P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 00:43:00 +02:00
Code Releases Activity

(v1.3.0.9039) lifecycle updates, added excess kurtosis

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-10-04 21:02:16 +02:00
parent baf510183c
commit c04dc852cf
30 changed files with 120 additions and 87 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
docs/reference/as.ab.html
View File

@ -82,7 +82,7 @@
</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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -288,12 +288,13 @@
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>

2
docs/reference/eucast_rules.html
View File

@ -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">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

9
docs/reference/guess_ab_col.html
View File

@ -82,7 +82,7 @@
</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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -267,12 +267,13 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <a href='antibiotics.html'>antibiotics</a> data set for any column containing a name or code of that antibiotic. <strong>Longer columns names take precendence over shorter column names.</strong></p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

2
docs/reference/index.html
View File

@ -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">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

27
docs/reference/kurtosis.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Kurtosis of the sample — kurtosis" />
<meta property="og:description" content="Kurtosis is a measure of the &quot;tailedness&quot; of the probability distribution of a real-valued random variable." />
<meta property="og:description" content="Kurtosis is a measure of the &quot;tailedness&quot; of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -82,7 +82,7 @@
</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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -239,19 +239,19 @@
</div>
<div class="ref-description">
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.</p>
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.</p>
</div>
<pre class="usage"><span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for default</span>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for matrix</span>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for data.frame</span>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)</pre>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -262,16 +262,21 @@
</tr>
<tr>
<th>na.rm</th>
<td><p>a logical value indicating whether <code>NA</code> values should be stripped before the computation proceeds.</p></td>
<td><p>a logical to indicate whether <code>NA</code> values should be stripped before the computation proceeds</p></td>
</tr>
<tr>
<th>excess</th>
<td><p>a logical to indicate whether the <em>excess kurtosis</em> should be returned, defined as the kurtosis minus 3.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

9
docs/reference/mdro.html
View File

@ -82,7 +82,7 @@
</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">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -337,12 +337,13 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://github.com/msberends/AMR/issues/new'>https://github.com/msberends/AMR/issues/new</a>.</p>
<p><strong>Note:</strong> Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named <em>order</em> Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu <em>et al.</em> in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this <code>mdro()</code> function makes sure that results from before 2016 and after 2016 are identical.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>

2
docs/reference/mo_source.html
View File

@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

15
docs/reference/skewness.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Skewness of the sample — skewness" />
<meta property="og:description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure." />
When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -241,7 +241,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<div class="ref-description">
<p>Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.</p>
<p>When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure.</p>
<p>When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.</p>
</div>
<pre class="usage"><span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
@ -264,16 +264,17 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</tr>
<tr>
<th>na.rm</th>
<td><p>a logical value indicating whether <code>NA</code> values should be stripped before the computation proceeds.</p></td>
<td><p>a logical value indicating whether <code>NA</code> values should be stripped before the computation proceeds</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>