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(v1.1.0.9021) 1st isolates update

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dr. M.S. (Matthijs) Berends
2020-05-28 10:51:56 +02:00
parent 86d44054f0
commit d9a4b0bcaf
51 changed files with 483 additions and 1106 deletions
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docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9021</span>
</span>
</div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1-1-0-9020" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0.9020">
<a href="#amr-1-1-0-9020" class="anchor"></a>AMR 1.1.0.9020<small> Unreleased </small>
<div id="amr-1-1-0-9021" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0.9021">
<a href="#amr-1-1-0-9021" class="anchor"></a>AMR 1.1.0.9021<small> Unreleased </small>
</h1>
<div id="last-updated-27-may-2020" class="section level2">
<div id="last-updated-28-may-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-27-may-2020" class="anchor"></a><small>Last updated: 27-May-2020</small>
<a href="#last-updated-28-may-2020" class="anchor"></a><small>Last updated: 28-May-2020</small>
</h2>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -260,7 +260,7 @@ Negative effects of this change are:
<ul>
<li>Taxonomy:
<ul>
<li>Updated the taxonomy of microorganisms tot May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020)</li>
<li>Updated the taxonomy of microorganisms tot May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). <strong>Note:</strong> a taxonomic update may always impact determination of first isolates (using <code><a href="../reference/first_isolate.html">first_isolate()</a></code>), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.</li>
<li>Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string)</li>
</ul>
</li>