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(v1.8.0.9001) as.mo improvement, fixes #52

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dr. M.S. (Matthijs) Berends
2022-02-26 21:58:23 +01:00
parent be792cc9eb
commit 18e8525d10
108 changed files with 568 additions and 399 deletions
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7
docs/reference/AMR-deprecated.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,13 +161,12 @@
<p>These functions are so-called '<a href="https://rdrr.io/r/base/Deprecated.html" class="external-link">Deprecated</a>'. <strong>They will be removed in a future release.</strong> Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
</div>
<div id="ref-usage">Usage,NULL</div>
<div id="retired-lifecycle">
<h2>Retired Lifecycle</h2>
<p><img src="figures/lifecycle_retired.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_retired.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
</div>
<div id="read-more-on-our-website-">
@ -189,7 +188,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

7
docs/reference/WHOCC.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,13 +161,12 @@
<p>All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.</p>
</div>
<div id="ref-usage">Usage,NULL</div>
<div id="whocc">
<h2>WHOCC</h2>
<p><img src="figures/logo_who.png" height="60px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_who.png" height="60" style='margin-bottom:"5"'><br>
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link">https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
@ -200,7 +199,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/ab_from_text.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Use this function on e.g. clinical texts from health care records. It returns a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> with all antimicrobial drugs, doses and forms of administration found in the texts.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ab_from_text</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ab_from_text</span><span class="op">(</span>
<span class="va">text</span>,
type <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">"drug"</span>, <span class="st">"dose"</span>, <span class="st">"administration"</span><span class="op">)</span>,
collapse <span class="op">=</span> <span class="cn">NULL</span>,
@ -169,7 +170,8 @@
thorough_search <span class="op">=</span> <span class="cn">NULL</span>,
info <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 class="va">...</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -217,7 +219,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -277,7 +279,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

13
docs/reference/ab_property.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Use these functions to return a specific property of an antibiotic from the <a href="antibiotics.html">antibiotics</a> data set. All input values will be evaluated internally with <code><a href="as.ab.html">as.ab()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ab_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, tolower <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ab_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, tolower <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_cid</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span>
@ -195,7 +196,8 @@
property <span class="op">=</span> <span class="st">"name"</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
snake_case <span class="op">=</span> <span class="cn">NULL</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -238,7 +240,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -247,7 +249,6 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">https://www.whocc.no/atc_ddd_index/</a></p>
<p>WHONET 2019 software: <a href="http://www.whonet.org/software.html" class="external-link">http://www.whonet.org/software.html</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div id="reference-data-publicly-available">
@ -347,7 +348,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/age.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>Calculates age in years based on a reference date, which is the sytem date at default.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">age</span><span class="op">(</span><span class="va">x</span>, reference <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>, exact <span class="op">=</span> <span class="cn">FALSE</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">age</span><span class="op">(</span><span class="va">x</span>, reference <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>, exact <span class="op">=</span> <span class="cn">FALSE</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -189,7 +191,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -228,7 +230,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/age_groups.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>Split ages into age groups defined by the <code>split</code> argument. This allows for easier demographic (antimicrobial resistance) analysis.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">age_groups</span><span class="op">(</span><span class="va">x</span>, split_at <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">12</span>, <span class="fl">25</span>, <span class="fl">55</span>, <span class="fl">75</span><span class="op">)</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">age_groups</span><span class="op">(</span><span class="va">x</span>, split_at <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">12</span>, <span class="fl">25</span>, <span class="fl">55</span>, <span class="fl">75</span><span class="op">)</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -190,7 +192,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -252,7 +254,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/antibiotic_class_selectors.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by <code>cephalosporins()</code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ab_class</span><span class="op">(</span><span class="va">ab_class</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ab_class</span><span class="op">(</span><span class="va">ab_class</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_selector</span><span class="op">(</span><span class="va">filter</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span>
@ -224,7 +225,8 @@
col_mo <span class="op">=</span> <span class="cn">NULL</span>,
version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -290,7 +292,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -432,7 +434,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

