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Built site for AMR: 1.8.2.9138@dad2530

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2023-02-22 13:47:35 +00:00
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4
reference/AMR-deprecated.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -160,7 +160,7 @@
<span></span>
<span><span class="fu">ggplot_rsi_predict</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">is.rsi</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">is.rsi</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">is.rsi.eligible</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span>

15
reference/AMR-options.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -154,12 +154,13 @@
<ul><li><p><code>AMR_custom_ab</code> <br> Allows to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
<li><p><code>AMR_custom_mo</code> <br> Allows to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
<li><p><code>AMR_eucastrules</code> <br> Used for setting the default types of rules for <code><a href="eucast_rules.html">eucast_rules()</a></code> function, must be one or more of: <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>.</p></li>
<li><p><code>AMR_guideline</code> <br> Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default is <code>"EUCAST 2022"</code>. Supported guideline are currently EUCAST (2013-2022) and CLSI (2013-2022).</p></li>
<li><p><code>AMR_ignore_pattern</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to define input that must be ignored in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions.</p></li>
<li><p><code>AMR_include_PKPD</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to <code>TRUE</code>.</p></li>
<li><p><code>AMR_include_screening</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that clinical breakpoints for screening are allowed, defaults to <code>FALSE</code>.</p></li>
<li><p><code>AMR_keep_synonyms</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names.</p></li>
<li><p><code>AMR_locale</code> <br> A language to use for the <code>AMR</code> package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk).</p></li>
<li><p><code>AMR_guideline</code> <br> Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2022"</code>. Supported guideline are currently EUCAST (2013-2022) and CLSI (2013-2022).</p></li>
<li><p><code>AMR_ignore_pattern</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to ignore (i.e., make <code>NA</code>) any match given in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions.</p></li>
<li><p><code>AMR_include_PKPD</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>.</p></li>
<li><p><code>AMR_include_screening</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>.</p></li>
<li><p><code>AMR_keep_synonyms</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>.</p></li>
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
<li><p><code>AMR_locale</code> <br> A language to use for the <code>AMR</code> package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported).</p></li>
<li><p><code>AMR_mo_source</code> <br> A file location for a manual code list to be used in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions. This is explained in <code><a href="mo_source.html">set_mo_source()</a></code>.</p></li>
</ul></div>
<div class="section level2">

2
reference/AMR.html
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@@ -18,7 +18,7 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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2
reference/WHOCC.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

91
reference/WHONET.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -178,7 +178,7 @@
<li><p><code>Inducible clindamycin resistance</code><br> Clindamycin can be induced?</p></li>
<li><p><code>Comment</code><br> Other comments</p></li>
<li><p><code>Date of data entry</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> this data was entered in WHONET</p></li>
<li><p><code>AMP_ND10:CIP_EE</code><br> 0 different antibiotics. You can lookup the abbreviations in the <a href="antibiotics.html">antibiotics</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href="as.sir.html">as.sir()</a></code>.</p></li>
<li><p><code>AMP_ND10:CIP_EE</code><br> 28 different antibiotics. You can lookup the abbreviations in the <a href="antibiotics.html">antibiotics</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href="as.sir.html">as.sir()</a></code>.</p></li>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -188,89 +188,8 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">WHONET</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi'</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> columns to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' columns</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> to 'sir' with as.sir(), e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> your_data %&gt;% mutate_if(is.rsi, as.sir)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 500 × 53</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Identif…¹ Speci…² Organ…³ Country Labor…⁴ Last …⁵ First…⁶ Sex Age Age c…⁷</span>
@@ -291,7 +210,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># `Organism type` &lt;chr&gt;, Serotype &lt;chr&gt;, `Beta-lactamase` &lt;lgl&gt;, ESBL &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Carbapenemase &lt;lgl&gt;, `MRSA screening test` &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># `Inducible clindamycin resistance` &lt;lgl&gt;, Comment &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># `Date of data entry` &lt;date&gt;, AMP_ND10 &lt;rsi[!]&gt;, AMC_ED20 &lt;rsi[!]&gt;, …</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># `Date of data entry` &lt;date&gt;, AMP_ND10 &lt;rsi&gt;, AMC_ED20 &lt;rsi&gt;, …</span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

9
reference/ab_from_text.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -174,7 +174,7 @@
<dt>translate_ab</dt>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>. Defaults to <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dt>thorough_search</dt>
@@ -182,7 +182,7 @@
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
@@ -224,12 +224,15 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mind the bad spelling of amoxicillin in this line,</span></span></span>
<span class="r-in"><span><span class="co"># straight from a true health care record:</span></span></span>
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"28/03/2020 regular amoxicilliin 500mg po tid"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] AMX</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] AMX CIP</span>

12
reference/ab_property.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -192,7 +192,7 @@
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>tolower</dt>
@@ -409,6 +409,8 @@
<span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Ampicillin"</span>
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="fl">6249</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Ampicillin"</span>
@@ -421,8 +423,10 @@
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"seephthriaaksone"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># use set_ab_names() for renaming columns</span></span></span>
@@ -492,6 +496,10 @@
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="va">NIT</span><span class="op">:</span><span class="va">VAN</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "patient" "age" "gender" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "ward" "mo" "PEN" "OXA" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "FLC" "AMX" "AMC" "AMP" </span>

22
reference/add_custom_antimicrobials.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -163,8 +163,8 @@
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
<p>There are two ways to automate this process:</p>
<p><strong>Method 1:</strong> Using the option <code><a href="AMR-options.html">AMR_custom_ab</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="antibiotics.html">antibiotics</a> data set (containing at the very least columns "ab" and "name") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_ab.rds"</code>, or any remote location.</p></li>
<li><p>Set the file location to the option <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
<p><strong>Method 1:</strong> Using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_ab</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="antibiotics.html">antibiotics</a> data set (containing at the very least columns "ab" and "name") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_ab.rds"</code>, or any remote location.</p></li>
<li><p>Set the file location to the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom antimicrobial codes:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_ab <span class="op">=</span> <span class="st">"~/my_custom_ab.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>Upon package load, this file will be loaded and run through the <code>add_custom_antimicrobials()</code> function.</p></li>
@@ -191,6 +191,22 @@
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/warning.html" class="external-link">suppressWarnings</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;NA&gt;</span>
<span class="r-in"><span></span></span>

6
reference/add_custom_microorganisms.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -164,8 +164,8 @@
<p>This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see <em>Examples</em>.</p>
<p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_microorganisms()</code> function has to be run in every <span style="R">R</span> session - added microorganisms are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
<p>There are two ways to automate this process:</p>
<p><strong>Method 1:</strong> Using the option <code><a href="AMR-options.html">AMR_custom_mo</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="microorganisms.html">microorganisms</a> data set (containing at the very least column "genus") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_mo.rds"</code>, or any remote location.</p></li>
<li><p>Set the file location to the option <code><a href="AMR-options.html">AMR_custom_mo</a></code>: <code>options(AMR_custom_mo = "~/my_custom_mo.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
<p><strong>Method 1:</strong> Using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_mo</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="microorganisms.html">microorganisms</a> data set (containing at the very least column "genus") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_mo.rds"</code>, or any remote location.</p></li>
<li><p>Set the file location to the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_mo</a></code>: <code>options(AMR_custom_mo = "~/my_custom_mo.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom microorganism codes:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_mo <span class="op">=</span> <span class="st">"~/my_custom_mo.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>Upon package load, this file will be loaded and run through the <code>add_custom_microorganisms()</code> function.</p></li>

