be namespaced with this package. This
 #' mechanism is used by `new()` to disambiguate if the class name clashes
 #' with a class defined in another package.
 #' @note This may not completely eliminate messages on standard error about
 #'   classes with the same name having been found in different packages. If
 #'   they appear, they will most likely have come from the call to the
-#'   [methods::initialize()] generic that `new()` issues at the end.
+#'   `methods::initialize()` generic that `new()` issues at the end.
 #' @param Class the name of the S4 class to be instantiated
-#' @param ... additional parameters for [methods::new()]
+#' @param ... additional parameters for `methods::new()`
 #' @importFrom methods new className packageSlot
 New <- function(Class, ...) {
   if (is.null(packageSlot(Class))) Class <- className(Class, "RNeXML")
diff -Nru r-cran-rnexml-2.4.4+ds/R/nexml_read.R r-cran-rnexml-2.4.5+ds/R/nexml_read.R
--- r-cran-rnexml-2.4.4+ds/R/nexml_read.R	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/R/nexml_read.R	2020-06-18 17:23:21.000000000 +0000
@@ -1,8 +1,8 @@
 #' Read NeXML files into various R formats
 #' 
-#' @param x Path to the file to be read in. Or an \code{\link[XML]{XMLInternalDocument-class}} 
-#' or \code{\link[XML]{XMLInternalNode-class}} 
-#' @param ... Further arguments passed on to \code{\link[XML]{xmlParse}}
+#' @param x Path to the file to be read in. An `XML::XMLDocument-class`
+#' or \code{\link[XML]{XMLNode-class}} 
+#' @param ... Further arguments passed on to \code{\link[XML]{xmlTreeParse}}
 #' @import XML
 #' @import httr
 #' @aliases nexml_read read.nexml 
diff -Nru r-cran-rnexml-2.4.4+ds/R/S4-utils.R r-cran-rnexml-2.4.5+ds/R/S4-utils.R
--- r-cran-rnexml-2.4.4+ds/R/S4-utils.R	2020-05-09 05:38:55.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/R/S4-utils.R	2020-06-18 17:16:46.000000000 +0000
@@ -3,9 +3,9 @@
 #' Finds the method that callNextMethod() should chain to
 #'
 #' Attempts to find the "next" method in the inheritance chain. This would
-#' (ideally) be the method that [methods::callNextMethod()] would chain to,
-#' as a result of the method [methods::addNextMethod()] would find (and return
-#' in the `nextMethod` slot of the [MethodWithNext][methods::MethodWithNext-class]
+#' (ideally) be the method that `methods::callNextMethod()` would chain to,
+#' as a result of the method `methods::addNextMethod()` would find (and return
+#' in the `nextMethod` slot of the `MethodWithNext`
 #' object). Hence, in theory one shouldn't ever need this, but unfortunately
 #' `addNextMethod()` is broken (and errors out) if one of the classes in the
 #' signature name-clashes with an S4 class defined in another package that is
@@ -16,18 +16,18 @@
 #' the signature that are defined in the package of the generic method from
 #' which this function was invoked (directly or indirectly). If there are
 #' no such parameters in the signature, or if there is more than one,
-#' finding the next method is handed off to [methods::addNextMethod()].
+#' finding the next method is handed off to `methods::addNextMethod()`.
 #' @note In theory a class name clash between packages shouldn't be a problem
-#'   because class names can be namespaced, and the [MethodDefinition][methods::MethodDefinition-class]
+#'   because class names can be namespaced, and the `MethodDefinition`
 #'   object passed to `addNextMethod()` has all the necessary namespace
 #'   information. Hopefully, at some point this gets fixed in R, and then we
 #'   don't need this anymore.
-#' @param method [MethodDefinition][methods::MethodDefinition-class]), the method for which to find
+#' @param method `MethodDefinition`, the method for which to find
 #'   the next method
-#' @param f [standardGeneric][methods::standardGeneric-class], the standard generic for which to find
+#' @param f `standardGeneric`, the standard generic for which to find
 #'   the next method. By default this will be obtained from `method`.
 #' @param envir the environment in which to find the method
-#' @return a [MethodDefinition][methods::MethodDefinition-class] object that is the next method in the
+#' @return a `MethodDefinition` object that is the next method in the
 #'   chain by inheritance
 #' @importFrom methods getClassDef selectMethod addNextMethod
 #' @importFrom utils packageName
@@ -74,17 +74,17 @@
 #' Saves the next method in the method meta data
 #'
 #' Promotes the given method definition to an instance of
-#' [MethodWithNext][methods::MethodWithNext-class], thereby recording the next
+#' `MethodWithNext`, thereby recording the next
 #' method in the `nextMethod` slot.
 #' @note `MethodWithNext` objects are normally returned by
-#'   [methods::addNextMethod()], but a constructor function for the class
+#'   `methods::addNextMethod()`, but a constructor function for the class
 #'   seems missing (or is undocumented?). This provides one.
