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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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -235,9 +235,7 @@
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
</div>
<pre class="usage"><span class='fu'>p.symbol</span>(<span class='no'>...</span>)
<span class='fu'>portion_R</span>(<span class='no'>...</span>)
<pre class="usage"><span class='fu'>portion_R</span>(<span class='no'>...</span>)
<span class='fu'>portion_IR</span>(<span class='no'>...</span>)
@ -277,7 +275,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
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<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">1.1.0.9004</span>
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<a href="../articles/AMR.html">
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Conduct AMR analysis
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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<h1>Methods for tidyverse</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/tidyverse.R'><code>R/tidyverse.R</code></a></small>
<div class="hidden name"><code>AMR-tidyverse.Rd</code></div>
</div>
<div class="ref-description">
<p>These methods are needed to support methods used by the tidyverse, like joining and transforming data, with new classes that come with this package.</p>
</div>
<pre class="usage"><span class='fu'>scale_type.mo</span>(<span class='no'>x</span>)
<span class='fu'>scale_type.ab</span>(<span class='no'>x</span>)
<span class='fu'>vec_ptype2.mo</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='no'>...</span>)
<span class='fu'>vec_cast.mo</span>(<span class='no'>x</span>, <span class='no'>to</span>, <span class='no'>...</span>)
<span class='fu'>vec_ptype2.ab</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='no'>...</span>)
<span class='fu'>vec_cast.ab</span>(<span class='no'>x</span>, <span class='no'>to</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
</div>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@ -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">1.1.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>

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@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -291,9 +291,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>mic_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>mic_data</span>)
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>mic_data</span>)</pre>
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>mic_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>mic_data</span>)</pre>
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@ -309,7 +308,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

