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

man/AMR-options.Rd

@@ -18,6 +18,7 @@ This is an overview of all the package-specific \code{\link[=options]{options()}
 \item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2024"}. Supported guideline are currently EUCAST (2011-2024) and CLSI (2011-2024).
 \item \code{AMR_ignore_pattern} \cr A \link[base:regex]{regular expression} to ignore (i.e., make \code{NA}) any match given in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions.
 \item \code{AMR_include_PKPD} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}.
+\item \code{AMR_substitute_missing_r_breakpoint} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that missing R breakpoints must be substituted with \code{"R"} - the default is \code{FALSE}.
 \item \code{AMR_include_screening} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}.
 \item \code{AMR_keep_synonyms} \cr A \link{logical} to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}.
 \item \code{AMR_locale} \cr A \link{character} to set the language for the \code{AMR} package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported, English otherwise).

man/as.sir.Rd

@@ -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}{

man/clinical_breakpoints.Rd

@@ -5,7 +5,7 @@
 \alias{clinical_breakpoints}
 \title{Data Set with Clinical Breakpoints for SIR Interpretation}
 \format{
-A \link[tibble:tibble]{tibble} with 34 063 observations and 14 variables:
+A \link[tibble:tibble]{tibble} with 34 382 observations and 14 variables:
 \itemize{
 \item \code{guideline}\cr Name of the guideline
 \item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
@@ -18,7 +18,7 @@ A \link[tibble:tibble]{tibble} with 34 063 observations and 14 variables:
 \item \code{ref_tbl}\cr Info about where the guideline rule can be found
 \item \code{disk_dose}\cr Dose of the used disk diffusion method
 \item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
-\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
+\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R", can be \code{NA}
 \item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
 \item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 24 breakpoints.
 }