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(v1.4.0.9018) reference_data in as.rsi()

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dr. M.S. (Matthijs) Berends
2020-11-11 18:54:03 +01:00
parent 01d9522434
commit f2edac3b67
15 changed files with 48 additions and 30 deletions
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docs/404.html
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</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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
</span>
</div>

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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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
</span>
</div>

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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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
</span>
</div>

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docs/authors.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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
</span>
</div>

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docs/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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
</span>
</div>

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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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409017" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9017">
<a href="#amr-1409017" class="anchor"></a>AMR 1.4.0.9017<small> Unreleased </small>
<div id="amr-1409018" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9018">
<a href="#amr-1409018" class="anchor"></a>AMR 1.4.0.9018<small> Unreleased </small>
</h1>
<div id="last-updated-11-november-2020" class="section level2">
<h2 class="hasAnchor">
@ -262,7 +262,7 @@
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Reference data used for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now be set by the user, using the <code>reference_data</code> parameter.</li>
<li>Reference data used for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now be set by the user, using the <code>reference_data</code> parameter. This allows for using own interpretation guidelines.</li>
<li>For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the <a href="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.</li>
<li>Deprecated function <code><a href="../reference/AMR-deprecated.html">p_symbol()</a></code> that not really fits the scope of this package. It will be removed in a future version. See <a href="https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R">here</a> for the source code to preserve it.</li>
<li>Better determination of disk zones and MIC values when running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame</li>

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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: 2020-11-11T15:44Z
last_built: 2020-11-11T17:53Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
</span>
</div>
@ -327,7 +327,7 @@ list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST In
</tr>
<tr>
<th>reference_data</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> to be used for interpretation, which defaults to the <a href='rsi_translation.html'>rsi_translation</a> data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the <a href='rsi_translation.html'>rsi_translation</a> data set (same column names and column types). Please note that the 'guideline' column in this data set must contain values set in the 'guideline' parameter of <code>as.rsi()</code>.</p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> to be used for interpretation, which defaults to the <a href='rsi_translation.html'>rsi_translation</a> data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the <a href='rsi_translation.html'>rsi_translation</a> data set (same column names and column types). Please note that the <code>guideline</code> parameter will be ignored when <code>reference_data</code> is manually set.</p></td>
</tr>
<tr>
<th>col_mo</th>
@ -365,7 +365,7 @@ list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST In
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> parameter.</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> parameter. The <code>guideline</code> parameter will then be ignored.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After interpretation</h3>

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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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</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">1.4.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
</span>
</div>