24
reference/age.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -158,7 +158,7 @@
<dt>reference</dt>
<dd><p>reference date(s) (defaults to today), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code></p></dd>
<dd><p>reference date(s) (default is today), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code></p></dd>
<dt>exact</dt>
@@ -205,16 +205,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1939-01-24 84 84.06849 60</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1951-10-09 71 71.36164 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1932-05-25 90 90.73699 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1968-09-21 54 54.41096 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1953-07-06 69 69.62192 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1991-10-10 31 31.35890 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1995-02-19 27 27.99726 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1961-04-11 61 61.85753 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-03-22 70 70.91233 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1967-09-04 55 55.45753 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1960-06-27 62 62.65753 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1970-01-19 53 53.09315 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1951-04-12 71 71.86575 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1934-02-03 89 89.05205 65</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1983-05-27 39 39.74247 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1944-08-01 78 78.56164 55</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1991-01-21 32 32.08767 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1957-12-02 65 65.22466 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1950-11-20 72 72.25753 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1959-07-23 63 63.58630 40</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

4
reference/age_groups.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -158,7 +158,7 @@
<dt>split_at</dt>
<dd><p>values to split <code>x</code> at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See <em>Details</em>.</p></dd>
<dd><p>values to split <code>x</code> at - the default is age groups 0-11, 12-24, 25-54, 55-74 and 75+. See <em>Details</em>.</p></dd>
<dt>na.rm</dt>

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69
reference/antibiogram.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -172,7 +172,13 @@
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for antibiogram</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, as_kable <span class="op">=</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, italicise <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> as_kable <span class="op">=</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> italicise <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> na <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"knitr.kable.NA"</span>, default <span class="op">=</span> <span class="st">""</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@@ -193,11 +199,11 @@
<dt>mo_transform</dt>
<dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt>ab_transform</dt>
<dd><p>a character to transform antibiotic input - must be one of the column names of the <a href="antibiotics.html">antibiotics</a> data set: "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units" or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dd><p>a character to transform antibiotic input - must be one of the column names of the <a href="antibiotics.html">antibiotics</a> data set: "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt>syndromic_group</dt>
@@ -205,7 +211,7 @@
<dt>add_total_n</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether total available numbers per pathogen should be added to the table (defaults to <code>TRUE</code>). This will add the lowest and highest number of available isolate per antibiotic (e.g, if for <em>E. coli</em> 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether total available numbers per pathogen should be added to the table (default is <code>TRUE</code>). This will add the lowest and highest number of available isolate per antibiotic (e.g, if for <em>E. coli</em> 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").</p></dd>
<dt>only_all_tested</dt>
@@ -217,7 +223,7 @@
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>language</dt>
@@ -229,7 +235,7 @@
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (defaults to <code>TRUE</code>)</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (default is <code>TRUE</code>)</p></dd>
<dt>sep</dt>
@@ -237,7 +243,7 @@
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
@@ -253,7 +259,11 @@
<dt>italicise</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the microorganism names in the output table should be made italic, using <code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code>. This only works when the output format is markdown, such as in HTML output.</p></dd>
<dd><p>(only when <code>as_kable = TRUE</code>) a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the microorganism names in the output table should be made italic, using <code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code>. This only works when the output format is markdown, such as in HTML output.</p></dd>
<dt>na</dt>
<dd><p>(only when <code>as_kable = TRUE</code>) character to use for showing <code>NA</code> values</p></dd>
</dl></div>
<div class="section level2">
@@ -289,7 +299,7 @@
<span> <span class="va">.</span><span class="op">$</span><span class="va">condition</span> <span class="op">==</span> <span class="st">"Heart Disease"</span>,</span>
<span> <span class="st">"Study Group"</span>, <span class="st">"Control Group"</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div></li>
</ol><p>All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>) or printed into R Markdown / Quarto formats for reports using <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code>. Use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. <code>flextable::as_flextable()</code> or <code>gt::gt()</code>.</p>
<p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (defaults to <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
<p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (default is <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>
@@ -342,7 +352,7 @@
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
@@ -364,7 +374,7 @@
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` J01GB01 J01GB03 J01GB04 J01GB06</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
@@ -394,11 +404,7 @@
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` TZP `TZP + GEN` `TZP + TOB`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 99 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044) 86 98 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
@@ -406,12 +412,7 @@
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> sep <span class="op">=</span> <span class="st">" &amp; "</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` `Piperacillin/tazobactam` Piperacillin/tazobactam &amp; …¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-550) 86 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with abbreviated variable name ¹​`Piperacillin/tazobactam &amp; Tobramycin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Syndromic antibiogram ------------------------------------------------</span></span></span>
@@ -422,7 +423,7 @@
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
@@ -457,7 +458,7 @@
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"es"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
@@ -477,13 +478,7 @@
<span class="r-in"><span> <span class="st">"WISCA Group 1"</span>, <span class="st">"WISCA Group 2"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Pathogen (N min-max)` AMC `AMC + CIP` TZP `TZP + TOB`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> WISCA Group 1 Gram-negative (261-285) 76 95 89 99</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> WISCA Group 2 Gram-negative (380-442) 76 98 88 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Print the output for R Markdown / Quarto -----------------------------</span></span></span>
<span class="r-in"><span></span></span>
@@ -519,16 +514,18 @@
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">ab1</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="antibiogram-1.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in ggplot2::autoplot(ab1):</span> Objects of class <span style="color: #0000BB;">&lt;numeric&gt;</span> are not supported by autoplot.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> have you loaded the required package?</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">ab2</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="antibiogram-2.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in ggplot2::autoplot(ab2):</span> Objects of class <span style="color: #0000BB;">&lt;numeric&gt;</span> are not supported by autoplot.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> have you loaded the required package?</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ab1</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="antibiogram-3.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="antibiogram-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ab2</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="antibiogram-4.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="antibiogram-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

