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dr. M.S. (Matthijs) Berends
2019-11-29 19:43:23 +01:00
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docs/reference/AMR-deprecated.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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

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<script src="../extra.js"></script>
<meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -234,7 +234,7 @@
</div>
<div class="ref-description">
<p>Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p>
<p>Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p>
</div>
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
@ -293,17 +293,19 @@
<p>Run <code><a href='https://rdrr.io/r/base/unique.html'>unique(AMR::rsi_translation$guideline)</a></code> for a list of all supported guidelines.</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-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
<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>
<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>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I 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>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. 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></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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>
</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='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>
@ -357,7 +359,7 @@
<li><a href="#arguments">Arguments</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>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>

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docs/reference/atc_online.html
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@ -86,7 +86,7 @@ This function requires an internet connection." />
</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

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docs/reference/availability.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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

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@ -86,7 +86,7 @@ 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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -278,7 +278,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</tr>
<tr>
<th>data</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
@ -306,18 +306,20 @@ 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>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><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="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>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>
<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>
<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>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I 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>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. 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></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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>
</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='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>
@ -423,7 +425,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<li><a href="#arguments">Arguments</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>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>

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docs/reference/eucast_rules.html
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@ -86,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -252,7 +252,7 @@
<li><p><code>gender</code><br /> gender of the patient</p></li>
<li><p><code>patient_id</code><br /> ID of the patient</p></li>
<li><p><code>mo</code><br /> ID of microorganism created with <code><a href='as.mo.html'>as.mo()</a></code>, see also <a href='microorganisms.html'>microorganisms</a></p></li>
<li><p><code>PEN:RIF</code><br /> 40 different antibiotics with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>); these column names occur in <a href='antibiotics.html'>antibiotics</a> data set and can be translated with <code><a href='ab_property.html'>ab_name()</a></code></p></li>
<li><p><code>PEN:RIF</code><br /> 40 different antibiotics with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>); these column names occur in <a href='antibiotics.html'>antibiotics</a> data set and can be translated with <code><a href='ab_property.html'>ab_name()</a></code></p></li>
</ul>
<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">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -300,7 +300,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>data</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with column(s) of class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with column(s) of class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
</tr>
<tr>
<th>position</th>
@ -393,7 +393,7 @@
<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><h3>The functions</h3>
<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>geom_rsi()</code> will take any variable from the data 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>) 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'>ggplot2::facet_wrap()</a></code>.</p>
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code>ggplot2::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>ggplot2::scale_brewer()</code>.</p>

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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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -248,24 +248,15 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a character vector where matches are sought, or an
object which can be coerced by <code>as.character</code> to a character
vector. <a href='https://rdrr.io/r/base/LongVectors.html'>Long vectors</a> are supported.</p></td>
<td><p>a character vector where matches are sought, or an object which can be coerced by <code><a href='https://rdrr.io/r/base/character.html'>as.character()</a></code> to a character vector.</p></td>
</tr>
<tr>
<th>pattern</th>
<td><p>character string containing a <a href='https://rdrr.io/r/base/regex.html'>regular expression</a>
(or character string for <code>fixed = TRUE</code>) to be matched
in the given character vector. Coerced by
<code><a href='https://rdrr.io/r/base/character.html'>as.character</a></code> to a character string if possible. If a
character vector of length 2 or more is supplied, the first element
is used with a warning. Missing values are allowed except for
<code>regexpr</code> and <code>gregexpr</code>.</p></td>
<td><p>a character string containing a regular expression (or <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> string for <code>fixed = TRUE</code>) to be matched in the given character vector. Coerced by <code><a href='https://rdrr.io/r/base/character.html'>as.character()</a></code> to a character string if possible. If a <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vector of length 2 or more is supplied, the first element is used with a warning.</p></td>
</tr>
<tr>
<th>ignore.case</th>
<td><p>if <code>FALSE</code>, the pattern matching is <em>case
sensitive</em> and if <code>TRUE</code>, case is ignored during matching.</p></td>
<td><p>if <code>FALSE</code>, the pattern matching is <em>case sensitive</em> and if <code>TRUE</code>, case is ignored during matching.</p></td>
</tr>
</table>

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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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -415,17 +415,19 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</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>
<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>
<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>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I 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>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. 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></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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>
</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='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>
@ -455,7 +457,7 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>

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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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

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@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

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@ -86,7 +86,7 @@ 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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -294,7 +294,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</tr>
<tr>
<th>data</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
@ -325,7 +325,7 @@ 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'>AMR::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>
<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>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
@ -357,17 +357,19 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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>
<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>
<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>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I 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>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. 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></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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>
</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>
@ -468,7 +470,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>

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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

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@ -90,7 +90,7 @@ 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">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -359,17 +359,19 @@
<li><p><code>"lin"</code> or <code>"linear"</code>: a linear regression model</p></li>
</ul>
<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>
<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>
<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>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I 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>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. 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></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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>
</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='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>
@ -437,7 +439,7 @@
<li><a href="#arguments">Arguments</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>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</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">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>