mirror of
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(v1.7.1) New CRAN release
This commit is contained in:
@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
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</span>
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</div>
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@ -236,40 +236,16 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1709002" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.0.9002">
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<a href="#amr-1709002" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0.9002</h1>
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<div id="last-updated-1-june-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-1-june-2021" class="anchor"></a><small>Last updated: 1 June 2021</small>
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</h2>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new" class="anchor"></a>New</h3>
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<ul>
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<li>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</li>
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</ul>
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</div>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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<a href="#changed" class="anchor"></a>Changed</h3>
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<ul>
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<li>
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<code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now supports grouping using the <code>dplyr</code> package</li>
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<li>As requested by CRAN administrators: decreased package size by 3 MB in costs of a ~50 times slower loading time of the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>)</li>
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</ul>
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</div>
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</div>
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</div>
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<div id="amr-170" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.0">
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<a href="#amr-170" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0</h1>
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<div id="amr-171" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1">
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<a href="#amr-171" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1</h1>
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<div id="breaking-change" class="section level3">
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<h3 class="hasAnchor">
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<a href="#breaking-change" class="anchor"></a>Breaking change</h3>
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<ul>
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<li><p>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</p></li>
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<li>
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<p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>, <code><a href="../reference/AMR-deprecated.html">filter_aminoglycosides()</a></code>). These functions are now deprecated and will be removed in a next release.</p>
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<p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>, <code><a href="../reference/AMR-deprecated.html">filter_aminoglycosides()</a></code>). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R">
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<span class="co"># select columns with results for carbapenems</span>
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@ -289,9 +265,9 @@
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</li>
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</ul>
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</div>
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<div id="new-1" class="section level3">
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new-1" class="anchor"></a>New</h3>
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<a href="#new" class="anchor"></a>New</h3>
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<ul>
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<li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
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</li>
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@ -313,10 +289,12 @@
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</li>
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</ul>
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</div>
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<div id="changed-1" class="section level3">
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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<a href="#changed-1" class="anchor"></a>Changed</h3>
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<a href="#changed" class="anchor"></a>Changed</h3>
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<ul>
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<li>
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<code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now supports grouping using the <code>dplyr</code> package</li>
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<li>Custom MDRO guidelines (<code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code>):
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<ul>
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<li>Custom MDRO guidelines can now be combined with other custom MDRO guidelines using <code><a href="https://rdrr.io/r/base/c.html">c()</a></code>
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@ -365,6 +343,7 @@
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<h3 class="hasAnchor">
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<a href="#other" class="anchor"></a>Other</h3>
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<ul>
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<li>As requested by CRAN administrators: decreased package size by 3 MB in costs of a slower loading time of the package</li>
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<li>All unit tests are now processed by the <code>tinytest</code> package, instead of the <code>testthat</code> package. The <code>testthat</code> package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the <code>tinytest</code> package is very lightweight and dependency-free.</li>
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</ul>
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</div>
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@ -372,9 +351,9 @@
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<div id="amr-160" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0">
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<a href="#amr-160" class="anchor"></a><small> 2021-03-14 </small><code>AMR</code> 1.6.0</h1>
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<div id="new-2" class="section level3">
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<div id="new-1" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new-2" class="anchor"></a>New</h3>
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<a href="#new-1" class="anchor"></a>New</h3>
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<ul>
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<li>
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<p>Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function and in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC and disk diffusion values. This is now the default guideline in this package.</p>
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@ -448,9 +427,9 @@
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</li>
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</ul>
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</div>
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<div id="changed-2" class="section level3">
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<div id="changed-1" class="section level3">
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<h3 class="hasAnchor">
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<a href="#changed-2" class="anchor"></a>Changed</h3>
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<a href="#changed-1" class="anchor"></a>Changed</h3>
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<ul>
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<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LPSN</a>)
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<ul>
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@ -509,9 +488,9 @@
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<div id="amr-150" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0">
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<a href="#amr-150" class="anchor"></a><small> 2021-01-06 </small><code>AMR</code> 1.5.0</h1>
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<div id="new-3" class="section level3">
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<div id="new-2" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new-3" class="anchor"></a>New</h3>
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<a href="#new-2" class="anchor"></a>New</h3>
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<ul>
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<li>
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<p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
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@ -527,9 +506,9 @@
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<li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
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</ul>
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</div>
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<div id="changed-3" class="section level3">
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<div id="changed-2" class="section level3">
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<h3 class="hasAnchor">
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<a href="#changed-3" class="anchor"></a>Changed</h3>
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||||
<a href="#changed-2" class="anchor"></a>Changed</h3>
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<ul>
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||||
