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v1.6.0

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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.5.0.9041 Version: 1.6.0
Date: 2021-03-11 Date: 2021-03-14
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

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NEWS.md
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# AMR 1.5.0.9041 # AMR 1.6.0
## <small>Last updated: 11 March 2021</small>
### New ### New
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package. * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@ -407,7 +407,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Speed improvements, especially for the *G. species* format (G for genus), like *E. coli* and *K pneumoniae* * Speed improvements, especially for the *G. species* format (G for genus), like *E. coli* and *K pneumoniae*
* Support for more common codes used in laboratory information systems * Support for more common codes used in laboratory information systems
* Input values for `as.disk()` limited to a maximum of 50 millimeters * Input values for `as.disk()` limited to a maximum of 50 millimeters
* Added a lifecycle state to every function, following [the lifecycle circle of the `tidyverse`](https://www.tidyverse.org/lifecycle) * Added a lifecycle state to every function, following the lifecycle circle of the `tidyverse`
* For in `as.ab()`: support for drugs starting with "co-" like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey) * For in `as.ab()`: support for drugs starting with "co-" like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)
* Changes to the `antibiotics` data set (thanks to Peter Dutey): * Changes to the `antibiotics` data set (thanks to Peter Dutey):
* Added more synonyms to colistin, imipenem and piperacillin/tazobactam * Added more synonyms to colistin, imipenem and piperacillin/tazobactam

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#' #'
#' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}} #' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
#' @inheritSection lifecycle Stable Lifecycle #' @inheritSection lifecycle Stable Lifecycle
#' @param only_rsi_columns a logical to indicate whether only columns of class [`<rsi>`]([rsi]) must be selected (defaults to `FALSE`) #' @param only_rsi_columns a logical to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
#' @inheritParams filter_ab_class #' @inheritParams filter_ab_class
#' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}} #' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
#' #'

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R/ggplot_pca.R
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#' 4. Added total amount of explained variance as a caption in the plot #' 4. Added total amount of explained variance as a caption in the plot
#' 5. Cleaned all syntax based on the `lintr` package, fixed grammatical errors and added integrity checks #' 5. Cleaned all syntax based on the `lintr` package, fixed grammatical errors and added integrity checks
#' 6. Updated documentation #' 6. Updated documentation
#' @details The colours for labels and points can be changed by adding another scale layer for colour, like `scale_colour_viridis_d()` or `scale_colour_brewer()`. #' @details The colours for labels and points can be changed by adding another scale layer for colour, such as `scale_colour_viridis_d()` and `scale_colour_brewer()`.
#' @rdname ggplot_pca #' @rdname ggplot_pca
#' @export #' @export
#' @examples #' @examples

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README.md
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<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" /> <img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](data-raw). The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/master/data-raw).
`AMR` is a free, open-source and independent R package 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. `AMR` is a free, open-source and independent R package 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. It is currently being used in over 150 countries.
After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package. This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package.

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cran-comments.md
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* Ever since one of the first CRAN releases, CHECK returns a NOTE for having a data and R directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. * This package has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software 4 weeks ago. We will add the paper as a vignette in the next version. Please allow this exception in package size for CRAN. We already compressed all data sets using `compression = "xz"` to make them as small as possible.

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docs/404.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

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docs/articles/datasets.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>
@ -211,7 +211,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2> <a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p> <p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 11 March 2021 09:32:27 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p> <p>It was last updated on 11 March 2021 20:59:32 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
@ -497,7 +497,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2> <a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p> <p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 8 March 2021 18:20:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p> <p>It was last updated on 11 March 2021 20:59:32 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

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// edit footer // edit footer
$('footer').html( $('footer').html(
'<div>' + '<div>' +
'<p><code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' + '<p><code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' +
'<a href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/master/docs/logo_rug.png" class="footer_logo"></a>' + '<a href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/master/docs/logo_rug.png" class="footer_logo"></a>' +
'</div>'); '</div>');
// all links should open in new tab/window // all links should open in new tab/window

