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(v1.4.0.9043) documentation update

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dr. M.S. (Matthijs) Berends
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docs/reference/ab_from_text.html
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -307,7 +307,7 @@
</tr>
<tr>
<th>...</th>
<td><p>parameters passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
<td><p>arguments passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
</tr>
</table>
@ -316,19 +316,19 @@
<p>A <a href='https://rdrr.io/r/base/list.html'>list</a>, or a <a href='https://rdrr.io/r/base/character.html'>character</a> if <code>collapse</code> is not <code>NULL</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Parameter <code>type</code></h3>
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Argument <code>type</code></h3>
<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Parameter <code>collapse</code></h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Argument <code>collapse</code></h3>
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
<code>df %&gt;% mutate(abx = ab_from_text(clinical_text))</code></p>
<p>The returned AB codes can be transformed to official names, groups, etc. with all <code><a href='ab_property.html'>ab_*</a></code> functions such as <code><a href='ab_property.html'>ab_name()</a></code> and <code><a href='ab_property.html'>ab_group()</a></code>, or by using the <code>translate_ab</code> parameter.</p>
<p>The returned AB codes can be transformed to official names, groups, etc. with all <code><a href='ab_property.html'>ab_*</a></code> functions such as <code><a href='ab_property.html'>ab_name()</a></code> and <code><a href='ab_property.html'>ab_group()</a></code>, or by using the <code>translate_ab</code> argument.</p>
<p>With using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/character.html'>character</a>:<br />
<code>df %&gt;% mutate(abx = ab_from_text(clinical_text, collapse = "|"))</code></p>

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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -316,7 +316,7 @@
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
<td><p>other arguments passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
</tr>
<tr>
<th>administration</th>
@ -356,7 +356,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

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docs/reference/age.html
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -296,7 +296,7 @@
</tr>
<tr>
<th>...</th>
<td><p>parameters passed on to <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code>, such as <code>origin</code></p></td>
<td><p>arguments passed on to <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code>, such as <code>origin</code></p></td>
</tr>
</table>
@ -312,7 +312,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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@ -76,7 +76,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Split ages into age groups — age_groups" />
<meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
<meta property="og:description" content="Split ages into age groups defined by the split argument. This allows for easier demographic (antimicrobial resistance) analysis." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -270,7 +270,7 @@
</div>
<div class="ref-description">
<p>Split ages into age groups defined by the <code>split</code> parameter. This allows for easier demographic (antimicrobial resistance) analysis.</p>
<p>Split ages into age groups defined by the <code>split</code> argument. This allows for easier demographic (antimicrobial resistance) analysis.</p>
</div>
<pre class="usage"><span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>x</span>, split_at <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span><span class='op'>)</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
@ -297,7 +297,7 @@
<p>Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>To split ages, the input for the <code>split_at</code> parameter can be:</p><ul>
<p>To split ages, the input for the <code>split_at</code> argument can be:</p><ul>
<li><p>A numeric vector. A value of e.g. <code><a href='https://rdrr.io/r/base/c.html'>c(10, 20)</a></code> will split <code>x</code> on 0-9, 10-19 and 20+. A value of only <code>50</code> will split <code>x</code> on 0-49 and 50+.
The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).</p></li>
<li><p>A character:</p><ul>
@ -314,7 +314,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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docs/reference/as.ab.html
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -326,7 +326,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>

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docs/reference/as.disk.html
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -302,7 +302,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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docs/reference/as.mic.html
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -302,7 +302,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

6
docs/reference/as.mo.html
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -327,7 +327,7 @@
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to functions</p></td>
<td><p>other arguments passed on to functions</p></td>
</tr>
</table>
@ -412,7 +412,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="matching-score-for-microorganisms"><a class="anchor" href="#matching-score-for-microorganisms"></a>Matching score for microorganisms</h2>