13
docs/reference/antibiotics.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,9 +161,11 @@
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href="as.ab.html">as.ab()</a></code> or one of the <code><a href="ab_property.html">ab_*</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">antibiotics</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">antibiotics</span>
<span class="va">antivirals</span></code></pre></div></div>
<span class="va">antivirals</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -206,7 +208,6 @@
<div id="source">
<h2>Source</h2>
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">https://www.whocc.no/atc_ddd_index/</a></p>
<p>WHONET 2019 software: <a href="http://www.whonet.org/software.html" class="external-link">http://www.whonet.org/software.html</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div id="details">
@ -233,7 +234,7 @@
<h2>WHOCC</h2>
<p><img src="figures/logo_who.png" height="60px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_who.png" height="60" style='margin-bottom:"5"'><br>
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link">https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
@ -262,7 +263,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

15
docs/reference/as.ab.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,9 +161,11 @@
<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href="antibiotics.html">antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.ab</span><span class="op">(</span><span class="va">x</span>, flag_multiple_results <span class="op">=</span> <span class="cn">TRUE</span>, info <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 class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.ab</span><span class="op">(</span><span class="va">x</span>, flag_multiple_results <span class="op">=</span> <span class="cn">TRUE</span>, info <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 class="va">...</span><span class="op">)</span>
<span class="fu">is.ab</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div></div>
<span class="fu">is.ab</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -195,14 +197,13 @@
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">https://www.whocc.no/atc_ddd_index/</a></p>
<p>WHONET 2019 software: <a href="http://www.whonet.org/software.html" class="external-link">http://www.whonet.org/software.html</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -210,7 +211,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<h2>WHOCC</h2>
<p><img src="figures/logo_who.png" height="60px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_who.png" height="60" style='margin-bottom:"5"'><br>
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link">https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
@ -283,7 +284,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/as.disk.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,11 +161,13 @@
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.disk</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.disk</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="va">NA_disk_</span>
<span class="fu">is.disk</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div></div>
<span class="fu">is.disk</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -191,7 +193,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -241,7 +243,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/as.mic.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,11 +161,13 @@
<p>This transforms vectors to a new class <code>mic</code>, which treats the input as decimal numbers, while maintaining operators (such as "&gt;=") and only allowing valid MIC values known to the field of (medical) microbiology.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.mic</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.mic</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="va">NA_mic_</span>
<span class="fu">is.mic</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div></div>
<span class="fu">is.mic</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -220,7 +222,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -275,7 +277,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

