mirror of https://github.com/msberends/AMR.git
(v1.7.1.9018) translation fix
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Package: AMR
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Version: 1.7.1.9017
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Date: 2021-07-08
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Version: 1.7.1.9018
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Date: 2021-07-11
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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7
NEWS.md
7
NEWS.md
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# `AMR` 1.7.1.9017
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## <small>Last updated: 8 July 2021</small>
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# `AMR` 1.7.1.9018
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## <small>Last updated: 11 July 2021</small>
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### Changed
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* Antibiotic class selectors (see `ab_class()`)
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@ -18,7 +18,8 @@
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* When warnings are throws because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
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* Taxonomic names now print in italic in tibbles, if created with `mo_name()`, `mo_fullname()`, `mo_shortname()`, `mo_genus()` or `mo_family()`
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* `ab_name()` gained argument `snake_case`, which is useful for column renaming
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* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is `ggplot2` bug #4511, soon to be fixed)
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* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is bug ggplot2#4511, soon to be fixed)
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* Fix for minor translation errors
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# `AMR` 1.7.1
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BIN
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@ -17,8 +17,8 @@ unknown species TRUE TRUE FALSE TRUE unbekannte Art onbekende soort especie desc
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unknown subspecies TRUE TRUE FALSE TRUE unbekannte Unterart onbekende ondersoort subespecie desconocida sottospecie sconosciute sous-espèce inconnue subespécies desconhecida
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unknown rank TRUE TRUE FALSE TRUE unbekannter Rang onbekende rang rango desconocido grado sconosciuto rang inconnu classificação desconhecido
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group TRUE TRUE FALSE TRUE Gruppe groep grupo gruppo groupe grupo
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CoNS FALSE TRUE FALSE FALSE KNS CNS SCN
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CoPS FALSE TRUE FALSE FALSE KPS CPS SCP
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CoNS FALSE TRUE FALSE TRUE KNS CNS SCN
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CoPS FALSE TRUE FALSE TRUE KPS CPS SCP
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Gram-negative TRUE TRUE FALSE FALSE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo
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Gram-positive TRUE TRUE FALSE FALSE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo
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^Bacteria$ TRUE TRUE FALSE FALSE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias
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@ -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="https://msberends.github.io/AMR//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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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@ -39,7 +39,7 @@
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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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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@ -192,7 +192,7 @@
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 class="date">08 July 2021</h4>
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<h4 class="date">11 July 2021</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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@ -382,17 +382,17 @@
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<div id="latest-development-version" class="section level4">
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<h4 class="hasAnchor">
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<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
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<p>[R-code-check][<a href="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" class="uri">https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master</a>](<a href="https://github.com/msberends/AMR/actions" class="uri">https://github.com/msberends/AMR/actions</a>) [CodeFactor][<a href="https://www.codefactor.io/repository/github/msberends/amr/badge" class="uri">https://www.codefactor.io/repository/github/msberends/amr/badge</a>](<a href="https://www.codefactor.io/repository/github/msberends/amr" class="uri">https://www.codefactor.io/repository/github/msberends/amr</a>) [Codecov][<a href="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" class="uri">https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg</a>](<a href="https://codecov.io/gh/msberends/AMR?branch=master" class="uri">https://codecov.io/gh/msberends/AMR?branch=master</a>)</p>
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<p><a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"></a> <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>
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<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
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<ol>
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<li>
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<p>Directly, using:</p>
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<p>Manually, using:</p>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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<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> <span class="co"># if you haven't already</span>
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<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
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</li>
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<li>
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<p>From the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’):</p>
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<p>Automatically, using the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’):</p>
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<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
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msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
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@ -405,7 +405,7 @@
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<div id="get-started" class="section level3">
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<h3 class="hasAnchor">
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<a href="#get-started" class="anchor"></a>Get started</h3>
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<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the links in the ‘How to’ menu.</p>
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<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
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</div>
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<div id="short-introduction" class="section level3">
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<h3 class="hasAnchor">
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@ -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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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@ -236,12 +236,12 @@