21
docs/reference/as.rsi.html
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -325,7 +325,7 @@
</tr>
<tr>
<th>...</th>
<td><p>for using on a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>: names of columns to apply <code>as.rsi()</code> on (supports tidy selection like <code>AMX:VAN</code>). Otherwise: parameters passed on to methods.</p></td>
<td><p>for using on a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>: names of columns to apply <code>as.rsi()</code> on (supports tidy selection like <code>AMX:VAN</code>). Otherwise: arguments passed on to methods.</p></td>
</tr>
<tr>
<th>threshold</th>
@ -357,7 +357,7 @@
</tr>
<tr>
<th>reference_data</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> to be used for interpretation, which defaults to the <a href='rsi_translation.html'>rsi_translation</a> data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the <a href='rsi_translation.html'>rsi_translation</a> data set (same column names and column types). Please note that the <code>guideline</code> parameter will be ignored when <code>reference_data</code> is manually set.</p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> to be used for interpretation, which defaults to the <a href='rsi_translation.html'>rsi_translation</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href='rsi_translation.html'>rsi_translation</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></td>
</tr>
<tr>
<th>col_mo</th>
@ -376,13 +376,13 @@
<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</pre></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.disk</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</pre></li>
@ -394,8 +394,8 @@
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported guidelines</h3>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> parameter. The <code>guideline</code> parameter will then be ignored.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After interpretation</h3>
@ -410,7 +410,7 @@
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>
<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>
<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> argument.</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>
@ -432,7 +432,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
@ -463,7 +463,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
CIP <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>0.256</span><span class='op'>)</span>,
GEN <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
TOB <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>16</span><span class='op'>)</span>,
NIT <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>32</span><span class='op'>)</span><span class='op'>)</span>
NIT <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>32</span><span class='op'>)</span>,
ERY <span class='op'>=</span> <span class='st'>"R"</span><span class='op'>)</span>
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
<span class='co'># for single values</span>

8
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -310,7 +310,7 @@
</tr>
<tr>
<th>...</th>
<td><p>parameters to pass on to <code>atc_property</code></p></td>
<td><p>arguments to pass on to <code>atc_property</code></p></td>
</tr>
</table>
@ -319,7 +319,7 @@
<p><a href='https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/'>https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/</a></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Options for parameter <code>administration</code>:</p><ul>
<p>Options for argument <code>administration</code>:</p><ul>
<li><p><code>"Implant"</code> = Implant</p></li>
<li><p><code>"Inhal"</code> = Inhalation</p></li>
<li><p><code>"Instill"</code> = Instillation</p></li>
@ -350,7 +350,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

4
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -300,7 +300,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

6
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -323,7 +323,7 @@
</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 interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
<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 argument <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation 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>
@ -365,7 +365,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

8
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@ -113,7 +113,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -326,11 +326,11 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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 interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
<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 argument <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation 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>
<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 argument <code>combine_SI</code>.</p></td>
</tr>
</table>
@ -349,7 +349,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>

6
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@ -113,7 +113,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -351,7 +351,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
</ol>
<p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p>
<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> parameter, or use <code>eucast_rules(..., rules = "all")</code>.</p>
<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
@ -366,7 +366,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>

4
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -335,7 +335,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='antibiotic_class_selectors.html'>antibiotic_class_selectors()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> equivalent.</p></div>

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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -356,11 +356,11 @@
</tr>
<tr>
<th>icu_exclude</th>
<td><p>logical whether ICU isolates should be excluded (rows with value <code>TRUE</code> in column <code>col_icu</code>)</p></td>
<td><p>logical whether ICU isolates should be excluded (rows with value <code>TRUE</code> in the column set with <code>col_icu</code>)</p></td>
</tr>
<tr>
<th>specimen_group</th>
<td><p>value in column <code>col_specimen</code> to filter on</p></td>
<td><p>value in the column set with <code>col_specimen</code> to filter on</p></td>
</tr>
<tr>
<th>type</th>
@ -384,7 +384,7 @@
</tr>
<tr>
<th>...</th>
<td><p>parameters passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, or parameters passed on to <code><a href='key_antibiotics.html'>key_antibiotics()</a></code> when using <code>filter_first_weighted_isolate()</code></p></td>
<td><p>arguments passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, or arguments passed on to <code><a href='key_antibiotics.html'>key_antibiotics()</a></code> when using <code>filter_first_weighted_isolate()</code></p></td>
</tr>
</table>
@ -397,7 +397,7 @@
<p>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> argument can be omitted, please see <em>Examples</em>.</p>
<p>The <code>first_isolate()</code> function is a wrapper around the <code><a href='is_new_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Why this is so important</h3>
@ -427,9 +427,9 @@
<p>There are two ways to determine whether isolates can be included as first <em>weighted</em> isolates which will give generally the same results:</p><ol>
<li><p>Using <code>type = "keyantibiotics"</code> and parameter <code>ignore_I</code></p>
<li><p>Using <code>type = "keyantibiotics"</code> and argument <code>ignore_I</code></p>
<p>Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the <code><a href='key_antibiotics.html'>key_antibiotics()</a></code> function.</p></li>
<li><p>Using <code>type = "points"</code> and parameter <code>points_threshold</code></p>
<li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code></p>
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which default to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
</ol>
@ -439,7 +439,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