21
docs/reference/as.mo.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Use this function to determine a valid microorganism code (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.mo</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.mo</span><span class="op">(</span>
<span class="va">x</span>,
Becker <span class="op">=</span> <span class="cn">FALSE</span>,
Lancefield <span class="op">=</span> <span class="cn">FALSE</span>,
@ -179,7 +180,8 @@
<span class="fu">mo_uncertainties</span><span class="op">(</span><span class="op">)</span>
<span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></code></pre></div></div>
<span class="fu">mo_renamed</span><span class="op">(</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -189,8 +191,8 @@
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker <em>et al.</em> (1,2,3).</p>
<p>This excludes <em>Staphylococcus aureus</em> at default, use <code>Becker = "all"</code> to also categorise <em>S. aureus</em> as "CoPS".</p></dd>
<dt>Lancefield</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether beta-haemolytic <em>Streptococci</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These <em>Streptococci</em> will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
<p>This excludes <em>Enterococci</em> at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all <em>Enterococci</em> as group D.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a beta-haemolytic <em>Streptococcus</em> should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These streptococci will be categorised in their first group, e.g. <em>Streptococcus dysgalactiae</em> will be group C, although officially it was also categorised into groups G and L.</p>
<p>This excludes enterococci at default (who are in group D), use <code>Lancefield = "all"</code> to also categorise all enterococci as group D.</p></dd>
<dt>allow_uncertain</dt>
<dd><p>a number between <code>0</code> (or <code>"none"</code>) and <code>3</code> (or <code>"all"</code>), or <code>TRUE</code> (= <code>2</code>) or <code>FALSE</code> (= <code>0</code>) to indicate whether the input should be checked for less probable results, see <em>Details</em></p></dd>
<dt>reference_df</dt>
@ -279,7 +281,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -288,7 +290,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<p>With ambiguous user input in <code>as.mo()</code> and all the <code><a href="mo_property.html">mo_*</a></code> functions, the returned results are chosen based on their matching score using <code><a href="mo_matching_score.html">mo_matching_score()</a></code>. This matching score \(m\), is calculated as:</p>
<p><img src="figures/mo_matching_score.png" width="300px" alt="mo matching score"></p>
<p><img src="figures/mo_matching_score.png" width="300" alt="mo matching score"></p>
<p>where:</p><ul><li><p><i>x</i> is the user input;</p></li>
<li><p><i>n</i> is a taxonomic name (genus, species, and subspecies);</p></li>
<li><p><i>l<sub>n</sub></i> is the length of <i>n</i>;</p></li>
@ -298,12 +300,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
<p>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> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<p>Since <code>AMR</code> version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.</p>
</div>
<div id="catalogue-of-life">
<h2>Catalogue of Life</h2>
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
@ -378,7 +381,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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12
docs/reference/as.rsi.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with levels <code>S &lt; I &lt; R</code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.rsi</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">as.rsi</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span>
<span class="va">NA_rsi_</span>
@ -204,7 +205,8 @@
conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</span>,
add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,
reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="rsi_translation.html">rsi_translation</a></span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -305,7 +307,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -425,7 +427,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/atc_online.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">atc_online_property</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">atc_online_property</span><span class="op">(</span>
<span class="va">atc_code</span>,
<span class="va">property</span>,
administration <span class="op">=</span> <span class="st">"O"</span>,
@ -173,7 +174,8 @@
<span class="fu">atc_online_ddd</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">atc_online_ddd_units</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu">atc_online_ddd_units</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -220,7 +222,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -259,7 +261,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/availability.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. <code><a href="proportion.html">susceptibility()</a></code> and <code><a href="proportion.html">resistance()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">availability</span><span class="op">(</span><span class="va">tbl</span>, width <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">availability</span><span class="op">(</span><span class="va">tbl</span>, width <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -182,7 +184,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -218,7 +220,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/bug_drug_combinations.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code> on the result to prettify it to a publishable/printable format, see <em>Examples</em>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, FUN <span class="op">=</span> <span class="va">mo_shortname</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, FUN <span class="op">=</span> <span class="va">mo_shortname</span>, <span class="va">...</span><span class="op">)</span>
<span class="co"># S3 method for bug_drug_combinations</span>
<span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span>
@ -176,7 +177,8 @@
decimal.mark <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">"OutDec"</span><span class="op">)</span>,
big.mark <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">decimal.mark</span> <span class="op">==</span> <span class="st">","</span>, <span class="st">"."</span>, <span class="st">","</span><span class="op">)</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -226,7 +228,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -267,7 +269,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

7
docs/reference/catalogue_of_life.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,13 +161,12 @@
<p>This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).</p>
</div>
<div id="ref-usage">Usage,NULL</div>
<div id="catalogue-of-life">
<h2>Catalogue of Life</h2>
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p>Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
@ -240,7 +239,7 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/catalogue_of_life_version.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>This function returns information about the included data from the Catalogue of Life.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">catalogue_of_life_version</span><span class="op">(</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">catalogue_of_life_version</span><span class="op">(</span><span class="op">)</span></code></pre></div>
</div>
<div id="value">
<h2>Value</h2>
@ -175,7 +177,7 @@
<h2>Catalogue of Life</h2>
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code>catalogue_of_life_version()</code>.</p>
</div>
@ -202,7 +204,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/count.html
View File

@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -163,7 +163,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">count_resistant</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">count_resistant</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="fu">count_susceptible</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
@ -187,7 +188,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
combine_IR <span class="op">=</span> <span class="cn">FALSE</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -221,7 +223,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -360,7 +362,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/custom_eucast_rules.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in <code><a href="eucast_rules.html">eucast_rules()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">custom_eucast_rules</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">custom_eucast_rules</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -265,7 +267,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -303,7 +305,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/eucast_rules.html
View File

