* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use LOINC code for input in any `ab_*` function:
* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2019 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows machine reading these guidelines**, which is currently almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
### Changes
* Bugfix for some WHONET microorganism codes that were not interpreted correctly when using `as.rsi()`
* Speed improvement for `as.mo()` (and consequently all `mo_*` functions that use `as.mo()` internally), especially for the *G. species* format (G for genus), like *E. coli* and *K penumoniae*
* Better support for determination of *Salmonella* biovars
* Input values for `as.disk()` limited to a maximum of 50 millimeters
#' @param guideline defaults to the latest included EUCAST guideline, run `unique(AMR::rsi_translation$guideline)` for all options
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
#' @param ... parameters passed on to methods
#' @details Run `unique(AMR::rsi_translation$guideline)` for a list of all supported guidelines.
#' @details Run `unique(AMR::rsi_translation$guideline)` for a list of all supported guidelines. The repository of this package contains [this machine readable version](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of these guidelines.
#'
#' These guidelines are machine readable, since [](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt).
#'
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">0.9.0.9013</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">0.9.0.9014</span>
</span>
</div>
@ -200,7 +200,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<ahref="#what-is-amr-for-r"class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
<p><em>(<helptitle="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <ahref="./articles/AMR.html">continue reading here to get started</a>.</em></p>
<p><code>AMR</code> is a free and open-source <ahref="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows <ahref="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <ahref="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code, and knows all about valid RSI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>After installing this package, R knows <ahref="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <ahref="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC and LOINC), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>We created this package for both routine data analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <ahref="./news">actively maintained</a> and is free software (see <ahref="#copyright">Copyright</a>).</p>
<divclass="main-content">
<p>
@ -238,7 +238,8 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<li>Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name) (<ahref="./reference/ab_property.html">manual</a>)</li>
<li>Get the LOINC code of an antibiotic, or get the name associated with a LOINC code (<ahref="./reference/ab_property.html">manual</a>)</li>
<li>Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code (<ahref="./reference/ab_property.html">manual</a>)</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2019 to translate MIC values and disk diffusion diameters to R/SI (<ahref="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
</ul>
<p>This package is ready-to-use for a professional environment by specialists in the following fields:</p>
<p>Medical Microbiology</p>
@ -330,7 +331,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<li>
<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
<ul>
<li>Use <code><ahref="reference/eucast_rules.html">eucast_rules()</a></code> to apply <ahref="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a> (not the translation from MIC to RSI values, use <code><ahref="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
<li>Use <code><ahref="reference/eucast_rules.html">eucast_rules()</a></code> to apply <ahref="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><ahref="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
<li>Use <code><ahref="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <ahref="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
<ul>
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><ahref="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use LOINC code for input in any <code>ab_*</code> function:</p>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><ahref="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
<li><p>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2019 to translate MIC and disk diffusion values to R/SI: <ahref="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt"class="uri">https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows machine reading these guidelines</strong>, which is currently almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p></li>
</ul>
</div>
<divid="changes"class="section level3">
<h3class="hasAnchor">
<ahref="#changes"class="anchor"></a>Changes</h3>
<ul>
<li>Bugfix for some WHONET microorganism codes that were not interpreted correctly when using <code><ahref="../reference/as.rsi.html">as.rsi()</a></code>
</li>
<li>Speed improvement for <code><ahref="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions that use <code><ahref="../reference/as.mo.html">as.mo()</a></code> internally), especially for the <em>G. species</em> format (G for genus), like <em>E. coli</em> and <em>K penumoniae</em>
</li>
<li>Better support for determination of <em>Salmonella</em> biovars</li>
@ -1441,7 +1446,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<p>Run <code><ahref='https://rdrr.io/r/base/unique.html'>unique(AMR::rsi_translation$guideline)</a></code> for a list of all supported guidelines.</p>
<p>Run <code><ahref='https://rdrr.io/r/base/unique.html'>unique(AMR::rsi_translation$guideline)</a></code> for a list of all supported guidelines. The repository of this package contains <ahref='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>this machine readable version</a> of these guidelines.</p>
<p>These guidelines are machine readable, since <ahref='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'></a>.</p>
<p>After using <code>as.rsi()</code>, you can use <code><ahref='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2class="hasAnchor"id="interpretation-of-r-and-s-i"><aclass="anchor"href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
`AMR` is a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code, and knows all about valid RSI and MIC values. It supports any data format, including WHONET/EARS-Net data.
After installing this package, R knows [**~70,000 distinct microbial species**](./reference/microorganisms.html) and all [**~550 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC and LOINC), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
We created this package for both routine data analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
@ -48,7 +48,8 @@ This package can be used for:
* Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name) ([manual](./reference/ab_property.html))
* Get the LOINC code of an antibiotic, or get the name associated with a LOINC code ([manual](./reference/ab_property.html))
* Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code ([manual](./reference/ab_property.html))
* Machine reading the EUCAST and CLSI guidelines from 2011-2019 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
This package is ready-to-use for a professional environment by specialists in the following fields:
@ -138,7 +139,7 @@ The `AMR` package basically does four important things:
2. It **enhances existing data** and **adds new data** from data sets included in this package.
* Use `eucast_rules()` to apply [EUCAST expert rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) (not the translation from MIC to RSI values, use `as.rsi()` for that).
* Use `eucast_rules()` to apply [EUCAST expert rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) (not the translation from MIC to R/SI values, use `as.rsi()` for that).
* Use `first_isolate()` to identify the first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute).
* You can also identify first *weighted* isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.
* Use `mdro()` to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos *et al.* (2012, [PMID 21793988](https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988)), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.
@ -44,7 +44,9 @@ Ordered factor with new class \code{\link{rsi}}
Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
}
\details{
Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines.
Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines. The repository of this package contains \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{this machine readable version} of these guidelines.
These guidelines are machine readable, since \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{}.
After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rules]{eucast_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