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docs/reference/as.mo.html
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@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -275,7 +275,7 @@
</tr>
<tr>
<th>reference_df</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> to use for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href='mo_source.html'>set_mo_source()</a></code> and <code><a href='mo_source.html'>get_mo_source()</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> to be used for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href='mo_source.html'>set_mo_source()</a></code> and <code><a href='mo_source.html'>get_mo_source()</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
</tr>
<tr>
<th>...</th>
@ -299,10 +299,10 @@
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ---&gt; subspecies, a 4-5 letter acronym
| | ----&gt; species, a 4-5 letter acronym
| ----&gt; genus, a 5-7 letter acronym
----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
| | | ---&amp;gt; subspecies, a 4-5 letter acronym
| | ----&amp;gt; species, a 4-5 letter acronym
| ----&amp;gt; genus, a 5-7 letter acronym
----&amp;gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</pre>
@ -455,7 +455,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -285,7 +285,7 @@
</tr>
<tr>
<th>guideline</th>
<td><p>defaults to the latest included EUCAST guideline, run <code><a href='https://rdrr.io/r/base/unique.html'>unique(rsi_translation$guideline)</a></code> for all options</p></td>
<td><p>defaults to the latest included EUCAST guideline, see Details for all options</p></td>
</tr>
<tr>
<th>uti</th>
@ -306,8 +306,9 @@
<p>Ordered factor with new class <code>rsi</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Run <code><a href='https://rdrr.io/r/base/unique.html'>unique(rsi_translation$guideline)</a></code> for a list of all supported guidelines. The repository of this package contains <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>this machine readable version</a> of these guidelines.</p>
<p>These guidelines are machine readable, since <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'></a>.</p>
<p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p>
<p>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". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p>
<p>The repository of this package <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This <strong>allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
<p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
@ -396,9 +397,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='no'>rsi_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
<span class='fu'>is.rsi</span>(<span class='no'>rsi_data</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span>
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>rsi_data</span>) <span class='co'># frequency table with informative header</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
@ -430,7 +430,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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8
docs/reference/catalogue_of_life_version.html
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@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -260,10 +260,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>kingdom</span>)
<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>kingdom</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>phylum</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -279,7 +275,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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22
docs/reference/count.html
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@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -304,7 +304,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<p>These functions are meant to count isolates. Use the <code><a href='proportion.html'>resistance()</a></code>/<code><a href='proportion.html'>susceptibility()</a></code> functions to calculate microbial resistance/susceptibility.</p>
<p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p>
<p>The function <code>n_rsi()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and counts the number of S's, I's and R's. The function <code><a href='proportion.html'>rsi_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and counts the number of S's, I's and R's. It also supports grouped variables. The function <code><a href='proportion.html'>rsi_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -338,21 +338,21 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
-------- -------- ---------- ----------- ---------- -----------
S or I S or I X X X X
R S or I X X X X
&lt;NA&gt; S or I X X - -
&amp;lt;NA&amp;gt; S or I X X - -
S or I R X X X X
R R - X - X
&lt;NA&gt; R - - - -
S or I &lt;NA&gt; X X - -
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
&amp;lt;NA&amp;gt; R - - - -
S or I &amp;lt;NA&amp;gt; X X - -
R &amp;lt;NA&amp;gt; - - - -
&amp;lt;NA&amp;gt; &amp;lt;NA&amp;gt; - - - -
--------------------------------------------------------------------
</pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span>() + <span class='fu'>count_I</span>() + <span class='fu'>count_R</span>() <span class='kw'>=</span> <span class='fu'>count_all</span>()
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() + <span class='fu'><a href='proportion.html'>proportion_I</a></span>() + <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &gt;= count_all()
proportion_S() + proportion_I() + proportion_R() &gt;= 1
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &amp;gt;= count_all()
proportion_S() + proportion_I() + proportion_R() &amp;gt;= 1
</pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
@ -399,7 +399,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>CIP</span>),
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
@ -437,7 +437,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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20
docs/reference/filter_ab_class.html
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Filter isolates on result in antibiotic class — filter_ab_class • AMR (for R)</title>
<title>Filter isolates on result in antimicrobial class — filter_ab_class • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,8 +48,8 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Filter isolates on result in antibiotic class — filter_ab_class" />
<meta property="og:description" content="Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
<meta property="og:title" content="Filter isolates on result in antimicrobial class — filter_ab_class" />
<meta property="og:description" content="Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -226,13 +226,13 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Filter isolates on result in antibiotic class</h1>
<h1>Filter isolates on result in antimicrobial class</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/filter_ab_class.R'><code>R/filter_ab_class.R</code></a></small>
<div class="hidden name"><code>filter_ab_class.Rd</code></div>
</div>
<div class="ref-description">
<p>Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.</p>
<p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.</p>
</div>
<pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='no'>x</span>, <span class='no'>ab_class</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
@ -298,7 +298,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># filter on isolates that have any result for any aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>()
@ -325,7 +326,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># all aminoglycosides and all fluoroquinolones</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)</pre>
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -341,7 +343,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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9
docs/reference/first_isolate.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">1.1.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -352,7 +352,7 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Methodology of this function is based on:</p>
<p>Methodology of this function is strictly based on:</p>
<p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@ -405,6 +405,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># Filter on first isolates:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
@ -425,14 +426,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># Have a look at A and B.</span>
<span class='co'># B is more reliable because every isolate is counted only once.</span>
<span class='co'># Gentamicin resitance in hospital D appears to be 3.7% higher than</span>
<span class='co'># Gentamicin resistance in hospital D appears to be 3.7% higher than</span>
<span class='co'># when you (erroneously) would have used all isolates for analysis.</span>
<span class='co'>## OTHER EXAMPLES:</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># Short-hand versions:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_isolate</span>()