@ -18,7 +18,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -163,7 +163,8 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see <em>Details</em>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">eucast_rules</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">eucast_rules</span><span class="op">(</span>
<span class="va">x</span>,
col_mo <span class="op">=</span> <span class="cn">NULL</span>,
info <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>,
@ -177,7 +178,8 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<span class="va">...</span>
<span class="op">)</span>
<span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">11</span><span class="op">)</span></code></pre></div></div>
<span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">11</span><span class="op">)</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -261,7 +263,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -336,7 +338,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/first_isolate.html
View File

@ -18,7 +18,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -163,7 +163,8 @@
). To determine patient episodes not necessarily based on microorganisms, use <code><a href="get_episode.html">is_new_episode()</a></code> that also supports grouping with the <code>dplyr</code> package.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">first_isolate</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">first_isolate</span><span class="op">(</span>
x <span class="op">=</span> <span class="cn">NULL</span>,
col_date <span class="op">=</span> <span class="cn">NULL</span>,
col_patient_id <span class="op">=</span> <span class="cn">NULL</span>,
@ -194,7 +195,8 @@
episode_days <span class="op">=</span> <span class="fl">365</span>,
method <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">"phenotype-based"</span>, <span class="st">"episode-based"</span>, <span class="st">"patient-based"</span>, <span class="st">"isolate-based"</span><span class="op">)</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -302,7 +304,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -373,7 +375,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/g.test.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p><code>g.test()</code> performs chi-squared contingency table tests and goodness-of-fit tests, just like <code><a href="https://rdrr.io/r/stats/chisq.test.html" class="external-link">chisq.test()</a></code> but is more reliable (1). A <em>G</em>-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a <strong><em>G</em>-test of goodness-of-fit</strong>), or to see whether the proportions of one variable are different for different values of the other variable (called a <strong><em>G</em>-test of independence</strong>).</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">g.test</span><span class="op">(</span><span class="va">x</span>, y <span class="op">=</span> <span class="cn">NULL</span>, p <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span><span class="op">/</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, rescale.p <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">g.test</span><span class="op">(</span><span class="va">x</span>, y <span class="op">=</span> <span class="cn">NULL</span>, p <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span><span class="op">/</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, rescale.p <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -258,7 +260,7 @@
<h2>Questioning Lifecycle</h2>
<p><img src="figures/lifecycle_questioning.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_questioning.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
</div>
<div id="read-more-on-our-website-">
@ -325,7 +327,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>questioni
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/get_episode.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,9 +161,11 @@
<p>These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis. The <code>get_episode()</code> function returns the index number of the episode per group, while the <code>is_new_episode()</code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span>, <span class="va">episode_days</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span>, <span class="va">episode_days</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">is_new_episode</span><span class="op">(</span><span class="va">x</span>, <span class="va">episode_days</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu">is_new_episode</span><span class="op">(</span><span class="va">x</span>, <span class="va">episode_days</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -189,7 +191,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -280,7 +282,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/ggplot_pca.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Produces a <code>ggplot2</code> variant of a so-called <a href="https://en.wikipedia.org/wiki/Biplot" class="external-link">biplot</a> for PCA (principal component analysis), but is more flexible and more appealing than the base <span style="R">R</span> <code><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot()</a></code> function.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ggplot_pca</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ggplot_pca</span><span class="op">(</span>
<span class="va">x</span>,
choices <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>,
scale <span class="op">=</span> <span class="fl">1</span>,
@ -184,7 +185,8 @@
arrows_alpha <span class="op">=</span> <span class="fl">0.75</span>,
base_textsize <span class="op">=</span> <span class="fl">10</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -260,7 +262,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -306,7 +308,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/ggplot_rsi.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Use these functions to create bar plots for AMR data analysis. All functions rely on <a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot2</a> functions.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ggplot_rsi</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ggplot_rsi</span><span class="op">(</span>
<span class="va">data</span>,
position <span class="op">=</span> <span class="cn">NULL</span>,
x <span class="op">=</span> <span class="st">"antibiotic"</span>,
@ -218,7 +219,8 @@
combine_IR <span class="op">=</span> <span class="cn">FALSE</span>,
datalabels.size <span class="op">=</span> <span class="fl">3</span>,
datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -291,7 +293,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -397,7 +399,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/guess_ab_col.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,12 +161,14 @@
<p>This tries to find a column name in a data set based on information from the <a href="antibiotics.html">antibiotics</a> data set. Also supports WHONET abbreviations.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">guess_ab_col</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">guess_ab_col</span><span class="op">(</span>
x <span class="op">=</span> <span class="cn">NULL</span>,
search_string <span class="op">=</span> <span class="cn">NULL</span>,
verbose <span class="op">=</span> <span class="cn">FALSE</span>,
only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -191,7 +193,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -245,7 +247,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