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docs/index.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>
@ -207,11 +207,11 @@ Since you are one of our users, we would like to know how you use the package an
<a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3> <a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
<p><em>(To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.)</em></p> <p><em>(To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.)</em></p>
<p><code>AMR</code> is a free, open-source and independent <a href="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><code>AMR</code> is a free, open-source and independent <a href="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 <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p> <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p> <p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
<div class="main-content" style="display: inline-block;"> <div class="main-content" style="display: inline-block;">
<p> <p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 148 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 148 countries. Click the map to enlarge and to see the country names. <a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 155 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 155 countries. Click the map to enlarge and to see the country names.
</p> </p>
</div> </div>
<div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5"> <div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5">
@ -349,7 +349,7 @@ Since you are one of our users, we would like to know how you use the package an
<a href="#partners" class="anchor"></a>Partners</h4> <a href="#partners" class="anchor"></a>Partners</h4>
<p>The development of this package is part of, related to, or made possible by:</p> <p>The development of this package is part of, related to, or made possible by:</p>
<div align="center"> <div align="center">
<p><a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a></p> <p><a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a></p>
</div> </div>
</div> </div>
</div> </div>
@ -372,7 +372,7 @@ Since you are one of our users, we would like to know how you use the package an
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li> <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li> <li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li> <li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li> <li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
<li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li> <li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
</ul> </ul>
</div> </div>

