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(v1.3.0.9037) pre-release
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Package: AMR
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Package: AMR
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Version: 1.3.0.9036
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Version: 1.3.0.9037
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Date: 2020-09-30
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Date: 2020-09-30
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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8
NEWS.md
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NEWS.md
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# AMR 1.3.0.9036
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# AMR 1.3.0.9037
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## <small>Last updated: 30 September 2020</small>
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## <small>Last updated: 30 September 2020</small>
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Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
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Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt about this package to. We are those reviewers very grateful for going through our code so thoroughly!
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### Breaking
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* Removed functions `portion_R()`, `portion_S()` and `portion_I()` that were deprecated since version 0.9.0 (November 2019) and were replaced with `proportion_R()`, `proportion_S()` and `proportion_I()`.
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### New
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### New
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* 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 `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` 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 `eucast_rules()` function consequently gained the parameters `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`.
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* 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 `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` 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 `eucast_rules()` function consequently gained the parameters `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`.
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@ -70,6 +67,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th
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* Added support for using `unique()` on classes `<rsi>`, `<mic>`, `<disk>`, `<ab>` and `<mo>`
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* Added support for using `unique()` on classes `<rsi>`, `<mic>`, `<disk>`, `<ab>` and `<mo>`
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### Other
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### Other
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* Removed functions `portion_R()`, `portion_S()` and `portion_I()` that were deprecated since version 0.9.0 (November 2019) and were replaced with `proportion_R()`, `proportion_S()` and `proportion_I()`
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* Removed unnecessary references to the `base` package
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* Removed unnecessary references to the `base` package
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* Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file
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* Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file
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2
R/mdro.R
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R/mdro.R
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"any")
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"any")
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trans_tbl(3,
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trans_tbl(3,
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which(x$mo %in% MO_CONS), # coagulase-negative Staphylococcus
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which(x$mo %in% MO_CONS), # coagulase-negative Staphylococcus
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c( VAN, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
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c(VAN, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
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"any")
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"any")
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trans_tbl(3,
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trans_tbl(3,
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which(x$genus == "Corynebacterium"),
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which(x$genus == "Corynebacterium"),
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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="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">1.3.0.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9037</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">1.3.0.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9037</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">1.3.0.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9037</span>
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</span>
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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">1.3.0.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9037</span>
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</span>
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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">1.3.0.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9037</span>
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</span>
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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">1.3.0.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9037</span>
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</span>
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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-1309036" class="section level1">
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<div id="amr-1309037" class="section level1">
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<h1 class="page-header" data-toc-text="1.3.0.9036">
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<h1 class="page-header" data-toc-text="1.3.0.9037">
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<a href="#amr-1309036" class="anchor"></a>AMR 1.3.0.9036<small> Unreleased </small>
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<a href="#amr-1309037" class="anchor"></a>AMR 1.3.0.9037<small> Unreleased </small>
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</h1>
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</h1>
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<div id="last-updated-30-september-2020" class="section level2">
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<div id="last-updated-30-september-2020" 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-30-september-2020" class="anchor"></a><small>Last updated: 30 September 2020</small>
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<a href="#last-updated-30-september-2020" class="anchor"></a><small>Last updated: 30 September 2020</small>
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</h2>
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</h2>
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<p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p>
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<p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt about this package to. We are those reviewers very grateful for going through our code so thoroughly!</p>
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<div id="breaking" class="section level3">
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<h3 class="hasAnchor">
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<a href="#breaking" class="anchor"></a>Breaking</h3>
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<ul>
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<li>Removed functions <code>portion_R()</code>, <code>portion_S()</code> and <code>portion_I()</code> that were deprecated since version 0.9.0 (November 2019) and were replaced with <code><a href="../reference/proportion.html">proportion_R()</a></code>, <code><a href="../reference/proportion.html">proportion_S()</a></code> and <code><a href="../reference/proportion.html">proportion_I()</a></code>.</li>
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</ul>
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</div>
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<h3 class="hasAnchor">
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<h3 class="hasAnchor">
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<a href="#new" class="anchor"></a>New</h3>
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<a href="#new" class="anchor"></a>New</h3>
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<h3 class="hasAnchor">
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<h3 class="hasAnchor">
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<a href="#other" class="anchor"></a>Other</h3>
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<a href="#other" class="anchor"></a>Other</h3>
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<ul>
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<ul>
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<li>Removed functions <code>portion_R()</code>, <code>portion_S()</code> and <code>portion_I()</code> that were deprecated since version 0.9.0 (November 2019) and were replaced with <code><a href="../reference/proportion.html">proportion_R()</a></code>, <code><a href="../reference/proportion.html">proportion_S()</a></code> and <code><a href="../reference/proportion.html">proportion_I()</a></code>
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</li>
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<li>Removed unnecessary references to the <code>base</code> package</li>
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<li>Removed unnecessary references to the <code>base</code> package</li>
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<li>Added packages that could be useful for some functions to the <code>Suggests</code> field of the <code>DESCRIPTION</code> file</li>
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<li>Added packages that could be useful for some functions to the <code>Suggests</code> field of the <code>DESCRIPTION</code> file</li>
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</ul>
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</ul>
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<h1 class="page-header" data-toc-text="1.2.0">
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<h1 class="page-header" data-toc-text="1.2.0">
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<a href="#amr-120" class="anchor"></a>AMR 1.2.0<small> 2020-05-28 </small>
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<a href="#amr-120" class="anchor"></a>AMR 1.2.0<small> 2020-05-28 </small>
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</h1>
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</h1>
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<li>
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<p>Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.</p>
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<p>Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.</p>
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<h1 class="page-header" data-toc-text="0.9.0">
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<h1 class="page-header" data-toc-text="0.9.0">
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<a href="#amr-090" class="anchor"></a>AMR 0.9.0<small> 2019-11-29 </small>
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<a href="#amr-090" class="anchor"></a>AMR 0.9.0<small> 2019-11-29 </small>
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</h1>
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<ul>
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<li>Adopted Adeolu <em>et al.</em> (2016), <a href="https://www.ncbi.nlm.nih.gov/pubmed/27620848">PMID 27620848</a> for the <code>microorganisms</code> data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like <em>Morganellaceae</em> and <em>Yersiniaceae</em>). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with <code><a href="../reference/mdro.html">mdro()</a></code> will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
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<li>Adopted Adeolu <em>et al.</em> (2016), <a href="https://www.ncbi.nlm.nih.gov/pubmed/27620848">PMID 27620848</a> for the <code>microorganisms</code> data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like <em>Morganellaceae</em> and <em>Yersiniaceae</em>). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with <code><a href="../reference/mdro.html">mdro()</a></code> will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
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<h1 class="page-header" data-toc-text="0.8.0">
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<h1 class="page-header" data-toc-text="0.8.0">
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<a href="#amr-080" class="anchor"></a>AMR 0.8.0<small> 2019-10-15 </small>
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<a href="#amr-080" class="anchor"></a>AMR 0.8.0<small> 2019-10-15 </small>
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<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
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<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
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pkgdown: 1.5.1.9000
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pkgdown: 1.5.1.9000
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pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
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pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
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articles: []
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articles: []
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last_built: 2020-09-30T08:23Z
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last_built: 2020-09-30T08:54Z
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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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</button>
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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">1.3.0.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9037</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9037</span>
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