NEWS.md
- Added official antimicrobial names to all filter_ab_class() functions, such as filter_aminoglycosides()
Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the antibiotics data set
Added Monuril as trade name for fosfomycin
Added parameter conserve_capped_values to as.rsi() for interpreting MIC values - it makes sure that values starting with “<” (but not “<=”) will always return “S” and values starting with “>” (but not “>=”) will always return “R”. The default behaviour of as.rsi() has not changed, so you need to specifically do as.rsi(..., conserve_capped_values = TRUE).
Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S < I < R. Invalid antimicrobial interpretations will be translated as NA with a warning.
Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S < I < R. Invalid antimicrobial interpretations will be translated as NA with a warning.
as.rsi(x, ...) @@ -244,6 +244,7 @@ ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, + conserve_capped_values = FALSE, ... ) @@ -254,11 +255,19 @@ ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, + conserve_capped_values = FALSE, ... ) # S3 method for data.frame -as.rsi(x, col_mo = NULL, guideline = "EUCAST", uti = NULL, ...) +as.rsi( + x, + col_mo = NULL, + guideline = "EUCAST", + uti = NULL, + conserve_capped_values = FALSE, + ... +) is.rsi(x) @@ -291,6 +300,10 @@uti + (Urinary Tract Infection) A vector with logicals (
TRUEorFALSE) to specify whether a UTI specific interpretation from the guideline should be chosen. For usingas.rsi()on a data.frame, this can also be a column containing logicals or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See Examples.+ conserve_capped_values ++ a logical to indicate that MIC values starting with
">"(but not">=") must always return "R" , and that MIC values starting with"<"(but not"<=") must always return "S"col_mo @@ -308,6 +321,7 @@ column name of the IDs of the microorganisms (see
as.mo()), defaults to the first column of classmo. Values will be coerced usingas.mo().When using
as.rsi()on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with classmic(usingas.mic()) or classdisk(usingas.disk()), the data will be interpreted based on the guideline set with theguidelineparameter.Supported guidelines to be used as input for the
+guidelineparameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using"CLSI"or"EUCAST"for input will automatically select the latest version of that guideline.When using
conserve_capped_values = TRUE, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (conserve_capped_values = FALSE) considers ">2" to be lower than ">=4" and will in this case return "S" or "I".The repository of this package contains a machine readable version of all guidelines. This is a CSV file consisting of 18,650 rows and 10 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 agent and the microorganism. 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.
After using
as.rsi(), you can useeucast_rules()to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.The function
diff --git a/docs/reference/index.html b/docs/reference/index.html index 19b76368..42e3fbef 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ diff --git a/docs/survey.html b/docs/survey.html index ed857061..d4288f74 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index d94e7c8f..569901e6 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -18,6 +18,7 @@ as.rsi(x, ...) ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, + conserve_capped_values = FALSE, ... ) @@ -27,10 +28,18 @@ as.rsi(x, ...) ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, + conserve_capped_values = FALSE, ... ) -\method{as.rsi}{data.frame}(x, col_mo = NULL, guideline = "EUCAST", uti = NULL, ...) +\method{as.rsi}{data.frame}( + x, + col_mo = NULL, + guideline = "EUCAST", + uti = NULL, + conserve_capped_values = FALSE, + ... +) is.rsi(x) @@ -49,6 +58,8 @@ is.rsi.eligible(x, threshold = 0.05) \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.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See \emph{Examples}.} +\item{conserve_capped_values}{a 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"} + \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} \item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}} @@ -57,13 +68,15 @@ is.rsi.eligible(x, threshold = 0.05) Ordered factor with new class \code{\link{rsi}} } \description{ -Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning. +Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning. } \details{ When using \code{\link[=as.rsi]{as.rsi()}} on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class \code{\link{mic}} (using \code{\link[=as.mic]{as.mic()}}) or class \code{\link{disk}} (using \code{\link[=as.disk]{as.disk()}}), the data will be interpreted based on the guideline set with the \code{guideline} parameter. Supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using \code{"CLSI"} or \code{"EUCAST"} for input will automatically select the latest version of that guideline. +When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and will in this case return "S" or "I". + The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,650 rows and 10 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 agent 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. After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rules]{eucast_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.is.rsi.eligible()returnsTRUEwhen a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), andFALSEotherwise. The threshold of 5% can be set with thethresholdparameter.