96
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9040</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>
@ -236,14 +236,10 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1509040" class="section level1"> <div id="amr-160" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9040"> <h1 class="page-header" data-toc-text="1.6.0">
<a href="#amr-1509040" class="anchor"></a>AMR 1.5.0.9040<small> Unreleased </small> <a href="#amr-160" class="anchor"></a>AMR 1.6.0<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-8-march-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-8-march-2021" class="anchor"></a><small>Last updated: 8 March 2021</small>
</h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3> <a href="#new" class="anchor"></a>New</h3>
@ -279,7 +275,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div> <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li> </li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li> <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li> <li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li> <li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p> <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
@ -302,60 +298,71 @@
<span class="co">#&gt; [1] "Hongos" "Levaduras"</span></code></pre></div> <span class="co">#&gt; [1] "Hongos" "Levaduras"</span></code></pre></div>
</li> </li>
<li><p>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</p></li> <li><p>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</p></li>
<li>
<p>MIC values (see <code><a href="../reference/as.mic.html">as.mic()</a></code>) can now be used in any mathematical processing, such as usage inside functions <code><a href="https://rdrr.io/r/base/Extremes.html">min()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html">max()</a></code>, <code><a href="https://rdrr.io/r/base/range.html">range()</a></code>, and with binary operators (<code><a href="https://rdrr.io/r/base/Arithmetic.html">+</a></code>, <code><a href="https://rdrr.io/r/base/Arithmetic.html">-</a></code>, etc.). This allows for easy distribution analysis and fast filtering on MIC values:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>
<span class="va">x</span>
<span class="co">#&gt; Class &lt;mic&gt;</span>
<span class="co">#&gt; [1] 128 0.5 2 0.125 64 0.25 &gt;=256 8 16 4</span>
<span class="va">x</span><span class="op">[</span><span class="va">x</span> <span class="op">&gt;</span> <span class="fl">4</span><span class="op">]</span>
<span class="co">#&gt; Class &lt;mic&gt;</span>
<span class="co">#&gt; [1] 128 64 &gt;=256 8 16</span>
<span class="fu"><a href="https://rdrr.io/r/base/range.html">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co">#&gt; [1] 0.125 256.000</span>
<span class="fu"><a href="https://rdrr.io/r/base/range.html">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html">log2</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; [1] -3 8</span></code></pre></div>
</li>
</ul> </ul>
</div> </div>
<div id="changed" class="section level3"> <div id="changed" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3> <a href="#changed" class="anchor"></a>Changed</h3>
<ul> <ul>
<li> <li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LSPN</a>)
<p>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LSPN</a>)</p>
<ul> <ul>
<li>Added 3,372 new species and 1,523 existing species became synomyms</li> <li>Added 3,372 new species and 1,523 existing species became synomyms</li>
<li>The URL of a bacterial species (<code><a href="../reference/mo_property.html">mo_url()</a></code>) will now lead to <a href="https://lpsn.dsmz.de" class="uri">https://lpsn.dsmz.de</a> <li>The URL of a bacterial species (<code><a href="../reference/mo_property.html">mo_url()</a></code>) will now lead to <a href="https://lpsn.dsmz.de" class="uri">https://lpsn.dsmz.de</a>
</li> </li>
</ul> </ul>
</li> </li>
<li> <li>Big update for plotting classes <code>rsi</code>, <code>&lt;mic&gt;</code>, and <code>&lt;disk&gt;</code>:
<p>Big update for plotting classes <code>rsi</code>, <code>&lt;mic&gt;</code>, and <code>&lt;disk&gt;</code>:</p>
<ul> <ul>
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li> <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li> <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li> <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li> <li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
</ul> </ul>
</li> </li>
<li><p><code><a href="../reference/as.rsi.html">is.rsi()</a></code> and <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now return a vector of <code>TRUE</code>/<code>FALSE</code> when the input is a data set, by iterating over all columns</p></li> <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
<li><p>Using functions without setting a data set (e.g., <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>) now work with <code>dplyr</code>s <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> again</p></li>
<li><p><code><a href="../reference/first_isolate.html">first_isolate()</a></code> can be used with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> (also when using a dot <code>.</code> as input for the data) and now returns the names of the groups</p></li>
<li> <li>
<p>MIC values (see <code><a href="../reference/as.mic.html">as.mic()</a></code>) can now be used in any mathematical processing, such as usage inside functions <code><a href="https://rdrr.io/r/base/Extremes.html">min()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html">max()</a></code>, <code><a href="https://rdrr.io/r/base/range.html">range()</a></code>, and with binary operators (+, -, etc.). This allows easy distribution analysis and fast filtering on MIC values:</p> <code><a href="../reference/as.rsi.html">is.rsi()</a></code> and <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now return a vector of <code>TRUE</code>/<code>FALSE</code> when the input is a data set, by iterating over all columns</li>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <li>Using functions without setting a data set (e.g., <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>) now work with <code>dplyr</code>s <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> again</li>
<code class="sourceCode R"> <li>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span> <code><a href="../reference/first_isolate.html">first_isolate()</a></code> can be used with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> (also when using a dot <code>.</code> as input for the data) and now returns the names of the groups</li>
<span class="va">x</span> <li>Updated the data set <code>microorganisms.codes</code> (which contains popular LIS and WHONET codes for microorganisms) for some species of <em>Mycobacterium</em> that previously incorrectly returned <em>M. africanum</em>
<span class="co">#&gt; Class &lt;mic&gt;</span>
<span class="co">#&gt; [1] 0.5 64 64 128 0.125 4 0.5 0.0625 0.0625 0.125 </span>
<span class="va">x</span><span class="op">[</span><span class="va">x</span> <span class="op">&gt;</span> <span class="fl">4</span><span class="op">]</span>
<span class="co">#&gt; Class &lt;mic&gt;</span>
<span class="co">#&gt; [1] 64 64 128</span></code></pre></div>
</li> </li>
<li><p>Updated the data set <code>microorganisms.codes</code> (which contains popular LIS and WHONET codes for microorganisms) for some species of <em>Mycobacterium</em> that previously incorrectly returned <em>M. africanum</em></p></li> <li>WHONET code <code>"PNV"</code> will now correctly be interpreted as <code>PHN</code>, the antibiotic code for phenoxymethylpenicillin (‘peni V’)</li>
<li><p>WHONET code <code>"PNV"</code> will now correctly be interpreted as <code>PHN</code>, the antibiotic code for phenoxymethylpenicillin (‘peni V’)</p></li> <li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only <em>P. aeruginosa</em>)</li>
<li><p>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only <em>P. aeruginosa</em>)</p></li> <li>
<li><p><code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</p></li> <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
<li><p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</p></li> <li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
<li><p>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</p></li> <li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
<li><p>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code></p></li> <li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
<li><p>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</p></li> </li>
<li><p>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</p></li> <li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
<li><p>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package (e.g., <code><a href="../reference/as.mo.html">as.mo()</a></code> is now up to 4 times faster)</p></li> <li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
<li><p><em>Staphylococcus cornubiensis</em> is now correctly categorised as coagulase-positive</p></li> <li>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package (e.g., <code><a href="../reference/as.mo.html">as.mo()</a></code> is now up to 4 times faster)</li>
<li><p><code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_mic()</a></code> now have an expanded range in their randomisation</p></li> <li>
<li><p>Support for GISA (glycopeptide-intermediate <em>S. aureus</em>), so e.g. <code><a href="../reference/mo_property.html">mo_genus("GISA")</a></code> will return <code>"Staphylococcus"</code></p></li> <em>Staphylococcus cornubiensis</em> is now correctly categorised as coagulase-positive</li>
<li><p>Added translations of German and Spanish for more than 200 antimicrobial drugs</p></li> <li>
<li><p>Speed improvement for <code><a href="../reference/as.ab.html">as.ab()</a></code> when the input is an official name or ATC code</p></li> <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_mic()</a></code> now have an expanded range in their randomisation</li>
<li><p>Added argument <code>include_untested_rsi</code> to the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> functions (defaults to <code>TRUE</code> to keep existing behaviour), to be able to exclude rows where all R/SI values (class <code>&lt;rsi&gt;</code>, see <code><a href="../reference/as.rsi.html">as.rsi()</a></code>) are empty</p></li> <li>Support for GISA (glycopeptide-intermediate <em>S. aureus</em>), so e.g. <code><a href="../reference/mo_property.html">mo_genus("GISA")</a></code> will return <code>"Staphylococcus"</code>
</li>
<li>Added translations of German and Spanish for more than 200 antimicrobial drugs</li>
<li>Speed improvement for <code><a href="../reference/as.ab.html">as.ab()</a></code> when the input is an official name or ATC code</li>
<li>Added argument <code>include_untested_rsi</code> to the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> functions (defaults to <code>TRUE</code> to keep existing behaviour), to be able to exclude rows where all R/SI values (class <code>&lt;rsi&gt;</code>, see <code><a href="../reference/as.rsi.html">as.rsi()</a></code>) are empty</li>
</ul> </ul>
</div> </div>
<div id="other" class="section level3"> <div id="other" class="section level3">
@ -366,7 +373,6 @@
<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li> <li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
</ul> </ul>
</div> </div>
</div>
</div> </div>
<div id="amr-150" class="section level1"> <div id="amr-150" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0"> <h1 class="page-header" data-toc-text="1.5.0">
@ -857,7 +863,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</ul> </ul>
</li> </li>
<li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li> <li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li>
<li>Added a lifecycle state to every function, following <a href="https://www.tidyverse.org/lifecycle">the lifecycle circle of the <code>tidyverse</code></a> <li>Added a lifecycle state to every function, following the lifecycle circle of the <code>tidyverse</code>
</li> </li>
<li>For in <code><a href="../reference/as.ab.html">as.ab()</a></code>: support for drugs starting with “co-” like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)</li> <li>For in <code><a href="../reference/as.ab.html">as.ab()</a></code>: support for drugs starting with “co-” like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)</li>
<li>Changes to the <code>antibiotics</code> data set (thanks to Peter Dutey): <li>Changes to the <code>antibiotics</code> data set (thanks to Peter Dutey):