4
docs/reference/index.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -416,7 +416,7 @@
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/italicise_taxonomy.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,9 +161,11 @@
<p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">italicise_taxonomy</span><span class="op">(</span><span class="va">string</span>, type <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">"markdown"</span>, <span class="st">"ansi"</span><span class="op">)</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">italicise_taxonomy</span><span class="op">(</span><span class="va">string</span>, type <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">"markdown"</span>, <span class="st">"ansi"</span><span class="op">)</span><span class="op">)</span>
<span class="fu">italicize_taxonomy</span><span class="op">(</span><span class="va">string</span>, type <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">"markdown"</span>, <span class="st">"ansi"</span><span class="op">)</span><span class="op">)</span></code></pre></div></div>
<span class="fu">italicize_taxonomy</span><span class="op">(</span><span class="va">string</span>, type <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">"markdown"</span>, <span class="st">"ansi"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -182,7 +184,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -223,7 +225,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/join.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Join the data set <a href="microorganisms.html">microorganisms</a> easily to an existing data set or to a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">inner_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, suffix <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">"2"</span>, <span class="st">""</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">inner_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, suffix <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">"2"</span>, <span class="st">""</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, suffix <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">"2"</span>, <span class="st">""</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
@ -171,7 +172,8 @@
<span class="fu">semi_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">anti_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu">anti_join_microorganisms</span><span class="op">(</span><span class="va">x</span>, by <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -197,7 +199,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -244,7 +246,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/key_antimicrobials.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see <code><a href="first_isolate.html">first_isolate()</a></code>). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">key_antimicrobials</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">key_antimicrobials</span><span class="op">(</span>
x <span class="op">=</span> <span class="cn">NULL</span>,
col_mo <span class="op">=</span> <span class="cn">NULL</span>,
universal <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">"ampicillin"</span>, <span class="st">"amoxicillin/clavulanic acid"</span>, <span class="st">"cefuroxime"</span>,
@ -185,7 +186,8 @@
ignore_I <span class="op">=</span> <span class="cn">TRUE</span>,
points_threshold <span class="op">=</span> <span class="fl">2</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -248,7 +250,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -310,7 +312,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/kurtosis.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">kurtosis</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, excess <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">kurtosis</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, excess <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="co"># S3 method for default</span>
<span class="fu">kurtosis</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, excess <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
@ -170,7 +171,8 @@
<span class="fu">kurtosis</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, excess <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="co"># S3 method for data.frame</span>
<span class="fu">kurtosis</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, excess <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div></div>
<span class="fu">kurtosis</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span>, excess <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -185,7 +187,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -212,7 +214,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