86
reference/antibiotic_class_selectors.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -221,11 +221,11 @@
<dt>only_sir_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code>sir</code> must be selected (defaults to <code>FALSE</code>), see <code><a href="as.sir.html">as.sir()</a></code></p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code>sir</code> must be selected (default is <code>FALSE</code>), see <code><a href="as.sir.html">as.sir()</a></code></p></dd>
<dt>only_treatable</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (defaults to <code>TRUE</code>), such as gentamicin-high (<code>GEH</code>) and imipenem/EDTA (<code>IPE</code>)</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is <code>TRUE</code>), such as gentamicin-high (<code>GEH</code>) and imipenem/EDTA (<code>IPE</code>)</p></dd>
<dt>...</dt>
@@ -237,11 +237,11 @@
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>version_expertrules</dt>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".</p></dd>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2", or "3.1".</p></dd>
</dl></div>
<div class="section level2">
@@ -265,31 +265,31 @@
<h2 id="full-list-of-supported-antibiotic-classes">Full list of supported (antibiotic) classes<a class="anchor" aria-label="anchor" href="#full-list-of-supported-antibiotic-classes"></a></h2>
<ul><li><p><code>aminoglycosides()</code> can select: <br> amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)</p></li>
<ul><li><p><code>aminoglycosides()</code> can select: <br> amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)</p></li>
<li><p><code>aminopenicillins()</code> can select: <br> amoxicillin (AMX) and ampicillin (AMP)</p></li>
<li><p><code>antifungals()</code> can select: <br> amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR)</p></li>
<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>carbapenems()</code> can select: <br> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)</p></li>
<li><p><code>cephalosporins()</code> can select: <br> cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_1st()</code> can select: <br> cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL) and cephradine (CED)</p></li>
<li><p><code>cephalosporins_2nd()</code> can select: <br> cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_3rd()</code> can select: <br> cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB) and latamoxef (LTM)</p></li>
<li><p><code>cephalosporins_4th()</code> can select: <br> cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)</p></li>
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1) and ceftolozane/tazobactam (CZT)</p></li>
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)</p></li>
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)</p></li>
<li><p><code>lincosamides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)</p></li>
<li><p><code>lipoglycopeptides()</code> can select: <br> dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)</p></li>
<li><p><code>macrolides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)</p></li>
<li><p><code>oxazolidinones()</code> can select: <br> cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)</p></li>
<li><p><code>penicillins()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>polymyxins()</code> can select: <br> colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)</p></li>
<li><p><code>quinolones()</code> can select: <br> besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)</p></li>
<li><p><code>antifungals()</code> can select: <br> amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)</p></li>
<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>carbapenems()</code> can select: <br> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)</p></li>
<li><p><code>cephalosporins()</code> can select: <br> cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_1st()</code> can select: <br> cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)</p></li>
<li><p><code>cephalosporins_2nd()</code> can select: <br> cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), and loracarbef (LOR)</p></li>
<li><p><code>cephalosporins_3rd()</code> can select: <br> cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)</p></li>
<li><p><code>cephalosporins_4th()</code> can select: <br> cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)</p></li>
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)</p></li>
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)</p></li>
<li><p><code>lincosamides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)</p></li>
<li><p><code>lipoglycopeptides()</code> can select: <br> dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)</p></li>
<li><p><code>macrolides()</code> can select: <br> acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)</p></li>
<li><p><code>oxazolidinones()</code> can select: <br> cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA)</p></li>
<li><p><code>penicillins()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>polymyxins()</code> can select: <br> colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)</p></li>
<li><p><code>quinolones()</code> can select: <br> besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<li><p><code>streptogramins()</code> can select: <br> pristinamycin (PRI) and quinupristin/dalfopristin (QDA)</p></li>
<li><p><code>tetracyclines()</code> can select: <br> cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY) and tigecycline (TGC)</p></li>
<li><p><code>trimethoprims()</code> can select: <br> brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP) and trimethoprim/sulfamethoxazole (SXT)</p></li>
<li><p><code>ureidopenicillins()</code> can select: <br> azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)</p></li>
<li><p><code>tetracyclines()</code> can select: <br> cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), and tigecycline (TGC)</p></li>
<li><p><code>trimethoprims()</code> can select: <br> brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)</p></li>
<li><p><code>ureidopenicillins()</code> can select: <br> azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP)</p></li>
</ul></div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
@@ -347,7 +347,7 @@
<span class="r-in"><span><span class="co"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span></span></span>
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo GEN TOB AMK KAN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -372,7 +372,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (rifampicin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 23</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX </span>
@@ -489,7 +489,7 @@
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 26 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -516,7 +516,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (piperacillin/tazobactam)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> PEN OXA FLC AMX AMC AMP TZP </span>
@@ -541,7 +541,7 @@
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),</span>
@@ -550,7 +550,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (rifampicin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP </span>
@@ -575,7 +575,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'KAN' (kanamycin), 'FOS'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (fosfomycin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'ERY' (erythromycin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'CLI' (clindamycin), 'MTR' (metronidazole) and 'CHL' (chloramphenicol)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'CLI' (clindamycin), 'MTR' (metronidazole), and 'CHL' (chloramphenicol)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP KAN FOS LNZ VAN ERY CLI MTR CHL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -600,7 +600,7 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span>, <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(aminoglycosides(), resistance)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 3: `ward = "Outpatient"`.</span>
@@ -620,7 +620,7 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),</span>
@@ -629,7 +629,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (rifampicin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX AMC AMP </span>
@@ -656,7 +656,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For not_intrinsic_resistant() removing columns 'PEN'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (benzylpenicillin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'TEC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (teicoplanin), 'ERY' (erythromycin), 'CLI' (clindamycin), 'AZM'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (azithromycin) and 'RIF' (rifampicin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (azithromycin), and 'RIF' (rifampicin)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 52 warnings in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(not_intrinsic_resistant(), resistance)`.</span>
@@ -716,7 +716,7 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo GEN TOB AMK KAN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -740,7 +740,7 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For cephalosporins_2nd() using columns 'CXM' (cefuroxime) and 'FOX'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (cefoxitin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 112 × 46</span></span>
@@ -770,7 +770,7 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 531 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -797,7 +797,7 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming a filter on all 4 aminoglycosides. Wrap around all() or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> any() to prevent this note.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 427 × 46</span></span>

2
reference/antibiotics.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

9
reference/as.ab.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -164,7 +164,7 @@
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
@@ -229,6 +229,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J 01 FA 01"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythromycin"</span><span class="op">)</span></span></span>
@@ -238,6 +239,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">" eryt 123"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"ERYT"</span><span class="op">)</span></span></span>
@@ -247,6 +251,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"eritromicine"</span><span class="op">)</span> <span class="co"># spelled wrong, yet works</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythrocin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>

4
reference/as.av.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -164,7 +164,7 @@
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>

2
reference/as.disk.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/as.mic.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -169,7 +169,7 @@
<dt>as.mic</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the <code>mic</code> class should be kept, defaults to <code>FALSE</code></p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the <code>mic</code> class should be kept - the default is <code>FALSE</code></p></dd>
<dt>...</dt>

33
reference/as.mo.html
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File diff suppressed because one or more lines are too long

34
reference/as.sir.html
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@@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -238,7 +238,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<dt>guideline</dt>
<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the option <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2013-2022) and CLSI (2013-2022), see <em>Details</em>.</p></dd>
<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2013-2022) and CLSI (2013-2022), see <em>Details</em>.</p></dd>
<dt>uti</dt>
@@ -258,15 +258,15 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<dt>include_screening</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that clinical breakpoints for screening are allowed, defaults to <code>FALSE</code>. Can also be set with the option <code><a href="AMR-options.html">AMR_include_screening</a></code>.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_screening</a></code>.</p></dd>
<dt>include_PKPD</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to <code>TRUE</code>. Can also be set with the option <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>clean</dt>
@@ -308,7 +308,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2022"</code> or <code>"CLSI 2022"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<p>You can set the default guideline with the option <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
<p>You can set the default guideline with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI 2018"</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"EUCAST 2020"</span>)</span>
@@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-18 <span style="color: #949494;">14:03:27</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-18 <span style="color: #949494;">14:03:26</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-18 <span style="color: #949494;">14:03:26</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-18 <span style="color: #949494;">14:03:25</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-22 <span style="color: #949494;">13:45:00</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-22 <span style="color: #949494;">13:44:59</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-22 <span style="color: #949494;">13:44:59</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-22 <span style="color: #949494;">13:44:58</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;, ab_considered &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mo_considered &lt;lgl&gt;, breakpoint_S &lt;lgl&gt;, breakpoint_R &lt;lgl&gt;,</span></span>
@@ -725,7 +725,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): 3 results in column '24' truncated (50%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B" and "C"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B", and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I R &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>