<li><p>New argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to correct for AmpC de-repressed cephalosporin-resistant mutants</p></li>
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<li>
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@ -622,9 +601,9 @@
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<div id="amr-140" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0">
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<a href="#amr-140" class="anchor"></a><small> 2020-10-08 </small><code>AMR</code> 1.4.0</h1>
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<div id="new-4" class="section level3">
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<div id="new-3" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new-4" class="anchor"></a>New</h3>
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<a href="#new-3" class="anchor"></a>New</h3>
|
||||
<ul>
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||||
<li><p>Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can now correct for more than 180 different antibiotics and the <code><a href="../reference/mdro.html">mdro()</a></code> function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function consequently gained the arguments <code>version_breakpoints</code> (at the moment defaults to v10.0, 2020) and <code>version_expertrules</code> (at the moment defaults to v3.2, 2020). The <code>example_isolates</code> data set now also reflects the change from v3.1 to v3.2. The <code><a href="../reference/mdro.html">mdro()</a></code> function now accepts <code>guideline == "EUCAST3.1"</code> and <code>guideline == "EUCAST3.2"</code>.</p></li>
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<li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
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@ -644,9 +623,9 @@
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<li><p>Support for skimming classes <code><rsi></code>, <code><mic></code>, <code><disk></code> and <code><mo></code> with the <code>skimr</code> package</p></li>
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</ul>
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</div>
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<div id="changed-4" class="section level3">
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<div id="changed-3" class="section level3">
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<h3 class="hasAnchor">
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<a href="#changed-4" class="anchor"></a>Changed</h3>
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<a href="#changed-3" class="anchor"></a>Changed</h3>
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<ul>
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<li><p>Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.</p></li>
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<li>
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<div id="amr-130" class="section level1">
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<h1 class="page-header" data-toc-text="1.3.0">
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<a href="#amr-130" class="anchor"></a><small> 2020-07-31 </small><code>AMR</code> 1.3.0</h1>
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<div id="new-5" class="section level3">
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<div id="new-4" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new-5" class="anchor"></a>New</h3>
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<a href="#new-4" class="anchor"></a>New</h3>
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<ul>
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<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
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<li>
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@ -749,9 +728,9 @@
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<li><p>Added argument <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “<” (but not “<=”) will always return “S” and values starting with “>” (but not “>=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
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</ul>
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</div>
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<h3 class="hasAnchor">
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<a href="#changed-5" class="anchor"></a>Changed</h3>
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<a href="#changed-4" class="anchor"></a>Changed</h3>
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<ul>
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<li>
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<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
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</li>
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<h3 class="hasAnchor">
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<a href="#changed-6" class="anchor"></a>Changed</h3>
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<a href="#changed-5" class="anchor"></a>Changed</h3>
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<ul>
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<li>Taxonomy:
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<ul>
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@ -870,17 +849,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<div id="amr-110" class="section level1">
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<h1 class="page-header" data-toc-text="1.1.0">
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<a href="#amr-110" class="anchor"></a><small> 2020-04-15 </small><code>AMR</code> 1.1.0</h1>
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<div id="new-6" class="section level3">
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<div id="new-5" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new-6" class="anchor"></a>New</h3>
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<a href="#new-5" class="anchor"></a>New</h3>
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<ul>
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<li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
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<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
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</ul>
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</div>
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<h3 class="hasAnchor">
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<a href="#changed-7" class="anchor"></a>Changed</h3>
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<a href="#changed-6" class="anchor"></a>Changed</h3>
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<ul>
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<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
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<ul>
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@ -911,9 +890,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<div id="amr-101" class="section level1">
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<h1 class="page-header" data-toc-text="1.0.1">
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<a href="#amr-101" class="anchor"></a><small> 2020-02-23 </small><code>AMR</code> 1.0.1</h1>
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<div id="changed-8" class="section level3">
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<div id="changed-7" class="section level3">
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<h3 class="hasAnchor">
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<a href="#changed-8" class="anchor"></a>Changed</h3>
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<a href="#changed-7" class="anchor"></a>Changed</h3>
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<ul>
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<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
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<li>
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@ -936,9 +915,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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<h1 class="page-header" data-toc-text="1.0.0">
|
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<a href="#amr-100" class="anchor"></a><small> 2020-02-17 </small><code>AMR</code> 1.0.0</h1>
|
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<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
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<div id="new-7" class="section level3">
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<div id="new-6" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new-7" class="anchor"></a>New</h3>
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<a href="#new-6" class="anchor"></a>New</h3>
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<ul>
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<li>Support for the newest <a href="https://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
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<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
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@ -1033,9 +1012,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
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</li>
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</ul>
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</div>
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<div id="new-8" class="section level3">
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<div id="new-7" class="section level3">
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<a href="#new-8" class="anchor"></a>New</h3>
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<a href="#new-7" class="anchor"></a>New</h3>
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<ul>
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<li>
|
||||
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
|
||||
@ -1152,9 +1131,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="new-9" class="section level3">
|
||||
<div id="new-8" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-9" class="anchor"></a>New</h3>
|
||||
<a href="#new-8" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
|
||||
@ -1219,9 +1198,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-9" class="section level3">
|
||||
<div id="changed-8" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-9" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-8" 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). Many thanks to all contributors that helped improving the algorithms.