-#' @param method the [MethodDefinition][methods::MethodDefinition-class] object to promote
-#' @param nextMethod the [MethodDefinition][methods::MethodDefinition-class]
+#' @param method the `MethodDefinition` object to promote
+#' @param nextMethod the `MethodDefinition`
 #'   object to record as the next method
 #' @param .cache whether to cache the promoted method definition object
-#'   (using [methods::cacheMethod()])
-#' @return an instance of [MethodWithNext][methods::MethodWithNext-class],
+#'   (using `methods::cacheMethod()`)
+#' @return an instance of `MethodWithNext`,
 #'   which has the next method in the `nextMethod` slot
 #' @importFrom methods getGeneric cacheMethod
 #' @importClassesFrom methods MethodWithNext
@@ -108,9 +108,9 @@
 #' Creates a label for a signature mirroring the result of `.sigLabel()`
 #' in the `methods` package, which unfortunately does not export the function.
 #' This is needed, for example, for the `excluded` slot in the
-#' [MethodWithNext][methods::MethodWithNext-class] class.
+#' `MethodWithNext` class.
 #' @param signature the signature for which to create a label, as a vector
-#'   or list of strings, or as an instance of [signature][methods::signature-class].
+#'   or list of strings, or as an instance of `signature`.
 #' @return a character string
 .sigLabel <- function(signature) {
   if (is(signature, "signature")) signature <- signature@.Data
@@ -121,13 +121,13 @@
 #'
 #' If the calling environment does not have the next method to be invoked
 #' in the inheritance chain cached yet, this will find the next method
-#' (using [findNextMethod()]), and cache it in the calling environment such
-#' that a subsequent call to [methods::callNextMethod()] will find and use
+#' (using `findNextMethod()`, and cache it in the calling environment such
+#' that a subsequent call to `methods::callNextMethod()` will find and use
 #' it.
 #'
 #' As per the description, what this function does would normally already
-#' be done by invoking [methods::callNextMethod()], so in theory this should
-#' be entirely redundant at best. However, [methods::addNextMethod()], which
+#' be done by invoking `methods::callNextMethod()`, so in theory this should
+#' be entirely redundant at best. However, `methods::addNextMethod()`, which
 #' is invoked by `callNextMethod()` if a next method isn't cached yet, is
 #' broken (errors out) if one of the classes in the signature name-clashes
 #' with a class defined in another package. Calling this function prior to
@@ -162,15 +162,15 @@
 #' Calls the given generic with the given arguments, using the method
 #' whose signature matches the arguments.
 #'
-#' Uses [methods::selectMethod()] to find the matching method. In theory,
+#' Uses `methods::selectMethod()` to find the matching method. In theory,
 #' this is at best wholly redundant with what standard S4 generics already
 #' do by themselves. However, the generics dispatch for S4 seems (at least
 #' currently) broken at least if the first argument in the signature is
 #' a class that name-clashes with a class defined in another package. In
 #' that case, whether the standard dispatch works correctly or not can depend
-#' on [search order][base::search()], and can change within a session
+#' on `search()` order, and can change within a session
 #' depending on the order in which packages are loaded.
-#' @param f the generic, as a character string or a [standardGeneric][methods::standardGeneric-class]
+#' @param f the generic, as a character string or a `standardGeneric`
 #'   object
 #' @param ... the arguments (named and/or unnamed) with which to call the
 #'   matching method
Binary files /tmp/tmphEnBrH/NqJhFZ_sZA/r-cran-rnexml-2.4.4+ds/tests/testthat/Rplots.pdf and /tmp/tmphEnBrH/GDK9lWVYoP/r-cran-rnexml-2.4.5+ds/tests/testthat/Rplots.pdf differ
diff -Nru r-cran-rnexml-2.4.4+ds/tests/testthat/test_01_utils.R r-cran-rnexml-2.4.5+ds/tests/testthat/test_01_utils.R
--- r-cran-rnexml-2.4.4+ds/tests/testthat/test_01_utils.R	2020-05-09 05:38:57.000000000 +0000
+++ r-cran-rnexml-2.4.5+ds/tests/testthat/test_01_utils.R	2020-06-17 03:51:37.000000000 +0000
@@ -126,8 +126,12 @@
   # (1) dplyr::coalesce is strict about type, and for some reason vectors
   # that are all NAs default to type logical
   testthat::expect_is(dta[, "col1"], "logical")
-  testthat::expect_error(dplyr::coalesce(dta$col1, dta$col3, last))
-  testthat::expect_error(dplyr::coalesce(dta$col3, last)) # col3 is a factor
+  
+  # EDIT: I believe these ungraceful behaviors in dplyr are resolved
+  # in the most recent version, and so these no longer throw errors:
+  
+  ## testthat::expect_error(dplyr::coalesce(dta$col1, dta$col3, last))
+  ## testthat::expect_error(dplyr::coalesce(dta$col3, last)) # col3 is a factor
   # (2) dplyr::coalesce doesn't gracefully deal with NULL arguments, which
   # can result from referencing column names that aren't there, requiring
   # a conditional testing for presence of the column