2
reference/atc_online.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/av_from_text.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -174,7 +174,7 @@
<dt>translate_av</dt>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antivirals</a> data set to translate the antibiotic abbreviations to, using <code><a href="av_property.html">av_property()</a></code>. Defaults to <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antivirals</a> data set to translate the antibiotic abbreviations to, using <code><a href="av_property.html">av_property()</a></code>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dt>thorough_search</dt>
@@ -182,7 +182,7 @@
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>

4
reference/av_property.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -180,7 +180,7 @@
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text - the default is system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>tolower</dt>

4
reference/availability.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -158,7 +158,7 @@
<dt>width</dt>
<dd><p>number of characters to present the visual availability, defaults to filling the width of the console</p></dd>
<dd><p>number of characters to present the visual availability - the default is filling the width of the console</p></dd>
</dl></div>
<div class="section level2">

10
reference/bug_drug_combinations.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
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@@ -172,11 +172,11 @@
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>FUN</dt>
<dd><p>the function to call on the <code>mo</code> column to transform the microorganism codes, defaults to <code><a href="mo_property.html">mo_shortname()</a></code></p></dd>
<dd><p>the function to call on the <code>mo</code> column to transform the microorganism codes - the default is <code><a href="mo_property.html">mo_shortname()</a></code></p></dd>
<dt>...</dt>
@@ -188,7 +188,7 @@
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>minimum</dt>
@@ -196,7 +196,7 @@
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values S and I should be summed, so resistance will be based on only R, defaults to <code>TRUE</code></p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values S and I should be summed, so resistance will be based on only R - the default is <code>TRUE</code></p></dd>
<dt>add_ab_group</dt>

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reference/clinical_breakpoints.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
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8
reference/count.html
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@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
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@@ -196,11 +196,11 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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), defaults to <code>TRUE</code></p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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) - the default is <code>TRUE</code></p></dd>
</dl></div>
<div class="section level2">
@@ -355,7 +355,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> <span class="fu">count_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward antibiotic interpretation value</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>

56
reference/custom_eucast_rules.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
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@@ -207,7 +207,7 @@
<h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
<span> <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
<span></span>
@@ -221,34 +221,34 @@
<h3 id="usage-of-antibiotic-group-names">Usage of antibiotic group names<a class="anchor" aria-label="anchor" href="#usage-of-antibiotic-group-names"></a></h3>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.</p><ul><li><p>"aminoglycosides"<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)</p></li>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.</p><ul><li><p>"aminoglycosides"<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>"aminopenicillins"<br>(amoxicillin and ampicillin)</p></li>
<li><p>"antifungals"<br>(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)</p></li>
<li><p>"antimycobacterials"<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide and viomycin)</p></li>
<li><p>"betalactams"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>"carbapenems"<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)</p></li>
<li><p>"cephalosporins"<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef and loracarbef)</p></li>
<li><p>"cephalosporins_1st"<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole and cephradine)</p></li>
<li><p>"cephalosporins_2nd"<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)</p></li>
<li><p>"cephalosporins_3rd"<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor and latamoxef)</p></li>
<li><p>"cephalosporins_4th"<br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)</p></li>
<li><p>"cephalosporins_5th"<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril and ceftolozane/tazobactam)</p></li>
<li><p>"cephalosporins_except_caz"<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef and loracarbef)</p></li>
<li><p>"fluoroquinolones"<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>"glycopeptides"<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)</p></li>
<li><p>"glycopeptides_except_lipo"<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)</p></li>
<li><p>"lincosamides"<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)</p></li>
<li><p>"lipoglycopeptides"<br>(dalbavancin, oritavancin and telavancin)</p></li>
<li><p>"macrolides"<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)</p></li>
<li><p>"oxazolidinones"<br>(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)</p></li>
<li><p>"penicillins"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)</p></li>
<li><p>"polymyxins"<br>(colistin, polymyxin B and polymyxin B/polysorbate 80)</p></li>
<li><p>"quinolones"<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)</p></li>
<li><p>"antifungals"<br>(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>"antimycobacterials"<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
<li><p>"betalactams"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>"carbapenems"<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)</p></li>
<li><p>"cephalosporins"<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>"cephalosporins_1st"<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)</p></li>
<li><p>"cephalosporins_2nd"<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)</p></li>
<li><p>"cephalosporins_3rd"<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)</p></li>
<li><p>"cephalosporins_4th"<br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)</p></li>
<li><p>"cephalosporins_5th"<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)</p></li>
<li><p>"cephalosporins_except_caz"<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>"fluoroquinolones"<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>"glycopeptides"<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>"glycopeptides_except_lipo"<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>"lincosamides"<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>"lipoglycopeptides"<br>(dalbavancin, oritavancin, and telavancin)</p></li>
<li><p>"macrolides"<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>"oxazolidinones"<br>(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)</p></li>
<li><p>"penicillins"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>"polymyxins"<br>(colistin, polymyxin B, and polymyxin B/polysorbate 80)</p></li>
<li><p>"quinolones"<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>"streptogramins"<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
<li><p>"tetracyclines"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline and tigecycline)</p></li>
<li><p>"tetracyclines_except_tgc"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline and tetracycline)</p></li>
<li><p>"trimethoprims"<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)</p></li>
<li><p>"ureidopenicillins"<br>(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)</p></li>
<li><p>"tetracyclines"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tigecycline)</p></li>
<li><p>"tetracyclines_except_tgc"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, and tetracycline)</p></li>
<li><p>"trimethoprims"<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>"ureidopenicillins"<br>(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)</p></li>
</ul></div>
</div>

6
reference/dosage.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -155,10 +155,10 @@
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 336 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>name</code><br> Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>type</code><br> Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti"</p></li>
<li><p><code>type</code><br> Type of the dosage, either "high_dosage", "standard_dosage", or "uncomplicated_uti"</p></li>
<li><p><code>dose</code><br> Dose, such as "2 g" or "25 mg/kg"</p></li>
<li><p><code>dose_times</code><br> Number of times a dose must be administered</p></li>
<li><p><code>administration</code><br> Route of administration, either "im", "iv" or "oral"</p></li>
<li><p><code>administration</code><br> Route of administration, either "im", "iv", or "oral"</p></li>
<li><p><code>notes</code><br> Additional dosage notes</p></li>
<li><p><code>original_txt</code><br> Original text in the PDF file of EUCAST</p></li>
<li><p><code>eucast_version</code><br> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply</p></li>