6
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -396,7 +396,7 @@
</tr>
<tr>
<th>...</th>
<td><p>Parameters passed on to functions</p></td>
<td><p>Arguments passed on to functions</p></td>
</tr>
</table>
@ -406,7 +406,7 @@
<p>As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:</p><ol>
<li><p>Rewritten code to remove the dependency on packages <code>plyr</code>, <code>scales</code> and <code>grid</code></p></li>
<li><p>Parametrised more options, like arrow and ellipse settings</p></li>
<li><p>Hardened all input possibilities by defining the exact type of user input for every parameter</p></li>
<li><p>Hardened all input possibilities by defining the exact type of user input for every argument</p></li>
<li><p>Added total amount of explained variance as a caption in the plot</p></li>
<li><p>Cleaned all syntax based on the <code>lintr</code> package, fixed grammatical errors and added integrity checks</p></li>
<li><p>Updated documentation</p></li>

12
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -372,11 +372,11 @@
</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 interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
<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 argument <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation 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>
<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 argument <code>combine_SI</code>.</p></td>
</tr>
<tr>
<th>minimum</th>
@ -428,13 +428,13 @@
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to <code>geom_rsi()</code></p></td>
<td><p>other arguments passed on to <code>geom_rsi()</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<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 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>The functions</h3>
<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> argument. See <code><a href='count.html'>count_df()</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>The functions</h3>
<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>
@ -483,7 +483,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># add other ggplot2 parameters as you like:</span>
<span class='co'># add other ggplot2 arguments as you like:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>width <span class='op'>=</span> <span class='fl'>0.5</span>,

4
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -304,7 +304,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

2
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@ -111,7 +111,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>

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@ -76,7 +76,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Determine (new) episodes for patients — is_new_episode" />
<meta property="og:description" content="This function determines which items in a vector can be considered (the start of) a new episode, based on the parameter episode_days. This can be used to determine clinical episodes for any epidemiological analysis." />
<meta property="og:description" content="This function determines which items in a vector can be considered (the start of) a new episode, based on the argument episode_days. This can be used to determine clinical episodes for any epidemiological analysis." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -270,7 +270,7 @@
</div>
<div class="ref-description">
<p>This function determines which items in a vector can be considered (the start of) a new episode, based on the parameter <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis.</p>
<p>This function determines which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis.</p>
</div>
<pre class="usage"><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>x</span>, episode_days <span class='op'>=</span> <span class='fl'>365</span>, <span class='va'>...</span><span class='op'>)</span></pre>
@ -306,7 +306,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

4
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -316,7 +316,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

12
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -336,7 +336,7 @@
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to functions</p></td>
<td><p>other arguments passed on to functions</p></td>
</tr>
<tr>
<th>y, z</th>
@ -362,7 +362,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>key_antibiotics()</code> function is context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>The <code>key_antibiotics()</code> function is context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> argument can be omitted, please see <em>Examples</em>.</p>
<p>The function <code>key_antibiotics()</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antibiotics()</code> and ignored by <code>key_antibiotics_equal()</code>.</p>
<p>The <code><a href='first_isolate.html'>first_isolate()</a></code> function only uses this function on the same microbial species from the same patient. Using this, e.g. an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) is found within the same patient episode. Without key antibiotic comparison it would not. See <code><a href='first_isolate.html'>first_isolate()</a></code> for more info.</p>
<p>At default, the antibiotics that are used for <strong>Gram-positive bacteria</strong> are:</p><ul>
@ -402,15 +402,15 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
<p>There are two ways to determine whether isolates can be included as first <em>weighted</em> isolates which will give generally the same results:</p><ol>
<li><p>Using <code>type = "keyantibiotics"</code> and parameter <code>ignore_I</code></p>
<li><p>Using <code>type = "keyantibiotics"</code> and argument <code>ignore_I</code></p>
<p>Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the <code>key_antibiotics()</code> function.</p></li>
<li><p>Using <code>type = "points"</code> and parameter <code>points_threshold</code></p>
<li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code></p>
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which default to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
</ol>

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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -307,7 +307,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

4
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@ -114,7 +114,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -297,7 +297,7 @@ The lifecycle of this function is <strong>maturing</strong>. The unlying code of
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired lifecycle</h2>

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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -318,7 +318,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -350,7 +350,7 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> argument can be omitted, please see <em>Examples</em>.</p>
<p>For the <code>pct_required_classes</code> argument, values above 1 will be divided by 100. This is to support both fractions (<code>0.75</code> or <code>3/4</code>) and percentages (<code>75</code>).</p>
<p>Currently supported guidelines are (case-insensitive):</p><ul>
<li><p><code>guideline = "CMI2012"</code> (default)</p>
@ -375,7 +375,7 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>

4
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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -311,7 +311,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
<p>Matthijs S. Berends</p>

