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dr. M.S. (Matthijs) Berends 2023-12-04 08:19:02 +01:00
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DESCRIPTION
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Package: AMR
Version: 2.1.1.9003
Date: 2023-12-03
Version: 2.1.1.9004
Date: 2023-12-04
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

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NEWS.md
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# AMR 2.1.1.9003
# AMR 2.1.1.9004
## Breaking
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents a year ago

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R/mic.R
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#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `mic` class.
#'
#' With [rescale_mic()], existing MIC ranges can be rescaled to a defined range of MIC values. This can be useful to better compare MIC distributions.
#'
#' For `ggplot2`, use one of the [`scale_*_mic()`][scale_x_mic()] functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
#' @aliases mic
#' @export

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R/plot.R
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#' @description
#' Functions to plot classes `sir`, `mic` and `disk`, with support for base \R and `ggplot2`.
#'
#' Especially the [scale_*_mic()] functions are relevant wrappers to plot MIC values for `ggplot2`. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
#' Especially the `scale_*_mic()` functions are relevant wrappers to plot MIC values for `ggplot2`. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
#' @param x,object values created with [as.mic()], [as.disk()] or [as.sir()] (or their `random_*` variants, such as [random_mic()])
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]

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R/sysdata.rda
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man/AMR.Rd
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@ -32,7 +32,7 @@ The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{fr
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated December 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{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 public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated december 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{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 public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
}

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man/as.mic.Rd
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@ -84,6 +84,8 @@ Use \code{\link[=droplevels]{droplevels()}} to drop unused levels. At default, i
With \code{\link[=rescale_mic]{rescale_mic()}}, existing MIC ranges can be rescaled to a defined range of MIC values. This can be useful to better compare MIC distributions.
For \code{ggplot2}, use one of the \code{\link[=scale_x_mic]{scale_*_mic()}} functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
\code{NA_mic_} is a missing value of the new \code{mic} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
}
\examples{

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man/plot.Rd
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\description{
Functions to plot classes \code{sir}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.
Especially the \code{\link[=scale_*_mic]{scale_*_mic()}} functions are relevant wrappers to plot MIC values for \code{ggplot2}. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC values for \code{ggplot2}. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
}
\details{
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.