22
reference/eucast_rules.html
View File

@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -188,15 +188,15 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions</p></dd>
<dt>rules</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>. The default value can be set to another value using the option <code><a href="AMR-options.html">AMR_eucastrules</a></code>: <code>options(AMR_eucastrules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>. The default value can be set to another value using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_eucastrules</a></code>: <code>options(AMR_eucastrules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dt>verbose</dt>
@@ -204,19 +204,19 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt>version_breakpoints</dt>
<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "12.0", "11.0" or "10.0".</p></dd>
<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "12.0", "11.0", or "10.0".</p></dd>
<dt>version_expertrules</dt>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".</p></dd>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2", or "3.1".</p></dd>
<dt>ampc_cephalosporin_resistance</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code> and higher; these version of '<em>EUCAST Expert Rules on Enterobacterales</em>' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of <code>NA</code> (the default) for this argument will remove results for these three drugs, while e.g. a value of <code>"R"</code> will make the results for these drugs resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using <code>TRUE</code> is equal to using <code>"R"</code>. <br> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, <em>Klebsiella aerogenes</em>, <em>Morganella morganii</em>, <em>Providencia</em> and <em>Serratia</em>.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code> and higher; these version of '<em>EUCAST Expert Rules on Enterobacterales</em>' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of <code>NA</code> (the default) for this argument will remove results for these three drugs, while e.g. a value of <code>"R"</code> will make the results for these drugs resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using <code>TRUE</code> is equal to using <code>"R"</code>. <br> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, <em>Klebsiella aerogenes</em>, <em>Morganella morganii</em>, <em>Providencia</em>, and <em>Serratia</em>.</p></dd>
<dt>only_sir_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dt>custom_rules</dt>
@@ -232,7 +232,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt>administration</dt>
<dd><p>route of administration, either "im", "iv" or "oral"</p></dd>
<dd><p>route of administration, either "im", "iv", or "oral"</p></dd>
</dl></div>
<div class="section level2">
@@ -262,7 +262,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol><li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li>
<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the same drug <strong>with</strong> enzyme inhibitor is R</p></li>
</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> argument, or use <code>eucast_rules(..., rules = "all")</code>. You can also set the option <code><a href="AMR-options.html">AMR_eucastrules</a></code>, i.e. run <code>options(AMR_eucastrules = "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>. You can also set the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_eucastrules</a></code>, i.e. run <code>options(AMR_eucastrules = "all")</code>.</p>
</div>
</div>
@@ -365,6 +365,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Tables' v12.0 (2022). This note will be shown once per session.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>

4
reference/example_isolates.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -157,7 +157,7 @@
<li><p><code>patient</code><br> ID of the patient</p></li>
<li><p><code>age</code><br> Age of the patient</p></li>
<li><p><code>gender</code><br> Gender of the patient, either "F" or "M"</p></li>
<li><p><code>ward</code><br> Ward type where the patient was admitted, either "Clinical", "ICU" or "Outpatient"</p></li>
<li><p><code>ward</code><br> Ward type where the patient was admitted, either "Clinical", "ICU", or "Outpatient"</p></li>
<li><p><code>mo</code><br> ID of microorganism created with <code><a href="as.mo.html">as.mo()</a></code>, see also the <a href="microorganisms.html">microorganisms</a> data set</p></li>
<li><p><code>PEN:RIF</code><br> 40 different antibiotics with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>); these column names occur in the <a href="antibiotics.html">antibiotics</a> data set and can be translated with <code><a href="ab_property.html">set_ab_names()</a></code> or <code><a href="ab_property.html">ab_name()</a></code></p></li>
</ul></div>

2
reference/example_isolates_unclean.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

12
reference/first_isolate.html
View File

@@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -197,15 +197,15 @@
<dt>col_date</dt>
<dd><p>column name of the result date (or date that is was received on the lab), defaults to the first column with a date class</p></dd>
<dd><p>column name of the result date (or date that is was received on the lab) - the default is the first column with a date class</p></dd>
<dt>col_patient_id</dt>
<dd><p>column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)</p></dd>
<dd><p>column name of the unique IDs of the patients - the default is the first column that starts with 'patient' or 'patid' (case insensitive)</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>col_testcode</dt>
@@ -221,7 +221,7 @@
<dt>col_keyantimicrobials</dt>
<dd><p>(only useful when <code>method = "phenotype-based"</code>) column name of the key antimicrobials to determine first isolates, see <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use <code>col_keyantimicrobials = FALSE</code> to prevent this. Can also be the output of <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>.</p></dd>
<dd><p>(only useful when <code>method = "phenotype-based"</code>) column name of the key antimicrobials to determine first isolates, see <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>. The default is the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use <code>col_keyantimicrobials = FALSE</code> to prevent this. Can also be the output of <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>.</p></dd>
<dt>episode_days</dt>
@@ -257,7 +257,7 @@
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>include_unknown</dt>

2
reference/g.test.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

110
reference/get_episode.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -192,27 +192,31 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 9 36 4 23 47 35 39 40 6 37 20 5 1 49 9 24 11 32 17 4 26 23 37 46 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 14 7 6 13 29 13 31 40 34 46 48 9 34 33 45 31 29 26 4 15 31 21 9 12 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 28 42 28 47 45 4 47 43 45 44 36 3 18 47 5 23 21 20 32 33 13 38 22 19 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 30 41 33 35 47 16 2 44 1 16 29 35 32 10 9 13 25 46 45 24 28 20 27 46 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 41 12 5 11 39 27 43 35 7 21 18 14 45 44 26 41 9 36 34 1 14 14 31 4 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 5 28 40 15 27 26 34 16 46 10 33 18 9 7 8 41 3 3 22 36 42 13 12 22 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 11 19 21 39 20 2 9 25 3 13 37 12 29 11 2 23 31 6 28 47 29 5 32 24 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 3 43 30 24 36 2 1 14 18 40 6 19 9 20 11 19 15 31 12 3 17 32 24 45 38</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-11-21 450741 77 F ICU B_STPHY_EPDR R NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-05-26 065187 76 F ICU B_STPHY_AURS R NA S R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2003-04-30 6BC362 62 M ICU B_STPHY_EPDR R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2003-06-01 CBC201 87 F Clinical B_STPHY_CONS S NA S NA </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2003-04-22 114570 74 M ICU B_STPHY_CONS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 2003-04-08 114570 74 M ICU B_STRPT_PYGN S NA S S </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;,</span></span>
@@ -247,19 +251,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [97]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 004531 2013-12-02 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 006827 2009-07-24 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 008218 2009-05-05 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 021368 2016-03-25 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 032343 2003-06-09 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 069276 2015-06-18 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 077922 2009-08-24 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 0DBB93 2009-05-08 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 125492 2017-09-15 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 126334 2009-11-26 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 065133 2011-12-19 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 065187 2003-05-26 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 080086 2007-10-26 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 114570 2003-04-08 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 114570 2003-04-22 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 126334 2009-11-26 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 146120 2011-09-23 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 15D386 2004-09-06 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 161740 2005-06-21 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 16F0F7 2010-01-17 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -273,19 +277,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2013-12-02 004531 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-07-24 006827 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2009-05-05 008218 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Outpatient 2016-03-25 021368 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2003-06-09 032343 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2015-06-18 069276 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2009-08-24 077922 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2009-05-08 0DBB93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2017-09-15 125492 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Outpatient 2009-11-26 126334 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2011-12-19 065133 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2003-05-26 065187 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2007-10-26 080086 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2003-04-08 114570 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2003-04-22 114570 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2009-11-26 126334 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2011-09-23 146120 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2004-09-06 15D386 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2005-06-21 161740 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2010-01-17 16F0F7 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -301,9 +305,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 74 14 41 54</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 20 7 16 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 4 2 3 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 60 13 33 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 27 9 21 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 8 6 7 7</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@@ -321,7 +325,7 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
<span class="r-in"><span><span class="co"># since you can now group on anything that seems relevant:</span></span></span>
@@ -335,16 +339,16 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 838694 B_ACNTB Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 919B60 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 032343 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 126334 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> BF4515 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B13995 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E99D61 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> C54153 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 822116 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B12887 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E52521 B_KLBSL_AERG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 6D6319 B_STPHY_CONS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 984417 B_STPHY_AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 161740 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 904640 B_PROTS_MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 387C40 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 59F400 B_STRPT_PNMN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> A97263 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 619705 B_KLBSL_PNMN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 314039 UNKNOWN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