17
docs/reference/lifecycle.html
View File

@ -19,7 +19,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,31 +161,30 @@ This page contains a section for every lifecycle (with text borrowed from the af
<div class="ref-description">
<p>Functions in this <code>AMR</code> package are categorised using <a href="https://lifecycle.r-lib.org/articles/stages.html" class="external-link">the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle</a>.</p>
<p><img src="figures/lifecycle_tidyverse.svg" height="200px" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_tidyverse.svg" height="200" style='margin-bottom:"5"'><br>
This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions.</p>
</div>
<div id="ref-usage">Usage,NULL</div>
<div id="experimental-lifecycle">
<h2>Experimental Lifecycle</h2>
<p><img src="figures/lifecycle_experimental.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_experimental.svg" style='margin-bottom:"5"'><br>
The lifecycle of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
</div>
<div id="maturing-lifecycle">
<h2>Maturing Lifecycle</h2>
<p><img src="figures/lifecycle_maturing.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_maturing.svg" style='margin-bottom:"5"'><br>
The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href="https://github.com/msberends/AMR/issues" class="external-link">to suggest changes at our repository</a> or <a href="AMR.html">write us an email (see section 'Contact Us')</a>.</p>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The lifecycle of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -193,14 +192,14 @@ The lifecycle of this function is <strong>stable</strong>. In a stable function,
<h2>Retired Lifecycle</h2>
<p><img src="figures/lifecycle_retired.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_retired.svg" style='margin-bottom:"5"'><br>
The lifecycle of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
</div>
<div id="questioning-lifecycle">
<h2>Questioning Lifecycle</h2>
<p><img src="figures/lifecycle_questioning.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_questioning.svg" style='margin-bottom:"5"'><br>
The lifecycle of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
</div>
@ -216,7 +215,7 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/like.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Convenient wrapper around <code><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl()</a></code> to match a pattern: <code>x %like% pattern</code>. It always returns a <code><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a></code> vector and is always case-insensitive (use <code>x %like_case% pattern</code> for case-sensitive matching). Also, <code>pattern</code> can be as long as <code>x</code> to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">like</span><span class="op">(</span><span class="va">x</span>, <span class="va">pattern</span>, ignore.case <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">like</span><span class="op">(</span><span class="va">x</span>, <span class="va">pattern</span>, ignore.case <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
<span class="va">x</span> <span class="op">%like%</span> <span class="va">pattern</span>
@ -169,7 +170,8 @@
<span class="va">x</span> <span class="op">%like_case%</span> <span class="va">pattern</span>
<span class="va">x</span> <span class="op">%unlike_case%</span> <span class="va">pattern</span></code></pre></div></div>
<span class="va">x</span> <span class="op">%unlike_case%</span> <span class="va">pattern</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -200,7 +202,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -262,7 +264,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/mdro.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mdro</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mdro</span><span class="op">(</span>
x <span class="op">=</span> <span class="cn">NULL</span>,
guideline <span class="op">=</span> <span class="st">"CMI2012"</span>,
col_mo <span class="op">=</span> <span class="cn">NULL</span>,
@ -183,7 +184,8 @@
<span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -287,7 +289,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -354,7 +356,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/microorganisms.codes.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href="mo_source.html">set_mo_source()</a></code>. They will all be searched when using <code><a href="as.mo.html">as.mo()</a></code> and consequently all the <code><a href="mo_property.html">mo_*</a></code> functions.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms.codes</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms.codes</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -178,7 +180,7 @@
<h2>Catalogue of Life</h2>
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
@ -205,7 +207,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
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10
docs/reference/microorganisms.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>A data set containing the full microbial taxonomy (<strong>last updated: 5 October 2021</strong>) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -223,7 +225,7 @@
<h2>Catalogue of Life</h2>
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
@ -256,7 +258,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/microorganisms.old.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href="as.mo.html">as.mo()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms.old</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms.old</span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
@ -179,7 +181,7 @@
<h2>Catalogue of Life</h2>
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
@ -212,7 +214,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

15
docs/reference/mo_matching_score.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>This algorithm is used by <code><a href="as.mo.html">as.mo()</a></code> and all the <code><a href="mo_property.html">mo_*</a></code> functions to determine the most probable match of taxonomic records based on user input.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_matching_score</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_matching_score</span><span class="op">(</span><span class="va">x</span>, <span class="va">n</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -175,7 +177,7 @@
<p>With ambiguous user input in <code><a href="as.mo.html">as.mo()</a></code> and all the <code><a href="mo_property.html">mo_*</a></code> functions, the returned results are chosen based on their matching score using <code>mo_matching_score()</code>. This matching score \(m\), is calculated as:</p>
<p><img src="figures/mo_matching_score.png" width="300px" alt="mo matching score"></p>
<p><img src="figures/mo_matching_score.png" width="300" alt="mo matching score"></p>
<p>where:</p><ul><li><p><i>x</i> is the user input;</p></li>
<li><p><i>n</i> is a taxonomic name (genus, species, and subspecies);</p></li>
<li><p><i>l<sub>n</sub></i> is the length of <i>n</i>;</p></li>
@ -185,12 +187,13 @@
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
<p>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> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<p>Since <code>AMR</code> version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.</p>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -208,7 +211,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div id="author">
<h2>Author</h2>
<p>Dr. Matthijs Berends</p>
<p>Dr Matthijs Berends</p>
</div>
<div id="ref-examples">
@ -232,7 +235,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

