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(v2.1.1.9195) add BTL-S, fix ranks in unknown microorganisms

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dr. M.S. (Matthijs) Berends
2025-03-13 14:30:14 +01:00
parent a7ef22a21e
commit 9aab129ea6
48 changed files with 1789 additions and 1710 deletions
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2
man/AMR-deprecated.Rd
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@ -8,7 +8,7 @@
\alias{ab_selector}
\title{Deprecated Functions}
\format{
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 494 rows and 14 columns.
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 495 rows and 14 columns.
}
\usage{
ab_class(...)

2
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{~79 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antimicrobials.html}{\strong{~610 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{~79 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antimicrobials.html}{\strong{~620 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.
}

12
man/antimicrobial_selectors.Rd
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@ -70,11 +70,13 @@ cephalosporins_4th(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_5th(only_sir_columns = FALSE, return_all = TRUE, ...)
fluoroquinolones(only_sir_columns = FALSE, return_all = TRUE, ...)
fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
isoxazolylpenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
lincosamides(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
@ -96,13 +98,15 @@ phenicols(only_sir_columns = FALSE, return_all = TRUE, ...)
polymyxins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
quinolones(only_sir_columns = FALSE, return_all = TRUE, ...)
quinolones(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)
streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)
tetracyclines(only_sir_columns = FALSE, return_all = TRUE, ...)
tetracyclines(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
trimethoprims(only_sir_columns = FALSE, return_all = TRUE, ...)

4
man/antimicrobials.Rd
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@ -4,9 +4,9 @@
\name{antimicrobials}
\alias{antimicrobials}
\alias{antivirals}
\title{Data Sets with 614 Antimicrobial Drugs}
\title{Data Sets with 615 Antimicrobial Drugs}
\format{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 494 observations and 14 variables:}{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 495 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr antimcrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
\item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}