6
reference/ggplot_pca.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -332,8 +332,8 @@
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "TOB". Total observations available: 7.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "TMP", and "TOB". Total observations available: 7.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Groups (n=4, named as 'order'):</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>

8
reference/ggplot_sir.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -240,7 +240,7 @@
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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), defaults to <code>TRUE</code></p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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) - the default is <code>TRUE</code></p></dd>
<dt>minimum</dt>
@@ -248,7 +248,7 @@
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>nrow</dt>
@@ -296,7 +296,7 @@
<dt>aesthetics</dt>
<dd><p>aesthetics to apply the colours to, defaults to "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"</p></dd>
<dd><p>aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"</p></dd>
</dl></div>
<div class="section level2">

4
reference/guess_ab_col.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -171,7 +171,7 @@
<dt>only_sir_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
</dl></div>
<div class="section level2">

4
reference/index.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -155,7 +155,7 @@
<code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_reset_session()</a></code> <code><a href="as.mo.html">mo_cleaning_regex()</a></code>
</dt>
<dd>Transform Input to a Microorganism Code</dd>
<dd>Transform Arbitrary Input to Valid Microbial Taxonomy</dd>
</dl><dl><dt>
<code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_status()</a></code> <code><a href="mo_property.html">mo_pathogenicity()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_gbif()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_current()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code>

2
reference/intrinsic_resistant.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/italicise_taxonomy.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/join.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/key_antimicrobials.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -182,7 +182,7 @@
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>universal</dt>
@@ -202,7 +202,7 @@
<dt>only_sir_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dt>...</dt>

6
reference/kurtosis.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -182,9 +182,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.147968</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.059277</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.003239662</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0744193</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/like.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

8
reference/mdro.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -188,11 +188,11 @@
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions</p></dd>
<dt>pct_required_classes</dt>
@@ -208,7 +208,7 @@
<dt>only_sir_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dt>...</dt>

84
reference/mean_amr_distance.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -170,7 +170,7 @@
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant), defaults to <code>TRUE</code></p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
<dt>amr_distance</dt>
@@ -201,30 +201,30 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I S S S S S S R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R S R R I R S S I</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.8973666 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4743416 -0.4743416 1.8973666 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.9486833 0.9486833 -0.9486833 0.9486833 0.9486833 -0.9486833</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.9486833 -0.9486833 -0.9486833 -0.9486833</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 0.001 0.01 1 4 0.125 0.125 8 2 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.0625 0.5 &gt;=64 &gt;=64 0.01 0.025 0.5 4 0.125 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.06516456 -1.92394777 -1.09443897 0.56457861 1.06399267 -0.18454247</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.18454247 1.31369970 0.81428564 -0.43424950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.65023906 -0.65023906 0.02162933 1.58932224 1.58932224 -1.24234686</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.94629296 0.02162933 0.69349772 -0.42628293</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.06516456 -1.92394777 -1.09443897 0.56457861 1.06399267 -0.18454247</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.18454247 1.31369970 0.81428564 -0.43424950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.65023906 -0.65023906 0.02162933 1.58932224 1.58932224 -1.24234686</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.94629296 0.02162933 0.69349772 -0.42628293</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 30 18 33 24 27 16 46 50 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 18 50 28 16 21 46 35 38 41 42</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.36485665 0.09748976 -0.87740785 0.34121416 -0.38995904 -0.14623464</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.03989078 1.39735324 1.72231911 0.25997270</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.2835219 1.3663298 -0.4554433 -1.4491377 -1.0350983 1.0350983</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.1242118 0.3726354 0.6210590 0.7038669</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -234,22 +234,22 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 24 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 20 &lt;=0.5 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 26 1 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 21 &lt;=0.5 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E R 26 2 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 18 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 21 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 29 2 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 23 1 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 19 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 31 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 31 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 19 &lt;=0.25 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 23 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E R 18 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 28 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 29 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 17 &gt;=16 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 26 &lt;=0.25 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 30 &lt;=0.25 2</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.584051604 -0.989329211 0.140243831 -0.328508012 0.257166131</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] -0.197313482 0.138976310 0.585319125 -0.187909163 -0.002697134</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.2343675231 0.3170884159 0.3733587992 -0.4531732369 0.1646099199</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] -0.2272860166 -0.2908156418 0.0641437661 -0.1815016525 -0.0007918763</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -263,19 +263,19 @@
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 26 1 8 0.140243831 0.000000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G R 21 2 1 0.138976310 0.001267521</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 E R 26 2 &lt;=0.25 0.257166131 0.116922299</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J R 19 2 1 -0.002697134 0.142940965</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I R 23 1 &lt;=0.25 -0.187909163 0.328152995</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 18 4 2 -0.197313482 0.337557314</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 A R 24 4 1 0.584051604 0.443807773</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 29 2 8 0.585319125 0.445075294</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 D S 21 &lt;=0.5 &gt;=16 -0.328508012 0.468751843</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 B S 20 &lt;=0.5 0.5 -0.989329211 1.129573042</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 19 &lt;=0.25 4 0.3733587992 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 31 0.5 1 0.3170884159 0.05627038</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 A S 31 8 1 0.2343675231 0.13899128</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E R 18 8 1 0.1646099199 0.20874888</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 H I 17 &gt;=16 2 0.0641437661 0.30921503</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 J I 30 &lt;=0.25 2 -0.0007918763 0.37415068</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 I I 26 &lt;=0.25 2 -0.1815016525 0.55486045</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 F I 28 1 1 -0.2272860166 0.60064482</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 G S 29 0.5 1 -0.2908156418 0.66417444</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D I 23 1 1 -0.4531732369 0.82653204</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -288,7 +288,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_genus()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_species()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM" and "MEM"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: mo [4]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo TCY IPM MEM dist</span>

2
reference/microorganisms.codes.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/microorganisms.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -165,7 +165,7 @@
<li><p><code>gbif</code><br> Identifier ('taxonID') of the Global Biodiversity Information Facility (GBIF)</p></li>
<li><p><code>gbif_parent</code><br> GBIF identifier of the parent taxon</p></li>
<li><p><code>gbif_renamed_to</code><br> GBIF identifier of the currently valid taxon</p></li>
<li><p><code>source</code><br> Either "GBIF", "LPSN" or "manually added" (see <em>Source</em>)</p></li>
<li><p><code>source</code><br> Either "GBIF", "LPSN", or "manually added" (see <em>Source</em>)</p></li>
<li><p><code>prevalence</code><br> Prevalence of the microorganism according to Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
), see <code><a href="mo_matching_score.html">mo_matching_score()</a></code> for the full explanation</p></li>
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of 1 July, 2021 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>