17
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View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with <code><a href="as.mo.html">as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. See <em>Examples</em>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
@ -217,7 +218,8 @@
<span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -260,7 +262,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -269,7 +271,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<p>With ambiguous user input in <code><a href="as.mo.html">as.mo()</a></code> and all the <code>mo_*</code> functions, the returned results are chosen based on their matching score using <code><a href="mo_matching_score.html">mo_matching_score()</a></code>. This matching score \(m\), is calculated as:</p>
<p><img src="figures/mo_matching_score.png" width="300px" alt="mo matching score"></p>
<p><img src="figures/mo_matching_score.png" width="300" alt="mo matching score"></p>
<p>where:</p><ul><li><p><i>x</i> is the user input;</p></li>
<li><p><i>n</i> is a taxonomic name (genus, species, and subspecies);</p></li>
<li><p><i>l<sub>n</sub></i> is the length of <i>n</i>;</p></li>
@ -279,12 +281,13 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</ul><p>The grouping into human pathogenic prevalence (\(p\)) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. <strong>Group 1</strong> (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is <em>Enterococcus</em>, <em>Staphylococcus</em> or <em>Streptococcus</em>. This group consequently contains all common Gram-negative bacteria, such as <em>Pseudomonas</em> and <em>Legionella</em> and all species within the order Enterobacterales. <strong>Group 2</strong> consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Absidia</em>, <em>Acremonium</em>, <em>Actinotignum</em>, <em>Alternaria</em>, <em>Anaerosalibacter</em>, <em>Apophysomyces</em>, <em>Arachnia</em>, <em>Aspergillus</em>, <em>Aureobacterium</em>, <em>Aureobasidium</em>, <em>Bacteroides</em>, <em>Basidiobolus</em>, <em>Beauveria</em>, <em>Blastocystis</em>, <em>Branhamella</em>, <em>Calymmatobacterium</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Catabacter</em>, <em>Chaetomium</em>, <em>Chryseobacterium</em>, <em>Chryseomonas</em>, <em>Chrysonilia</em>, <em>Cladophialophora</em>, <em>Cladosporium</em>, <em>Conidiobolus</em>, <em>Cryptococcus</em>, <em>Curvularia</em>, <em>Exophiala</em>, <em>Exserohilum</em>, <em>Flavobacterium</em>, <em>Fonsecaea</em>, <em>Fusarium</em>, <em>Fusobacterium</em>, <em>Hendersonula</em>, <em>Hypomyces</em>, <em>Koserella</em>, <em>Lelliottia</em>, <em>Leptosphaeria</em>, <em>Leptotrichia</em>, <em>Malassezia</em>, <em>Malbranchea</em>, <em>Mortierella</em>, <em>Mucor</em>, <em>Mycocentrospora</em>, <em>Mycoplasma</em>, <em>Nectria</em>, <em>Ochroconis</em>, <em>Oidiodendron</em>, <em>Phoma</em>, <em>Piedraia</em>, <em>Pithomyces</em>, <em>Pityrosporum</em>, <em>Prevotella</em>, <em>Pseudallescheria</em>, <em>Rhizomucor</em>, <em>Rhizopus</em>, <em>Rhodotorula</em>, <em>Scolecobasidium</em>, <em>Scopulariopsis</em>, <em>Scytalidium</em>, <em>Sporobolomyces</em>, <em>Stachybotrys</em>, <em>Stomatococcus</em>, <em>Treponema</em>, <em>Trichoderma</em>, <em>Trichophyton</em>, <em>Trichosporon</em>, <em>Tritirachium</em> or <em>Ureaplasma</em>. <strong>Group 3</strong> consists of all other microorganisms.</p>
<p>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> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<p>Since <code>AMR</code> version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.</p>
</div>
<div id="catalogue-of-life">
<h2>Catalogue of Life</h2>
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
@ -434,7 +437,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/mo_source.html
View File

