P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 19:01:51 +02:00
Code Releases Activity

fix SIR interpretation for uti

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-05-31 21:24:35 +02:00
parent 60c6c21e45
commit 7c1b564648
4 changed files with 70 additions and 36 deletions
Download Patch File Download Diff File Expand all files Collapse all files

18
man/as.sir.Rd
View File

@ -104,7 +104,7 @@ sir_interpretation_history(clean = FALSE)
\item{guideline}{defaults to EUCAST 2023 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2023) and CLSI (2011-2023), see \emph{Details}.}
\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
\item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
\item{conserve_capped_values}{a \link{logical} to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
@ -130,11 +130,11 @@ Ordered \link{factor} with new class \code{sir}
\description{
Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. \code{\link[=as.sir]{as.sir()}} transforms the input to a new class \code{\link{sir}}, which is an ordered \link{factor}.
These breakpoints are currently available:
These breakpoints are currently implemented:
\itemize{
\item For \strong{clinical microbiology} from EUCAST 2011-2023 and CLSI 2011-2023;
\item For \strong{veterinary microbiology} from EUCAST 2021-2023 and CLSI 2019-2023;
\item ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.
\item For \strong{clinical microbiology}: EUCAST 2011-2023 and CLSI 2011-2023;
\item For \strong{veterinary microbiology}: EUCAST 2021-2023 and CLSI 2019-2023;
\item ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
}
All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
@ -150,8 +150,10 @@ The \code{\link[=as.sir]{as.sir()}} function can work in four ways:
\itemize{
\item Using \code{dplyr}, SIR interpretation can be done very easily with either:
\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.mic, as.sir)
\if{html}{\out{<div class="sourceCode r">}}\preformatted{your_data \%>\% mutate_if(is.mic, as.sir)
your_data \%>\% mutate(across(where(is.mic), as.sir))
your_data \%>\% mutate_if(is.mic, as.sir, ab = "column_with_antibiotics", mo = "column_with_microorganisms")
your_data \%>\% mutate_if(is.mic, as.sir, ab = c("cipro", "ampicillin", ...), mo = c("E. coli", "K. pneumoniae", ...))
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.mic, as.sir, host = "column_with_animal_hosts", guideline = "CLSI")
@ -162,8 +164,10 @@ your_data \%>\% mutate_if(is.mic, as.sir, host = "column_with_animal_hosts", gui
\itemize{
\item Using \code{dplyr}, SIR interpretation can be done very easily with either:
\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.disk, as.sir)
\if{html}{\out{<div class="sourceCode r">}}\preformatted{your_data \%>\% mutate_if(is.disk, as.sir)
your_data \%>\% mutate(across(where(is.disk), as.sir))
your_data \%>\% mutate_if(is.disk, as.sir, ab = "column_with_antibiotics", mo = "column_with_microorganisms")
your_data \%>\% mutate_if(is.disk, as.sir, ab = c("cipro", "ampicillin", ...), mo = c("E. coli", "K. pneumoniae", ...))
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.disk, as.sir, host = "column_with_animal_hosts", guideline = "CLSI")