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expert rules 12.0

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dr. M.S. (Matthijs) Berends
2022-11-14 15:20:39 +01:00
parent 7ca44fb756
commit f6862a139d
35 changed files with 433 additions and 128 deletions
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4
man/dosage.Rd
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@@ -5,7 +5,7 @@
\alias{dosage}
\title{Data Set with Treatment Dosages as Defined by EUCAST}
\format{
A \link[tibble:tibble]{tibble} with 169 observations and 9 variables:
A \link[tibble:tibble]{tibble} with 336 observations and 9 variables:
\itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{name}\cr Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO
@@ -25,7 +25,7 @@ dosage
EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with \code{\link[=eucast_dosage]{eucast_dosage()}}.
}
\details{
This data set is based on \href{https://www.eucast.org/clinical_breakpoints/}{'EUCAST Clinical Breakpoint Tables' v11.0} (2021).
This data set is based on \href{https://www.eucast.org/clinical_breakpoints/}{'EUCAST Clinical Breakpoint Tables' v12.0} (2022) and \href{https://www.eucast.org/clinical_breakpoints/}{'EUCAST Clinical Breakpoint Tables' v11.0} (2021).
\subsection{Direct download}{
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.

6
man/eucast_rules.Rd
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@@ -25,7 +25,7 @@ eucast_rules(
info = interactive(),
rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
verbose = FALSE,
version_breakpoints = 11,
version_breakpoints = 12,
version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA,
only_rsi_columns = FALSE,
@@ -33,7 +33,7 @@ eucast_rules(
...
)
eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
}
\arguments{
\item{x}{a data set with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
@@ -46,7 +46,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\item{verbose}{a \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "11.0" or "10.0".}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "12.0", "11.0" or "10.0".}
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".}