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(v0.8.0.9027) adding susceptibility() and resistance()

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dr. M.S. (Matthijs) Berends
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14
docs/reference/AMR-deprecated.html
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@ -85,7 +85,7 @@
</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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -237,9 +237,17 @@
<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 Using the functions will give a warning with the name of the function it has been replaced by (if there is one).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'>as.atc</span>(<span class='no'>x</span>)
<pre class="usage"><span class='fu'>p.symbol</span>(<span class='no'>...</span>)
<span class='fu'>p.symbol</span>(<span class='no'>...</span>)</pre>
<span class='fu'>portion_R</span>(<span class='no'>...</span>)
<span class='fu'>portion_IR</span>(<span class='no'>...</span>)
<span class='fu'>portion_I</span>(<span class='no'>...</span>)
<span class='fu'>portion_SI</span>(<span class='no'>...</span>)
<span class='fu'>portion_S</span>(<span class='no'>...</span>)</pre>
<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>

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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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -244,27 +244,19 @@
<p><code>AMR</code> is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.</p>
<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul>
<li><p>Reference for microorganisms, since it contains all microbial (sub)species from the Catalogue of Life</p></li>
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life</p></li>
<li><p>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</p></li>
<li><p>Determining first isolates to be used for AMR analysis</p></li>
<li><p>Calculating antimicrobial resistance</p></li>
<li><p>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</p></li>
<li><p>Calculating empirical susceptibility of both mono therapy and combination therapy</p></li>
<li><p>Calculating (empirical) susceptibility of both mono therapy and combination therapies</p></li>
<li><p>Predicting future antimicrobial resistance using regression models</p></li>
<li><p>Getting properties for any microorganism (like Gram stain, species, genus or family)</p></li>
<li><p>Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)</p></li>
<li><p>Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)</p></li>
<li><p>Plotting antimicrobial resistance</p></li>
<li><p>Determining first isolates to be used for AMR analysis</p></li>
<li><p>Applying EUCAST expert rules</p></li>
<li><p>Descriptive statistics: frequency tables, kurtosis and skewness</p></li>
</ul>
<h2 class="hasAnchor" id="authors"><a class="anchor" href="#authors"></a>Authors</h2>
<p>Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] <br /></p>
<p>[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - <a href='https://www.rug.nl'>https://www.rug.nl</a> <a href='https://www.umcg.nl'>https://www.umcg.nl</a> <br />
[2] Certe Medical Diagnostics &amp; Advice, Groningen, the Netherlands - <a href='https://www.certe.nl'>https://www.certe.nl</a></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>
@ -289,7 +281,6 @@ Post Office Box 30001 <br />
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#details">Details</a></li>
<li><a href="#authors">Authors</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#contact-us">Contact us</a></li>
</ul>

2
docs/reference/WHOCC.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
docs/reference/WHONET.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
docs/reference/ab_property.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
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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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
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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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
docs/reference/antibiotics.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
docs/reference/as.ab.html
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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
docs/reference/as.disk.html
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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
docs/reference/as.mic.html
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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
docs/reference/as.mo.html
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@ -85,7 +85,7 @@
</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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

4
docs/reference/as.rsi.html
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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -306,7 +306,7 @@
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='portion.html'>portion_SI</a></code> to determine antimicrobial susceptibility and <code><a href='count.html'>count_SI</a></code> to count susceptible isolates.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a></code> (equal to <code><a href='proportion.html'>proportion_SI</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a></code> (equal to <code><a href='count.html'>count_SI</a></code>) to count susceptible isolates.</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/atc_online.html
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@ -85,7 +85,7 @@
</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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