@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -163,12 +163,14 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">set_mo_source</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">set_mo_source</span><span class="op">(</span>
<span class="va">path</span>,
destination <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">"AMR_mo_source"</span>, <span class="st">"~/mo_source.rds"</span><span class="op">)</span>
<span class="op">)</span>
<span class="fu">get_mo_source</span><span class="op">(</span>destination <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">"AMR_mo_source"</span>, <span class="st">"~/mo_source.rds"</span><span class="op">)</span><span class="op">)</span></code></pre></div></div>
<span class="fu">get_mo_source</span><span class="op">(</span>destination <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">"AMR_mo_source"</span>, <span class="st">"~/mo_source.rds"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -246,7 +248,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -269,7 +271,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/pca.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">pca</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">pca</span><span class="op">(</span>
<span class="va">x</span>,
<span class="va">...</span>,
retx <span class="op">=</span> <span class="cn">TRUE</span>,
@ -169,7 +170,8 @@
scale. <span class="op">=</span> <span class="cn">TRUE</span>,
tol <span class="op">=</span> <span class="cn">NULL</span>,
rank. <span class="op">=</span> <span class="cn">NULL</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -220,7 +222,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -268,7 +270,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/plot.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Functions to plot classes <code>rsi</code>, <code>mic</code> and <code>disk</code>, with support for base <span style="R">R</span> and <code>ggplot2</code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mic</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mic</span>
<span class="fu">plot</span><span class="op">(</span>
<span class="va">x</span>,
mo <span class="op">=</span> <span class="cn">NULL</span>,
@ -248,7 +249,8 @@
<span class="op">)</span>
<span class="co"># S3 method for rsi</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -288,7 +290,7 @@ The <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -334,7 +336,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/proportion.html
View File

@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -163,7 +163,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br></p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">resistance</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">resistance</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="fu">susceptibility</span><span class="op">(</span><span class="va">...</span>, minimum <span class="op">=</span> <span class="fl">30</span>, as_percent <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
@ -195,7 +196,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
as_percent <span class="op">=</span> <span class="cn">FALSE</span>,
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
combine_IR <span class="op">=</span> <span class="cn">FALSE</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="source">
<h2>Source</h2>
@ -267,7 +269,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -383,7 +385,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/random.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,11 +161,13 @@
<p>These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">random_mic</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">random_mic</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">random_disk</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">random_rsi</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, prob_RSI <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="fl">0.33</span>, <span class="fl">0.33</span>, <span class="fl">0.33</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu">random_rsi</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, prob_RSI <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="fl">0.33</span>, <span class="fl">0.33</span>, <span class="fl">0.33</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -193,7 +195,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -234,7 +236,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/resistance_predict.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,8 @@
<p>Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns <code>se_min</code> and <code>se_max</code>. See <em>Examples</em> for a real live example.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">resistance_predict</span><span class="op">(</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">resistance_predict</span><span class="op">(</span>
<span class="va">x</span>,
<span class="va">col_ab</span>,
col_date <span class="op">=</span> <span class="cn">NULL</span>,
@ -207,7 +208,8 @@
main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Resistance Prediction of"</span>, <span class="va">x_name</span><span class="op">)</span>,
ribbon <span class="op">=</span> <span class="cn">TRUE</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div></div>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -263,7 +265,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -360,7 +362,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

12
docs/reference/skewness.html
View File

@ -18,7 +18,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -163,7 +163,8 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<p>When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">skewness</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">skewness</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="co"># S3 method for default</span>
<span class="fu">skewness</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
@ -172,7 +173,8 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<span class="fu">skewness</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="co"># S3 method for data.frame</span>
<span class="fu">skewness</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div></div>
<span class="fu">skewness</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
@ -185,7 +187,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -212,7 +214,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

10
docs/reference/translate.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span>
</div>
@ -161,7 +161,9 @@
<p>For language-dependent output of AMR functions, like <code><a href="mo_property.html">mo_name()</a></code>, <code><a href="mo_property.html">mo_gramstain()</a></code>, <code><a href="mo_property.html">mo_type()</a></code> and <code><a href="ab_property.html">ab_name()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">get_AMR_locale</span><span class="op">(</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">get_AMR_locale</span><span class="op">(</span><span class="op">)</span></code></pre></div>
</div>
<div id="details">
<h2>Details</h2>
@ -181,7 +183,7 @@
<h2>Stable Lifecycle</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
@ -239,7 +241,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>