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(v1.4.0.9052) replaced all sapply's with type-safe vapply's

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dr. M.S. (Matthijs) Berends
2020-12-28 22:24:33 +01:00
parent ccf13dd6c0
commit 526f8afb08
37 changed files with 155 additions and 117 deletions
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2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>

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docs/LICENSE-text.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">1.4.0.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>

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docs/articles/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">1.4.0.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>

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docs/authors.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">1.4.0.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>

5
docs/index.html
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@ -43,7 +43,7 @@
</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">1.4.0.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>
@ -337,7 +337,7 @@ Since you are one of our users, we would like to know how you use the package an
<div id="latest-released-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
<p><img src="https://www.r-pkg.org/badges/version-ago/AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR"></p>
<p><a href="https://cran.r-project.org/package=AMR"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
@ -347,6 +347,7 @@ Since you are one of our users, we would like to know how you use the package an
<div id="latest-development-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
<p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
<p>The latest and unpublished development version can be installed from GitHub using:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span>

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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">1.4.0.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409051" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9051">
<a href="#amr-1409051" class="anchor"></a>AMR 1.4.0.9051<small> Unreleased </small>
<div id="amr-1409052" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9052">
<a href="#amr-1409052" class="anchor"></a>AMR 1.4.0.9052<small> Unreleased </small>
</h1>
<div id="last-updated-27-december-2020" class="section level2">
<div id="last-updated-28-december-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-27-december-2020" class="anchor"></a><small>Last updated: 27 December 2020</small>
<a href="#last-updated-28-december-2020" class="anchor"></a><small>Last updated: 28 December 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -317,6 +317,9 @@
<li>More extensive unit tests</li>
<li>Internal calls to <code><a href="https://rdrr.io/r/base/options.html">options()</a></code> were all removed in favour of a new internal environment <code>pkg_env</code>
</li>
<li>Improved internal type setting (among other things: replaced all <code><a href="https://rdrr.io/r/base/lapply.html">sapply()</a></code> calls with <code><a href="https://rdrr.io/r/base/lapply.html">vapply()</a></code>)</li>
<li>Added CodeFactor as a continuous code review to this package: <a href="https://www.codefactor.io/repository/github/msberends/amr/" class="uri">https://www.codefactor.io/repository/github/msberends/amr/</a>
</li>
<li>Added Dr. Rogier Schade as contributor</li>
</ul>
</div>

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docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-12-27T22:17Z
last_built: 2020-12-28T21:24Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>
@ -289,7 +289,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</tr>
<tr>
<th>ampc_cephalosporin_resistance</th>
<td><p>a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code>; '<em>EUCAST Expert Rules v3.2 on Enterobacterales</em>' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of <code>NA</code> for this argument will remove results for these agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. <br /> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Enterobacter</em>, <em>Klebsiella aerogenes</em>, <em>Citrobacter freundii</em>, <em>Hafnia alvei</em>, <em>Serratia</em>, <em>Morganella morganii</em>, <em>Providencia</em>.</p></td>
<td><p>a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code>; '<em>EUCAST Expert Rules v3.2 on Enterobacterales</em>' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of <code>NA</code> for this argument will remove results for these agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. <br /> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Enterobacter, Klebsiella aerogenes, Citrobacter freundii, Hafnia alvei, Serratia, Morganella morganii, Providencia</em>.</p></td>
</tr>
<tr>
<th>...</th>

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docs/reference/index.html
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</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">1.4.0.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>

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docs/survey.html
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</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">1.4.0.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9052</span>
</span>
</div>