8
docs/reference/availability.html
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@ -51,7 +51,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Check availability of columns — availability" />
<meta property="og:description" content="Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. portion_R." />
<meta property="og:description" content="Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. resistance." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -85,7 +85,7 @@
</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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -234,7 +234,7 @@
</div>
<div class="ref-description">
<p>Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. <code><a href='portion.html'>portion_R</a></code>.</p>
<p>Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. <code><a href='proportion.html'>resistance</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>availability</span>(<span class='no'>tbl</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
@ -257,7 +257,7 @@
<p><code>data.frame</code> with column names of <code>tbl</code> as row names</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function returns a <code>data.frame</code> with columns <code>"resistant"</code> and <code>"visual_resistance"</code>. The values in that columns are calculated with <code><a href='portion.html'>portion_R</a></code>.</p>
<p>The function returns a <code>data.frame</code> with columns <code>"resistant"</code> and <code>"visual_resistance"</code>. The values in that columns are calculated with <code><a href='proportion.html'>resistance</a></code>.</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/bug_drug_combinations.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
docs/reference/catalogue_of_life.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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docs/reference/catalogue_of_life_version.html
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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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docs/reference/count.html
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@ -52,7 +52,7 @@
<meta property="og:title" content="Count isolates — count" />
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in dplyrs summarise and support grouped variables, see Examples.
count_R and count_IR can be used to count resistant isolates, count_S and count_SI can be used to count susceptible isolates." />
count_resistant should be used to count resistant isolates, count_susceptible should be used to count susceptible isolates." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -86,7 +86,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -236,10 +236,14 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<div class="ref-description">
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>count_R</code> and <code>count_IR</code> can be used to count resistant isolates, <code>count_S</code> and <code>count_SI</code> can be used to count susceptible isolates.<br /></p>
<p><code>count_resistant</code> should be used to count resistant isolates, <code>count_susceptible</code> should be used to count susceptible isolates.<br /></p>
</div>
<pre class="usage"><span class='fu'>count_R</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>count_resistant</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_susceptible</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_R</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_IR</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
@ -289,18 +293,15 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Wickham H. <strong>Tidy Data.</strong> The Journal of Statistical Software, vol. 59, 2014. <a href='http://vita.had.co.nz/papers/tidy-data.html'>http://vita.had.co.nz/papers/tidy-data.html</a></p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Integer</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</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_S(...) + count_IR(...)</code>.</p>
<p>The function <code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of S, I and R. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
<p>The function <code>rsi_df</code> works exactly like <code>count_df</code>, but adds the percentage of S, I and R.</p>
<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>"rsi"</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>rsi_df</code> works exactly like <code>count_df</code>, but adds the percentage of S, I and R.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
@ -313,12 +314,12 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='portion.html'>portion_SI</a></code> to determine antimicrobial susceptibility and <code>count_SI</code> to count susceptible isolates.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a></code> (equal to <code><a href='proportion.html'>proportion_SI</a></code>) to determine antimicrobial susceptibility and <code>count_susceptible</code> (equal to <code>count_SI</code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how <code>portion_SI</code> works to calculate the %SI:</p>
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how <code>susceptibility</code> works to calculate the %SI:</p>
<pre>
--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
@ -339,11 +340,11 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre>
count_S() + count_I() + count_R() == count_all()
portion_S() + portion_I() + portion_R() == 1
count_S() + count_I() + count_R() = count_all()
proportion_S() + proportion_I() + proportion_R() = 1
</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()
portion_S() + portion_I() + portion_R() &gt;= 1
count_S() + count_I() + count_R() &gt;= count_all()
proportion_S() + proportion_I() + proportion_R() &gt;= 1
</pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
@ -354,29 +355,33 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<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 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>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='portion.html'>portion</a>_*</code> to calculate microbial resistance and susceptibility.</p></div>
<div class='dont-index'><p><code><a href='proportion.html'>proportion</a>_*</code> to calculate microbial resistance and susceptibility.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
?<span class='no'>example_isolates</span>
<span class='co'># Count resistant isolates</span>
<span class='fu'>count_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_resistant</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "R"</span>
<span class='fu'>count_susceptible</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "S" and "I"</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "S", "I" and "R"</span>
<span class='co'># Or susceptible isolates</span>
<span class='co'># be more specific</span>
<span class='fu'>count_S</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_I</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='co'># Count all available isolates</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='co'># Since n_rsi counts available isolates, you can</span>
<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
<span class='co'># This results in the same:</span>
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'><a href='portion.html'>portion_SI</a></span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='co'># n_rsi() is an alias of count_all().</span>
<span class='co'># Since it counts all available isolates, you can</span>
<span class='co'># calculate back to count e.g. susceptible isolates.</span>
<span class='co'># These results are the same:</span>
<span class='fu'>count_susceptible</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'><a href='proportion.html'>susceptibility</a></span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</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>
@ -390,19 +395,16 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<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>
<span class='co'># Please mind that `portion_SI` calculates percentages right away instead.</span>
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMC</span>) <span class='co'># 1433</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMC</span>) <span class='co'># 1879</span>
<span class='co'># Please mind that `susceptibility()` calculates percentages right away instead.</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>AMC</span>) <span class='co'># 1433</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>AMC</span>) <span class='co'># 1879</span>
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>GEN</span>) <span class='co'># 1399</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>GEN</span>) <span class='co'># 1855</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>GEN</span>) <span class='co'># 1399</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>GEN</span>) <span class='co'># 1855</span>
<span class='fu'><a href='https://rdrr.io/r/base/with.html'>with</a></span>(<span class='no'>example_isolates</span>,
<span class='fu'>count_SI</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># 1764</span>
<span class='fu'><a href='https://rdrr.io/r/base/with.html'>with</a></span>(<span class='no'>example_isolates</span>,
<span class='fu'>n_rsi</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># 1936</span>
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># 1764</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># 1936</span>
<span class='co'># Get number of S+I vs. R immediately of selected columns</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
@ -417,7 +419,6 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>