|
||||
<ul>
|
||||
@ -1285,9 +1264,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div id="amr-071" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="0.7.1">
|
||||
<a href="#amr-071" class="anchor"></a><small> 2019-06-23 </small><code>AMR</code> 0.7.1</h1>
|
||||
<div id="new-10" class="section level4">
|
||||
<div id="new-9" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-10" class="anchor"></a>New</h4>
|
||||
<a href="#new-9" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
|
||||
@ -1331,9 +1310,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-10" class="section level4">
|
||||
<div id="changed-9" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-10" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-9" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> are now lowercase</li>
|
||||
<li>Fixed bug in translation of microorganism names</li>
|
||||
@ -1369,9 +1348,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div id="amr-070" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="0.7.0">
|
||||
<a href="#amr-070" class="anchor"></a><small> 2019-06-03 </small><code>AMR</code> 0.7.0</h1>
|
||||
<div id="new-11" class="section level4">
|
||||
<div id="new-10" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-11" class="anchor"></a>New</h4>
|
||||
<a href="#new-10" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
|
||||
<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
|
||||
@ -1379,9 +1358,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-11" class="section level4">
|
||||
<div id="changed-10" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-11" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-10" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
|
||||
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
|
||||
@ -1465,9 +1444,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div id="amr-061" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="0.6.1">
|
||||
<a href="#amr-061" class="anchor"></a><small> 2019-03-29 </small><code>AMR</code> 0.6.1</h1>
|
||||
<div id="changed-12" class="section level4">
|
||||
<div id="changed-11" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-12" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-11" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
|
||||
</li>
|
||||
@ -1484,9 +1463,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Contains the complete manual of this package and all of its functions with an explanation of their arguments</li>
|
||||
<li>Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more.</li>
|
||||
</ul>
|
||||
<div id="new-12" class="section level4">
|
||||
<div id="new-11" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-12" class="anchor"></a>New</h4>
|
||||
<a href="#new-11" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li><p><strong>BREAKING</strong>: removed deprecated functions, arguments and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</p></li>
|
||||
<li>
|
||||
@ -1584,9 +1563,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-13" class="section level4">
|
||||
<div id="changed-12" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-13" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-12" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
|
||||
<ul>
|
||||
@ -1729,9 +1708,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div id="amr-050" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="0.5.0">
|
||||
<a href="#amr-050" class="anchor"></a><small> 2018-11-30 </small><code>AMR</code> 0.5.0</h1>
|
||||
<div id="new-13" class="section level4">
|
||||
<div id="new-12" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-13" class="anchor"></a>New</h4>
|
||||
<a href="#new-12" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Repository moved to GitLab</li>
|
||||
<li>Function <code>count_all</code> to get all available isolates (that like all <code>portion_*</code> and <code>count_*</code> functions also supports <code>summarise</code> and <code>group_by</code>), the old <code>n_rsi</code> is now an alias of <code>count_all</code>
|
||||
@ -1742,9 +1721,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-14" class="section level4">
|
||||
<div id="changed-13" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-14" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-13" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
|
||||
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
|
||||
@ -1852,9 +1831,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div id="amr-040" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="0.4.0">
|
||||
<a href="#amr-040" class="anchor"></a><small> 2018-10-01 </small><code>AMR</code> 0.4.0</h1>
|
||||
<div id="new-14" class="section level4">
|
||||
<div id="new-13" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-14" class="anchor"></a>New</h4>
|
||||
<a href="#new-13" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li><p>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</p></li>
|
||||
<li>
|
||||
@ -1932,9 +1911,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-15" class="section level4">
|
||||
<div id="changed-14" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-15" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-14" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
|
||||
<li>
|
||||
@ -2000,9 +1979,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div id="amr-030" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="0.3.0">
|
||||
<a href="#amr-030" class="anchor"></a><small> 2018-08-14 </small><code>AMR</code> 0.3.0</h1>
|
||||
<div id="new-15" class="section level4">
|
||||
<div id="new-14" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-15" class="anchor"></a>New</h4>
|
||||
<a href="#new-14" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
|
||||
@ -2073,9 +2052,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-16" class="section level4">
|
||||
<div id="changed-15" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-16" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-15" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
|
||||
<li>More antibiotics added as arguments for EUCAST rules</li>
|
||||
@ -2136,9 +2115,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div id="amr-020" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="0.2.0">
|
||||
<a href="#amr-020" class="anchor"></a><small> 2018-05-03 </small><code>AMR</code> 0.2.0</h1>
|
||||
<div id="new-16" class="section level4">
|
||||
<div id="new-15" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-16" class="anchor"></a>New</h4>
|
||||
<a href="#new-15" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Full support for Windows, Linux and macOS</li>
|
||||
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
|
||||
@ -2158,9 +2137,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-17" class="section level4">
|
||||
<div id="changed-16" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-17" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-16" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
|
||||
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>
|
||||
|
||||
Reference in New Issue
Block a user