2
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-03-11T20:23Z last_built: 2021-03-14T08:55Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

4
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@ -83,7 +83,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>
@ -283,7 +283,7 @@
</tr> </tr>
<tr> <tr>
<th>only_rsi_columns</th> <th>only_rsi_columns</th>
<td><p>a logical to indicate whether only columns of class <a href='[rsi]'><code>&lt;rsi&gt;</code></a> must be selected (defaults to <code>FALSE</code>)</p></td> <td><p>a logical to indicate whether only columns of class <code>&lt;rsi&gt;</code> must be selected (defaults to <code>FALSE</code>), see <code><a href='as.rsi.html'>as.rsi()</a></code></p></td>
</tr> </tr>
</table> </table>

2
docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/reference/filter_ab_class.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

4
docs/reference/ggplot_pca.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9040</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>
@ -383,7 +383,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The colours for labels and points can be changed by adding another scale layer for colour, like <code><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d()</a></code> or <code><a href='https://ggplot2.tidyverse.org/reference/scale_brewer.html'>scale_colour_brewer()</a></code>.</p> <p>The colours for labels and points can be changed by adding another scale layer for colour, such as <code><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d()</a></code> and <code><a href='https://ggplot2.tidyverse.org/reference/scale_brewer.html'>scale_colour_brewer()</a></code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2> <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

2
docs/reference/guess_ab_col.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/reference/lifecycle.html
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@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/reference/mdro.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/reference/microorganisms.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/reference/mo_matching_score.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/reference/mo_property.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9041</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0</span>
</span> </span>
</div> </div>