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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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -395,13 +395,13 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<span class='no'>A</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/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='AMR-deprecated.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</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>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='AMR-deprecated.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='co'># Have a look at A and B.</span>
<span class='co'># B is more reliable because every isolate is only counted once.</span>

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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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -274,7 +274,7 @@
</tr>
<tr>
<th>position</th>
<td><p>position adjustment of bars, either <code>"fill"</code> (default when <code>fun</code> is <code><a href='count.html'>count_df</a></code>), <code>"stack"</code> (default when <code>fun</code> is <code><a href='portion.html'>portion_df</a></code>) or <code>"dodge"</code></p></td>
<td><p>position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code></p></td>
</tr>
<tr>
<th>x</th>
@ -362,7 +362,7 @@
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df</a></code>.</p>
<p><strong>The functions</strong><br />
<code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code><a href='portion.html'>rsi_df</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code><a href='proportion.html'>rsi_df</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>facet_wrap</a></code>.</p>
<p><code>scale_y_percent</code> transforms the y axis to a 0 to 100% range using <code>scale_continuous</code>.</p>
<p><code>scale_rsi_colours</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code>scale_brewer</code>.</p>
@ -397,7 +397,7 @@
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>()
<span class='co'># get only portions and no counts:</span>
<span class='co'># get only proportions and no counts:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)

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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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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@ -84,7 +84,7 @@
</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">0.8.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -428,15 +428,15 @@
</tr><tr>
<td>
<p><code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
<p><code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
</td>
<td><p>Count isolates</p></td>
</tr><tr>
<td>
<p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> <code><a href="portion.html">rsi_df()</a></code> </p>
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
</td>
<td><p>Calculate resistance of isolates</p></td>
<td><p>Calculate microbial resistance</p></td>
</tr><tr>
<td>
@ -562,7 +562,7 @@
<tr>
<td>
<p><code><a href="AMR-deprecated.html">as.atc()</a></code> <code><a href="AMR-deprecated.html">p.symbol()</a></code> </p>
<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> </p>
</td>
<td><p>Deprecated functions</p></td>
</tr>

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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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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@ -85,7 +85,7 @@
</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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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@ -85,7 +85,7 @@
</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">0.8.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>
@ -411,7 +411,7 @@
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='portion.html'>portion_SI</a></code> to determine antimicrobial susceptibility and <code><a href='count.html'>count_SI</a></code> to count susceptible isolates.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a></code> (equal to <code><a href='proportion.html'>proportion_SI</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a></code> (equal to <code><a href='count.html'>count_SI</a></code>) to count susceptible isolates.</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>