6
reference/mo_matching_score.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -186,7 +186,7 @@
</ul><p>Furthermore,</p><ul><li><p>Any genus present in the <strong>established</strong> list also has <code>prevalence = 1.0</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any other genus present in the <strong>putative</strong> list has <code>prevalence = 1.25</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any other species or subspecies of which the genus is present in the two aforementioned groups, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set;</p></li>
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Pediculus</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em> or <em>Wuchereria</em>;</p></li>
<li><p>Any <em>non-bacterial</em> genus, species or subspecies of which the genus is present in the following list, has <code>prevalence = 1.5</code> in the <a href="microorganisms.html">microorganisms</a> data set: <em>Absidia</em>, <em>Acanthamoeba</em>, <em>Acremonium</em>, <em>Aedes</em>, <em>Alternaria</em>, <em>Amoeba</em>, <em>Ancylostoma</em>, <em>Angiostrongylus</em>, <em>Anisakis</em>, <em>Anopheles</em>, <em>Apophysomyces</em>, <em>Aspergillus</em>, <em>Aureobasidium</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Blastomyces</em>, <em>Candida</em>, <em>Capillaria</em>, <em>Chaetomium</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Contracaecum</em>, <em>Cordylobia</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Demodex</em>, <em>Dermatobia</em>, <em>Dientamoeba</em>, <em>Diphyllobothrium</em>, <em>Dirofilaria</em>, <em>Echinostoma</em>, <em>Entamoeba</em>, <em>Enterobius</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Fasciola</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Giardia</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Hendersonula</em>, <em>Heterophyes</em>, <em>Histomonas</em>, <em>Histoplasma</em>, <em>Hymenolepis</em>, <em>Hypomyces</em>, <em>Hysterothylacium</em>, <em>Leishmania</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Metagonimus</em>, <em>Meyerozyma</em>, <em>Microsporidium</em>, <em>Microsporum</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Necator</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oesophagostomum</em>, <em>Oidiodendron</em>, <em>Opisthorchis</em>, <em>Pediculus</em>, <em>Phlebotomus</em>, <em>Phoma</em>, <em>Pichia</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Pneumocystis</em>, <em>Pseudallescheria</em>, <em>Pseudoterranova</em>, <em>Pulex</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Saccharomyces</em>, <em>Sarcoptes</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Spirometra</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Strongyloides</em>, <em>Syngamus</em>, <em>Taenia</em>, <em>Toxocara</em>, <em>Trichinella</em>, <em>Trichobilharzia</em>, <em>Trichoderma</em>, <em>Trichomonas</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Trichostrongylus</em>, <em>Trichuris</em>, <em>Tritirachium</em>, <em>Trombicula</em>, <em>Trypanosoma</em>, <em>Tunga</em>, or <em>Wuchereria</em>;</p></li>
<li><p>All other records have <code>prevalence = 2.0</code> in the <a href="microorganisms.html">microorganisms</a> data set.</p></li>
</ul><p>When calculating the matching score, all characters in \(x\) and \(n\) are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.</p>
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.159\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
@@ -228,7 +228,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> Enterobacter cancerogenus (0.540), Ezakiella coagulans (0.484),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Effusibacillus consociatus (0.462), Enterococcus crotali (0.433),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Erwinia coffeiphila (0.404), Eubacterium coprostanoligenes (0.402),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Enterococcus columbae (0.397), Enterococcus camelliae (0.394) and</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Enterococcus columbae (0.397), Enterococcus camelliae (0.394), and</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Eubacterium cellulosolvens (0.385) [showing first 25]</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>

37
reference/mo_property.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -389,7 +389,7 @@
<dt>keep_synonyms</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the option <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
<dt>...</dt>
@@ -405,7 +405,7 @@
<dt>property</dt>
<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed", or must be <code>"shortname"</code></p></dd>
<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be <code>"shortname"</code></p></dd>
</dl></div>
<div class="section level2">
@@ -433,7 +433,7 @@
<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be 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_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antibiotics).</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>
<p>SNOMED codes (<code>mo_snomed()</code>) are from the version of 1 July, 2021. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code>, the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code> (which will have the scientific reference as <a href="https://rdrr.io/r/base/names.html" class="external-link">name</a>), the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
<p>All output <a href="translate.html">will be translated</a> where possible.</p>
</div>
<div class="section level2">
@@ -527,18 +527,19 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># scientific reference -----------------------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_ref</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Trevisan, 1887"</span>
<span class="r-in"><span><span class="fu">mo_authors</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Trevisan"</span>
<span class="r-in"><span><span class="fu">mo_year</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1887</span>
<span class="r-in"><span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "777151"</span>
<span class="r-in"><span><span class="fu">mo_gbif</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "3221874"</span>
<span class="r-in"><span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> NULL</span>
<span class="r-in"><span><span class="fu">mo_ref</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Tindall et al., 2017"</span>
<span class="r-in"><span><span class="fu">mo_authors</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Tindall et al."</span>
<span class="r-in"><span><span class="fu">mo_year</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2017</span>
<span class="r-in"><span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "777146"</span>
<span class="r-in"><span><span class="fu">mo_gbif</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "9281703"</span>
<span class="r-in"><span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Hormaeche et al., 1960 Bascomb et al., 1971 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "Enterobacter aerogenes" "Klebsiella mobilis" </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># abbreviations known in the field -----------------------------------------</span></span></span>
@@ -554,8 +555,10 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Escherichia"</span>
<span class="r-in"><span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"EIEC"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "coli"</span>
<span class="r-in"><span><span class="fu">mo_name</span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Escherichia coli"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># known subspecies ---------------------------------------------------------</span></span></span>

6
reference/mo_source.html
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@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -166,13 +166,13 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<dt>destination</dt>
<dd><p>destination of the compressed data file, default to the user's home directory.</p></dd>
<dd><p>destination of the compressed data file - the default is the user's home directory.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></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" class="external-link">data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href="microorganisms.html">microorganisms$mo</a></code> or <code><a href="microorganisms.html">microorganisms$fullname</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 with the option <code><a href="AMR-options.html">AMR_mo_source</a></code>, e.g. <code>options(AMR_mo_source = "my/location/file.rds")</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" class="external-link">data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href="microorganisms.html">microorganisms$mo</a></code> or <code><a href="microorganisms.html">microorganisms$fullname</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 with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_mo_source</a></code>, e.g. <code>options(AMR_mo_source = "my/location/file.rds")</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 <a href="https://rdrr.io/r/base/attributes.html" class="external-link">attribute</a> 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" class="external-link">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>

6
reference/pca.html
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@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -265,8 +265,8 @@
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "TOB". Total observations available: 7.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "TMP", and "TOB". Total observations available: 7.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Groups (n=4, named as 'order'):</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>

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8
reference/plot.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -254,7 +254,7 @@
<dt>guideline</dt>
<dd><p>interpretation guideline to use, defaults to the latest included EUCAST guideline, see <em>Details</em></p></dd>
<dd><p>interpretation guideline to use - the default is the latest included EUCAST guideline, see <em>Details</em></p></dd>
<dt>main, title</dt>
@@ -270,7 +270,7 @@
<dt>language</dt>
<dd><p>language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the option <code><a href="AMR-options.html">AMR_locale</a></code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>expand</dt>
@@ -293,7 +293,7 @@
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</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: "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014" and "CLSI 2013".</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: "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", and "CLSI 2013".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
</div>