3
git_premaster.sh
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@ -124,7 +124,8 @@ echo "••••••••••••••••••••"
echo "• Building package •" echo "• Building package •"
echo "••••••••••••••••••••" echo "••••••••••••••••••••"
echo "• Building 'data-raw/AMR_latest.tar.gz'..." echo "• Building 'data-raw/AMR_latest.tar.gz'..."
Rscript -e "x <- devtools::build(path = 'data-raw/AMR_latest.tar.gz', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)" Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz
echo "• Installing..." echo "• Installing..."
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)" Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
echo echo

12
index.md
View File

@ -13,15 +13,15 @@
`AMR` is a free, open-source and independent [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. `AMR` is a free, open-source and independent [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 (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI 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, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)). This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
<div class="main-content" style="display: inline-block;"> <div class="main-content" style="display: inline-block;">
<p> <p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
<strong>Used in 148 countries</strong><br> <strong>Used in 155 countries</strong><br>
Since its first public release in early 2018, this package has been downloaded from 148 countries. Click the map to enlarge and to see the country names.</p> Since its first public release in early 2018, this package has been downloaded from 155 countries. Click the map to enlarge and to see the country names.</p>
</div> </div>
##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side! ##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!
@ -75,7 +75,7 @@ The development of this package is part of, related to, or made possible by:
<div align="center"> <div align="center">
<a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a>
<a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a>
<a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation"><img src="./logo_certe.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a>
<a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a>
</div> </div>
@ -98,7 +98,7 @@ This package can be used for:
* Applying EUCAST expert rules ([manual](./reference/eucast_rules.html)) * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
* Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](./reference/mo_property.html)) * Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](./reference/mo_property.html))
* Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code ([manual](./reference/ab_property.html)) * Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code ([manual](./reference/ab_property.html))
* Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](./articles/datasets.html)) * Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI ([link](./articles/datasets.html))
* Principal component analysis for AMR ([tutorial](./articles/PCA.html)) * Principal component analysis for AMR ([tutorial](./articles/PCA.html))
### Get this package ### Get this package

2
man/antibiotic_class_selectors.Rd
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@ -52,7 +52,7 @@ tetracyclines(only_rsi_columns = FALSE)
\arguments{ \arguments{
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.} \item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
\item{only_rsi_columns}{a logical to indicate whether only columns of class \href{[rsi]}{\verb{<rsi>}} must be selected (defaults to \code{FALSE})} \item{only_rsi_columns}{a logical to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
} }
\description{ \description{
These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}} These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}

2
man/ggplot_pca.Rd
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@ -106,7 +106,7 @@ ggplot_pca(
Produces a \code{ggplot2} variant of a so-called \href{https://en.wikipedia.org/wiki/Biplot}{biplot} for PCA (principal component analysis), but is more flexible and more appealing than the base \R \code{\link[=biplot]{biplot()}} function. Produces a \code{ggplot2} variant of a so-called \href{https://en.wikipedia.org/wiki/Biplot}{biplot} for PCA (principal component analysis), but is more flexible and more appealing than the base \R \code{\link[=biplot]{biplot()}} function.
} }
\details{ \details{
The colours for labels and points can be changed by adding another scale layer for colour, like \code{scale_colour_viridis_d()} or \code{scale_colour_brewer()}. The colours for labels and points can be changed by adding another scale layer for colour, such as \code{scale_colour_viridis_d()} and \code{scale_colour_brewer()}.
} }
\section{Stable Lifecycle}{ \section{Stable Lifecycle}{

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pkgdown/extra.js
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@ -66,7 +66,7 @@ $(document).ready(function() {
// edit footer // edit footer
$('footer').html( $('footer').html(
'<div>' + '<div>' +
'<p><code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' + '<p><code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' +
'<a href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/master/docs/logo_rug.png" class="footer_logo"></a>' + '<a href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/master/docs/logo_rug.png" class="footer_logo"></a>' +
'</div>'); '</div>');
// all links should open in new tab/window // all links should open in new tab/window

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tests/testthat.R
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@ -24,8 +24,8 @@
# ==================================================================== # # ==================================================================== #
# the testthat package is in Suggests, but very old R versions will not be # the testthat package is in Suggests, but very old R versions will not be
# able to install it. Yet, we want checks in those R versions as well, so # able to install it. Yet, we want basic R CMD CHECK's in those R versions
# only run unit tests in later R versions: # as well, so only run unit tests in later R versions:
if (require("testthat")) { if (require("testthat")) {
library(testthat, warn.conflicts = FALSE) library(testthat, warn.conflicts = FALSE)
library(AMR) library(AMR)