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Code Releases Activity

(v0.7.1.9074) CI updates

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dr. M.S. (Matthijs) Berends
2019-09-16 12:00:56 +02:00
parent 398c5bdc4f
commit f553a08a7b
19 changed files with 322 additions and 173 deletions
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@ -78,7 +78,7 @@
</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">0.7.1.9072</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9074</span>
</span>
</div>
@ -225,11 +225,11 @@
</div>
<div id="amr-0-7-1-9072" class="section level1">
<div id="amr-0-7-1-9074" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9072" class="anchor"></a>AMR 0.7.1.9072<small> Unreleased </small>
<a href="#amr-0-7-1-9074" class="anchor"></a>AMR 0.7.1.9074<small> Unreleased </small>
</h1>
<p><small>Last updated: 12-Sep-2019</small></p>
<p><small>Last updated: 16-Sep-2019</small></p>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -305,6 +305,17 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set):
<ul>
<li>Self-learning algorithm - the function now gains experience from previously determined microorganism IDs and learns from it (yielding 80-95% speed improvement for any guess after the first try)</li>
<li>Big improvement for misspelled input</li>
<li>These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus</li>
<li>Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology</li>
<li>Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)</li>
<li>Added support for 5,000 new fungi</li>
<li>Added support for unknown yeasts and fungi</li>
</ul>
</li>
<li>Renamed data set <code>septic_patients</code> to <code>example_isolates</code>
</li>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
@ -323,16 +334,6 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
</li>
<li>Fix and speed improvement for <code><a href="../reference/mo_property.html">mo_shortname()</a></code>
</li>
<li>Algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (by which some additions were made to the <code>microorganisms</code> data set:
<ul>
<li>Big improvement for misspelled input</li>
<li>These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus</li>
<li>Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology</li>
<li>Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)</li>
<li>Added support for 5,000 new fungi</li>
<li>Added support for unknown yeasts and fungi</li>
</ul>
</li>
<li>Fix for using <code>mo_*</code> functions where the coercion uncertainties and failures would not be available through <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> and <code><a href="../reference/as.mo.html">mo_failures()</a></code> anymore</li>
<li>Deprecated the <code>country</code> parameter of <code><a href="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li>
<li>The <code>name</code> of <code>RIF</code> is now Rifampicin instead of Rifampin</li>
@ -1264,7 +1265,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9072">0.7.1.9072</a></li>
<li><a href="#amr-0-7-1-9074">0.7.1.9074</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>