10
reference/proportion.html
View File

@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -227,7 +227,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt>side</dt>
<dd><p>the side of the confidence interval to return. Defaults to <code>"both"</code> for a length 2 vector, but can also be (abbreviated as) <code>"min"</code>/<code>"left"</code>/<code>"lower"</code>/<code>"less"</code> or <code>"max"</code>/<code>"right"</code>/<code>"higher"</code>/<code>"greater"</code>.</p></dd>
<dd><p>the side of the confidence interval to return. The default is <code>"both"</code> for a length 2 vector, but can also be (abbreviated as) <code>"min"</code>/<code>"left"</code>/<code>"lower"</code>/<code>"less"</code> or <code>"max"</code>/<code>"right"</code>/<code>"higher"</code>/<code>"greater"</code>.</p></dd>
<dt>data</dt>
@@ -239,11 +239,11 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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), defaults to <code>TRUE</code></p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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) - the default is <code>TRUE</code></p></dd>
</dl></div>
<div class="section level2">
@@ -407,7 +407,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `KAN = (function (..., minimum = 30, as_percent = FALSE,</span>

37
reference/random.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -193,43 +193,44 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.001 0.01 0.5 0.005 16 0.01 0.125 2 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 8 0.5 0.01 64 128 256 128 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 256 0.005 0.125 1 &lt;=0.001 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.002 0.001 0.5 0.5 0.01 8 0.0625 0.125 0.025 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 16 0.25 0.0625 0.025 0.01 &gt;=128 4 64 &gt;=128 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4 0.005 &gt;=128 0.0625 0.5 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 49 14 6 19 16 27 29 24 37 47 22 42 45 48 38 50 50 44 29 42 9 34 48 42 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 50 29 8 33 45 24 41 40 50 48 33 41 8 8 46 26 48 11 13 17 8 26 29 15</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R S S R I S I R R R S I R S R I S S R R S I I S R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I S R S I R S R S I S R S S S I I R I S S S I S S</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001 8 0.001 0.025 0.5 16 0.5 0.005 1 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.0625 16 0.025 0.5 0.5 64 0.125 0.25 0.001 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.025 32 2 2 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.001 &lt;=0.001 0.005 0.005 0.5 0.002 0.125 16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 4 8 16 64 0.0625 4 64 64 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.002 8 1 0.0625 0.0625 2 1 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 &gt;=32 &gt;=32 8 16 4 1 &lt;=0.5 &gt;=32 1 1 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 8 2 &lt;=0.5 8 8 16 4 16 2 &gt;=32 16 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 16 &lt;=0.5 4 32 4 4 16 16 &lt;=0.5 32 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 8 16 32 &lt;=0.5 &lt;=0.5 64 16 8 &lt;=0.5 1 4 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 64 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5 4 0.125 2 1 0.0625 0.0625 8 0.5 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.0625 0.125 0.025 4 8 1 4 0.0625 0.0625 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.025 0.025 2 8 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 4 4 2 1 2 0.25 &lt;=0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 4 1 0.125 1 0.125 4 0.125 &lt;=0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 0.125 2 0.125 &gt;=8 4 2 0.5 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] &gt;=8 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 48 32 50 49 47 30 38 18 49 32 25 47 11 48 17 38 12 42 50 43 45 46 43 48 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 48 8 8 30 49 17 48 32 32 43 43 28 21 43 27 42 46 22 49 41 30 33 45 36 18</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 15 13 16 12 17 17 14 15 12 12 14 17 13 17 11 12 15 14 11 17 17 15 15 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 16 12 12 11 15 16 16 13 14 13 12 16 17 12 17 11 14 11 17 14 12 11 14 11</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 26 20 22 24 25 19 19 20 21 21 16 19 24 22 23 17 18 25 26 22 17 15 19 19 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 17 20 17 26 27 26 19 18 21 24 19 19 27 23 17 17 21 24 16 18 21 18 26 19</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

6
reference/resistance_predict.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -208,7 +208,7 @@
<dt>col_date</dt>
<dd><p>column name of the date, will be used to calculate years if this column doesn't consist of years already, defaults to the first column of with a date class</p></dd>
<dd><p>column name of the date, will be used to calculate years if this column doesn't consist of years already - the default is the first column of with a date class</p></dd>
<dt>year_min</dt>
@@ -216,7 +216,7 @@
<dt>year_max</dt>
<dd><p>highest year to use in the prediction model, defaults to 10 years after today</p></dd>
<dd><p>highest year to use in the prediction model - the default is 10 years after today</p></dd>
<dt>year_every</dt>

4
reference/skewness.html
View File

@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001867225</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01904674</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

17
reference/translate.html
View File

@@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -160,7 +160,7 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>language</dt>
<dd><p>language to choose. Use one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk).</p></dd>
<dd><p>language to choose. Use one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk).</p></dd>
<dt>x</dt>
@@ -169,8 +169,8 @@
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The currently 20 supported languages are English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) and Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.</p>
<p>To permanently silence the once-per-session language note on a non-English operating system, you can set the option <code><a href="AMR-options.html">AMR_locale</a></code> in your <code>.Rprofile</code> file like this:</p>
<p>The currently 20 supported languages are English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), and Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.</p>
<p>To permanently silence the once-per-session language note on a non-English operating system, you can set the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code> in your <code>.Rprofile</code> file like this:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Open .Rprofile file</span></span>
<span><span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span>
<span></span>
@@ -181,10 +181,10 @@
<h3 id="changing-the-default-language">Changing the Default Language<a class="anchor" aria-label="anchor" href="#changing-the-default-language"></a></h3>
<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale("LC_COLLATE")</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the option <code><a href="AMR-options.html">AMR_locale</a></code>, either by using e.g. <code>set_AMR_locale("German")</code> or by running e.g. <code>options(AMR_locale = "German")</code>.</p>
<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale("LC_COLLATE")</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>, either by using e.g. <code>set_AMR_locale("German")</code> or by running e.g. <code>options(AMR_locale = "German")</code>.</p>
<p>Note that setting an <span style="R">R</span> option only works in the same session. Save the command <code>options(AMR_locale = "(your language)")</code> to your <code>.Rprofile</code> file to apply it for every session. Run <code>utils::file.edit("~/.Rprofile")</code> to edit your <code>.Rprofile</code> file.</p></li>
<li><p>Setting the system variable <code>LANGUAGE</code> or <code>LANG</code>, e.g. by adding <code>LANGUAGE="de_DE.utf8"</code> to your <code>.Renviron</code> file in your home directory.</p></li>
</ol><p>Thus, if the option <code><a href="AMR-options.html">AMR_locale</a></code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p>
</ol><p>Thus, if the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p>
</div>
</div>
@@ -229,7 +229,10 @@
<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"de"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using German (Deutsch) for the AMR package for this session.</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"amox/clav"</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>More than one result was found for item 1: amoxicillin and clavulansäure</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "here"</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ More than one result was found for item 1: amoxicillin and clavulansäure</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Amoxicillin/Clavulansäure"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># reset to system default</span></span></span>