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(v1.6.0.9019) website fix
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Package: AMR
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Package: AMR
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Version: 1.6.0.9018
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Version: 1.6.0.9019
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Date: 2021-05-04
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Date: 2021-05-05
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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Authors@R: c(
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person(role = c("aut", "cre"),
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person(role = c("aut", "cre"),
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6
NEWS.md
6
NEWS.md
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# `AMR` 1.6.0.9018
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# `AMR` 1.6.0.9019
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## <small>Last updated: 4 May 2021</small>
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## <small>Last updated: 5 May 2021</small>
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### New
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### New
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* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
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* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
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* Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
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* Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
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* Support for all four methods to determine first isolates as summarised by Hindler *et al* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
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* Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
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* The `first_isolate()` function gained the argument `method` that has to be "phenotype-based", "episode-based", "patient-based", or "isolate-based". The old behaviour is equal to "episode-based". The new default is "phenotype-based" if antimicrobial test results are available, and "episode-based" otherwise. This new default will yield slightly more isolates for selection (which is a good thing).
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* The `first_isolate()` function gained the argument `method` that has to be "phenotype-based", "episode-based", "patient-based", or "isolate-based". The old behaviour is equal to "episode-based". The new default is "phenotype-based" if antimicrobial test results are available, and "episode-based" otherwise. This new default will yield slightly more isolates for selection (which is a good thing).
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* Since fungal isolates can also be selected, the functions `key_antibiotics()` and `key_antibiotics_equal()` are now deprecated in favour of the `key_antimicrobials()` and `antimicrobial_equal()` functions. Also, the new `all_antimicrobials()` function works like the old `key_antibiotics()` function, but includes any column with antimicrobial test results. Using `key_antimicrobials()` still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new `antifungal` argument to set antifungal agents (antimycotics).
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* Since fungal isolates can also be selected, the functions `key_antibiotics()` and `key_antibiotics_equal()` are now deprecated in favour of the `key_antimicrobials()` and `antimicrobial_equal()` functions. Also, the new `all_antimicrobials()` function works like the old `key_antibiotics()` function, but includes any column with antimicrobial test results. Using `key_antimicrobials()` still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new `antifungal` argument to set antifungal agents (antimycotics).
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* Using `type == "points"` in the `first_isolate()` function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the new `all_antimicrobials()`
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* Using `type == "points"` in the `first_isolate()` function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the new `all_antimicrobials()`
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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</span>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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</div>
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}
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}
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// remove leading newline in code examples on changelog
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// remove leading newline in code examples on changelog
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$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
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if ($("body .template-news").length > 0) {
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$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
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}
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// PR for 'R for Data Science' on How To pages
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// PR for 'R for Data Science' on How To pages
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if ($(".template-article").length > 0) {
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if ($(".template-article").length > 0) {
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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</span>
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</div>
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</div>
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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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<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>
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<div id="amr-1609018" class="section level1">
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<div id="amr-1609019" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9018">
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<h1 class="page-header" data-toc-text="1.6.0.9019">
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<a href="#amr-1609018" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9018</h1>
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<a href="#amr-1609019" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9019</h1>
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<div id="last-updated-4-may-2021" class="section level2">
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<div id="last-updated-5-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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<a href="#last-updated-4-may-2021" class="anchor"></a><small>Last updated: 4 May 2021</small>
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<a href="#last-updated-5-may-2021" class="anchor"></a><small>Last updated: 5 May 2021</small>
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</h2>
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</h2>
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<div id="new" class="section level3">
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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<h3 class="hasAnchor">
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@ -250,7 +250,7 @@
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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>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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</li>
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<li>Function <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to make taxonomic names within a string italic, with support for markdown and ANSI</li>
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<li>Function <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to make taxonomic names within a string italic, with support for markdown and ANSI</li>
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<li>Support for all four methods to determine first isolates as summarised by Hindler <em>et al</em> (doi: <a href="https://doi.org/10.1086/511864">10.1086/511864</a>): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
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<li>Support for all four methods to determine first isolates as summarised by Hindler <em>et al.</em> (doi: <a href="https://doi.org/10.1086/511864">10.1086/511864</a>): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
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<ul>
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<ul>
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<li>The <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function gained the argument <code>method</code> that has to be “phenotype-based”, “episode-based”, “patient-based”, or “isolate-based”. The old behaviour is equal to “episode-based”. The new default is “phenotype-based” if antimicrobial test results are available, and “episode-based” otherwise. This new default will yield slightly more isolates for selection (which is a good thing).</li>
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<li>The <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function gained the argument <code>method</code> that has to be “phenotype-based”, “episode-based”, “patient-based”, or “isolate-based”. The old behaviour is equal to “episode-based”. The new default is “phenotype-based” if antimicrobial test results are available, and “episode-based” otherwise. This new default will yield slightly more isolates for selection (which is a good thing).</li>
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<li>Since fungal isolates can also be selected, the functions <code><a href="../reference/AMR-deprecated.html">key_antibiotics()</a></code> and <code><a href="../reference/AMR-deprecated.html">key_antibiotics_equal()</a></code> are now deprecated in favour of the <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code>antimicrobial_equal()</code> functions. Also, the new <code><a href="../reference/key_antimicrobials.html">all_antimicrobials()</a></code> function works like the old <code><a href="../reference/AMR-deprecated.html">key_antibiotics()</a></code> function, but includes any column with antimicrobial test results. Using <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new <code>antifungal</code> argument to set antifungal agents (antimycotics).</li>
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<li>Since fungal isolates can also be selected, the functions <code><a href="../reference/AMR-deprecated.html">key_antibiotics()</a></code> and <code><a href="../reference/AMR-deprecated.html">key_antibiotics_equal()</a></code> are now deprecated in favour of the <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code>antimicrobial_equal()</code> functions. Also, the new <code><a href="../reference/key_antimicrobials.html">all_antimicrobials()</a></code> function works like the old <code><a href="../reference/AMR-deprecated.html">key_antibiotics()</a></code> function, but includes any column with antimicrobial test results. Using <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new <code>antifungal</code> argument to set antifungal agents (antimycotics).</li>
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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datasets: datasets.html
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resistance_predict: resistance_predict.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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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-05-04T13:19Z
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last_built: 2021-05-05T13:26Z
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urls:
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urls:
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reference: https://msberends.github.io/AMR//reference
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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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article: https://msberends.github.io/AMR//articles
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.6.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9019</span>
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</span>
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}
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}
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// remove leading newline in code examples on changelog
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// remove leading newline in code examples on changelog
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$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
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if ($("body .template-news").length > 0) {
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$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
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}
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// PR for 'R for Data Science' on How To pages
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// PR for 'R for Data Science' on How To pages
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if ($(".template-article").length > 0) {
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if ($(".template-article").length > 0) {
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