8
docs/reference/ggplot_pca.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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -382,6 +382,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>pca_model</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
@ -394,7 +395,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_model</span>)
<span class='co'># new </span>
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)</pre>
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -410,7 +412,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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28
docs/reference/ggplot_rsi.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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -484,30 +484,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>,
<span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># genuine analysis: check 3 most prevalent microorganisms</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on top three bacterial ID's</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'>top_freq</span>(<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on first isolates</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='co'># get short MO names (like "E. coli")</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>bug</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># select this short name and some antiseptic drugs</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>bug</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='co'># group by MO</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>bug</span>) <span class='kw'>%&gt;%</span>
<span class='co'># plot the thing, putting MOs on the facet</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"bug"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Top Three Microorganisms In Blood Culture Isolates"</span>,
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/expression.html'>expression</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Only First Isolates, CoNS grouped according to Becker "</span>,
<span class='fu'><a href='https://rdrr.io/r/grDevices/plotmath.html'>italic</a></span>(<span class='st'>"et al."</span>), <span class='st'>" (2014)"</span>)),
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (EARS-Net code)"</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -524,7 +500,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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18
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">1.1.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -350,7 +350,7 @@
<td>
<p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p>
</td>
<td><p>Join a table with microorganisms</p></td>
<td><p>Join microorganisms to a data set</p></td>
</tr><tr>
<td>
@ -429,7 +429,7 @@
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Filter isolates on result in antibiotic class</p></td>
<td><p>Filter isolates on result in antimicrobial class</p></td>
</tr><tr>
<td>
@ -585,12 +585,6 @@
<td><p>Translate strings from AMR package</p></td>
</tr><tr>
<td>
<p><code><a href="extended-functions.html">scale_type.mo()</a></code> <code><a href="extended-functions.html">scale_type.ab()</a></code> </p>
</td>
<td><p>Extended functions</p></td>
</tr><tr>
<td>
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
</td>
@ -604,9 +598,9 @@
</tr><tr>
<td>
<p><code><a href="AMR-vctrs.html">vec_ptype2.mo()</a></code> <code><a href="AMR-vctrs.html">vec_cast.mo()</a></code> <code><a href="AMR-vctrs.html">vec_ptype2.ab()</a></code> <code><a href="AMR-vctrs.html">vec_cast.ab()</a></code> </p>
<p><code><a href="AMR-tidyverse.html">scale_type.mo()</a></code> <code><a href="AMR-tidyverse.html">scale_type.ab()</a></code> <code><a href="AMR-tidyverse.html">vec_ptype2.mo()</a></code> <code><a href="AMR-tidyverse.html">vec_cast.mo()</a></code> <code><a href="AMR-tidyverse.html">vec_ptype2.ab()</a></code> <code><a href="AMR-tidyverse.html">vec_cast.ab()</a></code> </p>
</td>
<td><p><code>vctrs</code> methods</p></td>
<td><p>Methods for tidyverse</p></td>
</tr>
</tbody><tbody>
<tr>
@ -623,7 +617,7 @@
<tr>
<td>
<p><code><a href="AMR-deprecated.html">p.symbol()</a></code> <code><a href="AMR-deprecated.html">portion_R()</a></code> <code><a href="AMR-deprecated.html">portion_IR()</a></code> <code><a href="AMR-deprecated.html">portion_I()</a></code> <code><a href="AMR-deprecated.html">portion_SI()</a></code> <code><a href="AMR-deprecated.html">portion_S()</a></code> <code><a href="AMR-deprecated.html">portion_df()</a></code> </p>
<p><code><a href="AMR-deprecated.html">portion_R()</a></code> <code><a href="AMR-deprecated.html">portion_IR()</a></code> <code><a href="AMR-deprecated.html">portion_I()</a></code> <code><a href="AMR-deprecated.html">portion_SI()</a></code> <code><a href="AMR-deprecated.html">portion_S()</a></code> <code><a href="AMR-deprecated.html">portion_df()</a></code> </p>
</td>
<td><p>Deprecated functions</p></td>
</tr>

19
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Join a table with <a href='microorganisms.html'>microorganisms</a> — join • AMR (for R)</title>
<title>Join <a href='microorganisms.html'>microorganisms</a> to a data set — join • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Join a table with <a href='microorganisms.html'>microorganisms</a> — join" />
<meta property="og:title" content="Join <a href='microorganisms.html'>microorganisms</a> to a data set — join" />
<meta property="og:description" content="Join the data set microorganisms easily to an existing table or character vector." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -226,7 +226,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Join a table with <a href='microorganisms.html'>microorganisms</a></h1>
<h1>Join <a href='microorganisms.html'>microorganisms</a> to a data set</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/join_microorganisms.R'><code>R/join_microorganisms.R</code></a></small>
<div class="hidden name"><code>join.Rd</code></div>
</div>
@ -264,13 +264,14 @@
</tr>
<tr>
<th>...</th>
<td><p>other parameters to pass on to <code><a href='https://dplyr.tidyverse.org/reference/mutate-joins.html'>dplyr::join()</a></code></p></td>
<td><p>other parameters to pass on to <code><a href='https://dplyr.tidyverse.org/reference/join.html'>dplyr::join()</a></code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>Note:</strong> As opposed to the <code><a href='https://dplyr.tidyverse.org/reference/mutate-joins.html'>dplyr::join()</a></code> functions of <code>dplyr</code>, <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='https://dplyr.tidyverse.org/reference/mutate-joins.html'>dplyr::join()</a></code> for more information.</p>
<p><strong>Note:</strong> As opposed to the <code>join()</code> functions of <code>dplyr</code>, <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix.</p>
<p>These functions rely on <code><a href='https://rdrr.io/r/base/merge.html'>merge()</a></code>, a base R function to do joins.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -288,6 +289,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<pre class="examples"><span class='fu'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))
<span class='fu'>left_join_microorganisms</span>(<span class='st'>"B_KLBSL_PNE"</span>)
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>left_join_microorganisms</span>()
@ -299,7 +301,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='no'>df</span>)
<span class='no'>df_joined</span> <span class='kw'>&lt;-</span> <span class='fu'>left_join_microorganisms</span>(<span class='no'>df</span>, <span class='st'>"bacteria"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='no'>df_joined</span>)</pre>
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='no'>df_joined</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -315,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