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@ -85,7 +85,7 @@
</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">0.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
</span>
</div>

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resistance should be used to calculate resistance, susceptibility should be used to calculate susceptibility." />
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<h1>Calculate microbial resistance</h1>
<div class="hidden name"><code>proportion.Rd</code></div>
</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>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, 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>
<pre class="usage"><span class='fu'>resistance</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>susceptibility</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_R</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_IR</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_I</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_SI</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_S</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>proportion_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>rsi_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>...</th>
<td><p>one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with <code><a href='as.rsi.html'>as.rsi</a></code> if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.</p></td>
</tr>
<tr>
<th>minimum</th>
<td><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
</tr>
<tr>
<th>as_percent</th>
<td><p>a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of <code>0.123456</code> will then be returned as <code>"12.3%"</code>.</p></td>
</tr>
<tr>
<th>only_all_tested</th>
<td><p>(for combination therapies, i.e. using more than one variable for <code>...</code>) a logical to indicate that isolates must be tested for all antibiotics, see section <em>Combination therapy</em> below</p></td>
</tr>
<tr>
<th>data</th>
<td><p>a <code>data.frame</code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property</a></code></p></td>
</tr>
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
</tr>
<tr>
<th>combine_SI</th>
<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
</tr>
<tr>
<th>combine_IR</th>
<td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter <code>combine_SI</code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<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>
<p>Double or, when <code>as_percent = TRUE</code>, a character.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<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> functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code>count_susceptible() / count_all()</code>. <em>Low counts can infuence 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>"rsi"</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>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how <code>susceptibility</code> works to calculate the %SI:</p>
<pre>
--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as
numerator denominator numerator denominator
-------- -------- ---------- ----------- ---------- -----------
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 - -
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; - - - -
--------------------------------------------------------------------
</pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre>
count_S() + count_I() + count_R() = count_all()
proportion_S() + proportion_I() + proportion_R() = 1
</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
</pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p>
<ul>
<li><p><strong>S</strong> - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I</strong> - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
<li><p><strong>R</strong> - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code>susceptibility</code> (equal to <code>proportion_SI</code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a></code> (equal to <code><a href='count.html'>count_SI</a></code>) to count susceptible isolates.</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 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>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='count.html'>count</a>_*</code> to count resistant and susceptible isolates.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
?<span class='no'>example_isolates</span>
<span class='fu'>resistance</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># determines %R</span>
<span class='fu'>susceptibility</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># determines %S+I</span>
<span class='co'># be more specific</span>
<span class='fu'>proportion_S</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_I</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>proportion_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='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>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>r</span> <span class='kw'>=</span> <span class='fu'>resistance</span>(<span class='no'>CIP</span>),
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</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>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>resistance</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<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/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>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>) <span class='co'># %SI = 76.3%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='no'>GEN</span>) <span class='co'># %SI = 75.4%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># %SI = 94.1%</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># n = 1939</span>
<span class='co'># See Details on how `only_all_tested` works. Example:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
<span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>),
<span class='kw'>proportion</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>numerator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>denominator</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>proportion</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</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'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>),
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>),
<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>))
<span class='co'># Get proportions S/I/R immediately of all rsi columns</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</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='co'># It also supports grouping variables</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</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>
<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>,
<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>), <span class='co'># amoxicillin with metronidazole</span>
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>))
}</pre>
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<li><a href="#details">Details</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
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<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 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>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>The <code><a href='portion.html'>portion</a></code> function to calculate resistance, <br /> <code><a href='https://rdrr.io/r/stats/lm.html'>lm</a></code> <code><a href='https://rdrr.io/r/stats/glm.html'>glm</a></code></p></div>
<div class='dont-index'><p>The <code><a href='proportion.html'>portion</a></code> function to calculate resistance, <br /> <code><a href='https://rdrr.io/r/stats/lm.html'>lm</a></code> <code><a href='https://rdrr.io/r/stats/glm.html'>glm</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>resistance_predict</span>(<span class='no'>example_isolates</span>, <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>)

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