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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-1719017" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9017">
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<a href="#amr-1719017" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9017</h1>
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<div id="last-updated-8-july-2021" class="section level2">
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<div id="amr-1719018" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9018">
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<a href="#amr-1719018" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9018</h1>
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<div id="last-updated-11-july-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-8-july-2021" class="anchor"></a><small>Last updated: 8 July 2021</small>
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<a href="#last-updated-11-july-2021" class="anchor"></a><small>Last updated: 11 July 2021</small>
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</h2>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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@ -273,7 +273,8 @@
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</li>
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<li>
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<code><a href="../reference/ab_property.html">ab_name()</a></code> gained argument <code>snake_case</code>, which is useful for column renaming</li>
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<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is <code>ggplot2</code> bug <a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li>
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<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is bug ggplot2<a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li>
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<li>Fix for minor translation errors</li>
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</ul>
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</div>
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</div>
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-07-08T21:03Z
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last_built: 2021-07-11T11:19Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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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">1.7.1.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
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</span>
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</div>
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15
index.md
15
index.md
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@ -110,30 +110,33 @@ It will be downloaded and installed automatically. For RStudio, click on the men
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#### Latest development version
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![R-code-check][https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master](https://github.com/msberends/AMR/actions)
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![CodeFactor][https://www.codefactor.io/repository/github/msberends/amr/badge](https://www.codefactor.io/repository/github/msberends/amr)
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![Codecov][https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg](https://codecov.io/gh/msberends/AMR?branch=master)
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[](https://codecov.io/gh/msberends/AMR?branch=master)
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[](https://www.codefactor.io/repository/github/msberends/amr)
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[](https://codecov.io/gh/msberends/AMR?branch=master)
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The latest and unpublished development version can be installed from GitHub in two ways:
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1. Directly, using:
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1. Manually, using:
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```r
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install.packages("remotes") # if you haven't already
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remotes::install_github("msberends/AMR")
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```
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2. From the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), by adding [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'):
|
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2. Automatically, using the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), by adding [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'):
|
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```r
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options(repos = c(getOption("repos"),
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msberends = "https://msberends.r-universe.dev"))
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```
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After this, you can install and update this `AMR` package like any official release (e.g., using `install.packages("AMR")` or in RStudio via *Tools* > *Check for Package Updates...*).
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You can also download the latest build from our repository: <https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz>
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### Get started
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To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
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To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://msberends.github.io/AMR/articles/).
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### Short introduction
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@ -23,12 +23,10 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_identical(as.character(mo_genus("B_GRAMP", language = "pt")),
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"(Gram positivos desconhecidos)")
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expect_identical(as.character(mo_fullname("CoNS", "en")), "Coagulase-negative Staphylococcus (CoNS)")
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expect_identical(as.character(mo_fullname("CoNS", "de")), "Koagulase-negative Staphylococcus (KNS)")
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expect_identical(as.character(mo_fullname("CoNS", "nl")), "Coagulase-negatieve Staphylococcus (CNS)")
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expect_identical(as.character(mo_fullname("CoNS", "es")), "Staphylococcus coagulasa negativo (SCN)")
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expect_identical(as.character(mo_fullname("CoNS", "it")), "Staphylococcus negativo coagulasi (CoNS)")
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expect_identical(as.character(mo_fullname("CoNS", "pt")), "Staphylococcus coagulase negativo (CoNS)")
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expect_identical(mo_genus("B_GRAMP", language = "pt"), "(Gram positivos desconhecidos)")
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expect_identical(mo_fullname("CoNS", "en"), "Coagulase-negative Staphylococcus (CoNS)")
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expect_identical(mo_fullname("CoNS", "de"), "Koagulase-negative Staphylococcus (KNS)")
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expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")
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expect_identical(mo_fullname("CoNS", "es"), "Staphylococcus coagulasa negativo (SCN)")
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expect_identical(mo_fullname("CoNS", "it"), "Staphylococcus negativo coagulasi (CoNS)")
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expect_identical(mo_fullname("CoNS", "pt"), "Staphylococcus coagulase negativo (CoNS)")
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