7
docs/reference/key_antibiotics.html
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@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -324,7 +324,8 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>key_antibiotics()</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate()</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate()</a></code>). Without key antibiotic comparison it would not.</p>
<p>The function <code>key_antibiotics()</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antibiotics()</code> and ignored by <code>key_antibiotics_equal()</code>.</p>
<p>The <code><a href='first_isolate.html'>first_isolate()</a></code> function only uses this function on the same microbial species from the same patient. Using this, e.g. an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) is found within the same patient episode. Without key antibiotic comparison it would not. See <code><a href='first_isolate.html'>first_isolate()</a></code> for more info.</p>
<p>At default, the antibiotics that are used for <strong>Gram-positive bacteria</strong> are:</p><ul>
<li><p>Amoxicillin</p></li>
<li><p>Amoxicillin/clavulanic acid</p></li>
@ -427,7 +428,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

18
docs/reference/like.html
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@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -260,13 +260,19 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/master/R/like.R'><code>like</code> function from the <code>data.table</code> package</a>, but made it case insensitive at default and let it support multiple patterns. Also, if the regex fails the first time, it tries again with <code>perl = TRUE</code>.</p>
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/master/R/like.R'><code>like</code> function from the <code>data.table</code> package</a></p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>When running a regular expression fails, these functions try again with <code><a href='https://rdrr.io/r/base/grep.html'>base::grepl(..., perl = TRUE)</a></code>.</p>
<p>The <code>%like%</code> function:</p><ul>
<li><p>Is case insensitive (use <code>%like_case%</code> for case-sensitive matching)</p></li>
<li><p>Supports multiple patterns</p></li>
<li><p>Checks if <code>pattern</code> is a regular expression and sets <code>fixed = TRUE</code> if not, to greatly improve speed</p></li>
<li><p>Tries again with <code>perl = TRUE</code> if regex fails</p></li>
</ul>
<p>Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like <code>Ctrl+Shift+L</code> or <code>Cmd+Shift+L</code> (see <code>Tools</code> &gt; <code>Modify Keyboard Shortcuts...</code>).</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -299,11 +305,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
<span class='co'>#&gt; TRUE TRUE TRUE</span>
<span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</span>
<span class='co'># get isolates whose name start with 'Ent' or 'ent'</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>"^ent"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>))</pre>
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>mo</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -319,7 +325,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

4
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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -467,7 +467,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

2
docs/reference/microorganisms.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">1.1.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>

2
docs/reference/mo_property.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">1.1.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>

10
docs/reference/pca.html
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@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -254,7 +254,7 @@
</tr>
<tr>
<th>...</th>
<td><p>columns of <code>x</code> to be selected for PCA</p></td>
<td><p>columns of <code>x</code> to be selected for PCA, can be unquoted since it supports quasiquotation.</p></td>
</tr>
<tr>
<th>retx</th>
@ -315,6 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># calculate the resistance per group first</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>resistance_data</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
@ -329,7 +330,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='no'>pca_result</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>pca_result</span>)
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_result</span>)
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='no'>pca_result</span>) <span class='co'># a new and convenient plot function</span></pre>
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='no'>pca_result</span>) <span class='co'># a new and convenient plot function</span>
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -345,7 +347,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

