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(v2.1.1.9194) new argument for missing R breakpoints - updated from WHONET

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dr. M.S. (Matthijs) Berends
2025-03-12 16:24:38 +01:00
parent e1b7252ff6
commit a7ef22a21e
27 changed files with 15755 additions and 15399 deletions
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13
man/as.sir.Rd
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@ -40,7 +40,8 @@ is_sir_eligible(x, threshold = 0.05)
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
conserve_capped_values = FALSE, add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
include_screening = getOption("AMR_include_screening", FALSE),
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE, ...)
@ -49,7 +50,8 @@ is_sir_eligible(x, threshold = 0.05)
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
include_screening = getOption("AMR_include_screening", FALSE),
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE, ...)
@ -58,7 +60,8 @@ is_sir_eligible(x, threshold = 0.05)
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
conserve_capped_values = FALSE, add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
include_screening = getOption("AMR_include_screening", FALSE),
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE)
@ -88,6 +91,8 @@ sir_interpretation_history(clean = FALSE)
\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
\item{substitute_missing_r_breakpoint}{a \link{logical} to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is \code{FALSE}. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning the outcome can only be \code{"S"} or \code{NA}. Setting this to \code{TRUE} will convert the \code{NA}s to \code{"R"} only if the R breakpoint is missing. Can also be set with the package option \code{\link[=AMR-options]{AMR_substitute_missing_r_breakpoint}}.}
\item{include_screening}{a \link{logical} to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_screening}}.}
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
@ -190,7 +195,7 @@ To determine which isolates are multi-drug resistant, be sure to run \code{\link
\subsection{Machine-Readable Clinical Breakpoints}{
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 34 063 rows and 14 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 34 382 rows and 14 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
}
\subsection{Other}{