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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -340,7 +340,7 @@
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to <code><a href='as.mo.html'>as.mo()</a></code>, such as 'allow_uncertain' and 'ignore_pattern'</p></td>
<td><p>other arguments passed on to <code><a href='as.mo.html'>as.mo()</a></code>, such as 'allow_uncertain' and 'ignore_pattern'</p></td>
</tr>
<tr>
<th>ab</th>
@ -378,7 +378,7 @@
<p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href='as.mo.html'>as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> from 2020. The <code>mo_is_intrinsic_resistant()</code> can be vectorised over parameters <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> from 2020. The <code>mo_is_intrinsic_resistant()</code> can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -387,7 +387,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="matching-score-for-microorganisms"><a class="anchor" href="#matching-score-for-microorganisms"></a>Matching score for microorganisms</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -298,7 +298,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an <span style="R">R</span> object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p>
<p><code>set_mo_source()</code> will check the file for validity: it must be a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href='microorganisms.html'>microorganisms$mo</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into <span style="R">R</span> and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> parameter and defaults to the user's home directory. It can also be set as an <span style="R">R</span> option, using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_mo_source = "my/location/file.rds")</a></code>.</p>
<p><code>set_mo_source()</code> will check the file for validity: it must be a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href='microorganisms.html'>microorganisms$mo</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into <span style="R">R</span> and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> argument and defaults to the user's home directory. It can also be set as an <span style="R">R</span> option, using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_mo_source = "my/location/file.rds")</a></code>.</p>
<p>The created compressed data file <code>"mo_source.rds"</code> will be used at default for MO determination (function <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>). The location and timestamp of the original file will be saved as an attribute to the compressed data file.</p>
<p>The function <code>get_mo_source()</code> will return the data set by reading <code>"mo_source.rds"</code> with <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>. If the original file has changed (by checking the location and timestamp of the original file), it will call <code>set_mo_source()</code> to update the data file automatically if used in an interactive session.</p>
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p>
@ -368,7 +368,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -355,7 +355,7 @@
</tr>
<tr>
<th>...</th>
<td><p>Parameters passed on to functions</p></td>
<td><p>Arguments passed on to functions</p></td>
</tr>
<tr>
<th>height</th>
@ -394,7 +394,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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@ -113,7 +113,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -342,11 +342,11 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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 interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
<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 argument <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation 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>
<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 argument <code>combine_SI</code>.</p></td>
</tr>
</table>
@ -360,7 +360,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p>The function <code>resistance()</code> is equal to the function <code>proportion_R()</code>. The function <code>susceptibility()</code> is equal to the function <code>proportion_SI()</code>.</p>
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href='first_isolate.html'>first_isolate()</a></code> to determine them in your data set.</p>
<p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href='count.html'>count()</a></code> functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code>count_susceptible() / count_all()</code>. <em>Low counts can influence the outcome - the <code>proportion</code> functions may camouflage this, since they only return the proportion (albeit being dependent on the <code>minimum</code> parameter).</em></p>
<p>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 influence the outcome - the <code>proportion</code> functions may camouflage this, since they only return the proportion (albeit being dependent on the <code>minimum</code> argument).</em></p>
<p>The function <code>proportion_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and calculates the proportions R, I and S. It also supports grouped variables. The function <code>rsi_df()</code> works exactly like <code>proportion_df()</code>, but adds the number of isolates.</p>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
@ -399,7 +399,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -310,7 +310,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The base R function <code><a href='https://rdrr.io/r/base/sample.html'>sample()</a></code> is used for generating values.</p>
<p>Generated values are based on the latest EUCAST guideline implemented in the <a href='rsi_translation.html'>rsi_translation</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> parameter.</p>
<p>Generated values are based on the latest EUCAST guideline implemented in the <a href='rsi_translation.html'>rsi_translation</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -362,7 +362,7 @@
</tr>
<tr>
<th>...</th>
<td><p>parameters passed on to functions</p></td>
<td><p>arguments passed on to functions</p></td>
</tr>
<tr>
<th>main</th>
@ -389,7 +389,7 @@
<p>Furthermore, the model itself is available as an attribute: <code>attributes(x)$model</code>, please see <em>Examples</em>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Valid options for the statistical model (parameter <code>model</code>) are:</p><ul>
<p>Valid options for the statistical model (argument <code>model</code>) are:</p><ul>
<li><p><code>"binomial"</code> or <code>"binom"</code> or <code>"logit"</code>: a generalised linear regression model with binomial distribution</p></li>
<li><p><code>"loglin"</code> or <code>"poisson"</code>: a generalised log-linear regression model with poisson distribution</p></li>
<li><p><code>"lin"</code> or <code>"linear"</code>: a linear regression model</p></li>

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@ -113,7 +113,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -305,7 +305,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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@ -112,7 +112,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
</span>
</div>
@ -296,7 +296,7 @@
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -304,7 +304,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># The 'language' parameter of below functions</span>
<pre class="examples"><span class='co'># The 'language' argument of below functions</span>
<span class='co'># will be set automatically to your system language</span>
<span class='co'># with get_locale()</span>