30
docs/reference/proportion.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Calculate microbial resistance — proportion" />
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise()][dplyr::summarise()] and also support grouped variables, please see Examples.
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also supports grouped variables, please see Examples.
resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -233,7 +233,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</div>
<div class="ref-description">
<p>These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>summarise()</code>][dplyr::summarise()] and also support grouped variables, please see <em>Examples</em>.</p>
<p>These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>summarise()</code> from the <code>dplyr</code> package and also supports grouped variables, please see <em>Examples</em>.</p>
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
</div>
@ -323,7 +323,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p>The function <code>resistance()</code> is equal to the function <code>proportion_R()</code>. The function <code>susceptibility()</code> is equal to the function <code>proportion_SI()</code>.</p>
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href='first_isolate.html'>first_isolate()</a></code> to determine them in your data set.</p>
<p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href='count.html'>count()</a></code>][AMR::count()] functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code>count_susceptible() / count_all()</code>. <em>Low counts can influence the outcome - the <code>proportion</code> functions may camouflage this, since they only return the proportion (albeit being dependent on the <code>minimum</code> parameter).</em></p>
<p>The function <code>proportion_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and calculates the proportions R, I and S. The function <code>rsi_df()</code> works exactly like <code>proportion_df()</code>, but adds the number of isolates.</p>
<p>The function <code>proportion_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and calculates the proportions R, I and S. It also supports grouped variables. The function <code>rsi_df()</code> works exactly like <code>proportion_df()</code>, but adds the number of isolates.</p>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
@ -336,21 +336,21 @@ resistance() should be used to calculate resistance, susceptibility() should be
-------- -------- ---------- ----------- ---------- -----------
S or I S or I X X X X
R S or I X X X X
&lt;NA&gt; S or I X X - -
&amp;lt;NA&amp;gt; S or I X X - -
S or I R X X X X
R R - X - X
&lt;NA&gt; R - - - -
S or I &lt;NA&gt; X X - -
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
&amp;lt;NA&amp;gt; R - - - -
S or I &amp;lt;NA&amp;gt; X X - -
R &amp;lt;NA&amp;gt; - - - -
&amp;lt;NA&amp;gt; &amp;lt;NA&amp;gt; - - - -
--------------------------------------------------------------------
</pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() + <span class='fu'><a href='count.html'>count_I</a></span>() + <span class='fu'><a href='count.html'>count_R</a></span>() <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
<span class='fu'>proportion_S</span>() + <span class='fu'>proportion_I</span>() + <span class='fu'>proportion_R</span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &gt;= count_all()
proportion_S() + proportion_I() + proportion_R() &gt;= 1
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &amp;gt;= count_all()
proportion_S() + proportion_I() + proportion_R() &amp;gt;= 1
</pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
@ -398,6 +398,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'>proportion_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
@ -410,7 +411,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='kw'>SI</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
@ -455,9 +456,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>proportion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># calculate current empiric combination therapy of Helicobacter gastritis:</span>
<span class='no'>my_table</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
@ -480,7 +478,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
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4
docs/reference/reexports.html
View File

@ -87,7 +87,7 @@ below to see their documentation.
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -263,7 +263,7 @@ below to see their documentation.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

34
docs/reference/resistance_predict.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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -266,7 +266,7 @@
)
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='no'>x_name</span>), <span class='no'>...</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='no'>x_name</span>), <span class='no'>...</span>)
<span class='fu'>ggplot_rsi_predict</span>(
<span class='no'>x</span>,
@ -392,25 +392,25 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
<span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>,
<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='fu'>ggplot_rsi_predict</span>(<span class='no'>x</span>)
<span class='co'># use dplyr so you can actually read it:</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='co'># get the model from the object</span>
<span class='no'>mymodel</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span>(<span class='no'>x</span>)$<span class='no'>model</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>mymodel</span>)
<span class='co'># using dplyr:</span>
<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</span>)
<span class='co'># get the model from the object</span>
<span class='no'>mymodel</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span>(<span class='no'>x</span>)$<span class='no'>model</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>mymodel</span>)
}
<span class='co'># create nice plots with ggplot2 yourself</span>
<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>ggplot2</span>)) {
<span class='kw'>if</span> (!<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>ggplot2</span>) <span class='kw'>&amp;</span> !<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
@ -451,7 +451,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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12
docs/reference/translate.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Translate strings from AMR package — translate" />
<meta property="og:description" content="For language-dependent output of AMR functions, like mo_name(), mo_type() and ab_name()." />
<meta property="og:description" content="For language-dependent output of AMR functions, like mo_name(), mo_gramstain(), mo_type() and ab_name()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
</span>
</div>
@ -232,7 +232,7 @@
</div>
<div class="ref-description">
<p>For language-dependent output of AMR functions, like <code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code> and <code><a href='ab_property.html'>ab_name()</a></code>.</p>
<p>For language-dependent output of AMR functions, like <code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code> and <code><a href='ab_property.html'>ab_name()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>get_locale</span>()</pre>
@ -241,9 +241,9 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>.</p>
<p>Currently supported languages can be found if running: <code><a href='https://rdrr.io/r/base/unique.html'>unique(AMR:::translations_file$lang)</a></code>.</p>
<p>Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Not all these languages currently have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p>Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property()</a></code> functions (<code><a href='mo_property.html'>mo_fullname()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.).</p>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property()</a></code> functions (<code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.).</p>
<p>The system language will be used at default, if that language is supported. The system language can be overwritten with <code><a href='https://rdrr.io/r/base/Sys.setenv.html'>Sys.setenv(AMR_locale = yourlanguage)</a></code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -301,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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