docs

man/AMR-options.Rd

@@ -15,6 +15,7 @@ This is an overview of all the package-specific \code{\link[=options]{options()}
 \item \code{AMR_guideline} \cr Used for setting 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 2023"}. Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).
 \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_ecoff} \cr A \link{logical} use in \code{\link[=as.sir]{as.sir()}}, to indicate that ECOFF (Epidemiological Cut-Off) values must be used - 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_cleaning_regex} \cr A \link[base:regex]{regular expression} (case-insensitive) to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to clean the user input. The default is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar".

man/as.sir.Rd

@@ -43,6 +43,7 @@ is_sir_eligible(x, threshold = 0.05)
   reference_data = AMR::clinical_breakpoints,
   include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
+  ecoff = getOption("AMR_ecoff", FALSE),
   ...
 )
 
@@ -56,6 +57,7 @@ is_sir_eligible(x, threshold = 0.05)
   reference_data = AMR::clinical_breakpoints,
   include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
+  ecoff = getOption("AMR_ecoff", FALSE),
   ...
 )
 
@@ -69,7 +71,8 @@ is_sir_eligible(x, threshold = 0.05)
   add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
   include_screening = getOption("AMR_include_screening", FALSE),
-  include_PKPD = getOption("AMR_include_PKPD", TRUE)
+  include_PKPD = getOption("AMR_include_PKPD", TRUE),
+  ecoff = getOption("AMR_ecoff", FALSE)
 )
 
 sir_interpretation_history(clean = FALSE)
@@ -99,6 +102,8 @@ sir_interpretation_history(clean = FALSE)
 
 \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 \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_PKPD}}.}
 
+\item{ecoff}{a \link{logical} to indicate that ECOFF (Epidemiological Cut-Off) values must be used - the default is \code{FALSE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_ecoff}}.}
+
 \item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
 \item{clean}{a \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results}

man/clinical_breakpoints.Rd

@@ -17,7 +17,7 @@ A \link[tibble:tibble]{tibble} with 42 599 observations and 12 variables:
 \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{ecoff}\cr Epidemiological cut-off (ECOFF) value, used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi (use \link{as.sir(..., ecoff = TRUE)} to interpret raw data using ECOFF values)
+\item \code{ecoff}\cr Epidemiological cut-off (ECOFF) value, used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi (use \code{\link[=as.sir]{as.sir(..., ecoff = TRUE)}} to interpret raw data using ECOFF values)
 \item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
 }
 }