mirror of https://github.com/msberends/AMR.git
158 lines
7.3 KiB
R
Executable File
158 lines
7.3 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/key_antibiotics.R
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\name{key_antibiotics}
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\alias{key_antibiotics}
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\alias{key_antibiotics_equal}
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\title{Key antibiotics for first \emph{weighted} isolates}
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\usage{
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key_antibiotics(
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x,
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col_mo = NULL,
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universal_1 = guess_ab_col(x, "amoxicillin"),
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universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
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universal_3 = guess_ab_col(x, "cefuroxime"),
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universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
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universal_5 = guess_ab_col(x, "ciprofloxacin"),
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universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
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GramPos_1 = guess_ab_col(x, "vancomycin"),
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GramPos_2 = guess_ab_col(x, "teicoplanin"),
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GramPos_3 = guess_ab_col(x, "tetracycline"),
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GramPos_4 = guess_ab_col(x, "erythromycin"),
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GramPos_5 = guess_ab_col(x, "oxacillin"),
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GramPos_6 = guess_ab_col(x, "rifampin"),
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GramNeg_1 = guess_ab_col(x, "gentamicin"),
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GramNeg_2 = guess_ab_col(x, "tobramycin"),
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GramNeg_3 = guess_ab_col(x, "colistin"),
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GramNeg_4 = guess_ab_col(x, "cefotaxime"),
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GramNeg_5 = guess_ab_col(x, "ceftazidime"),
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GramNeg_6 = guess_ab_col(x, "meropenem"),
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warnings = TRUE,
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...
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)
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key_antibiotics_equal(
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y,
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z,
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type = c("keyantibiotics", "points"),
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ignore_I = TRUE,
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points_threshold = 2,
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info = FALSE
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)
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}
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\arguments{
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\item{x}{table with antibiotics coloms, like \code{AMX} or \code{amox}}
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\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()}}.}
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\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link[=guess_ab_col]{guess_ab_col()}}.}
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\item{GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6}{column names of antibiotics for \strong{Gram-positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link[=guess_ab_col]{guess_ab_col()}}.}
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\item{GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6}{column names of antibiotics for \strong{Gram-negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link[=guess_ab_col]{guess_ab_col()}}.}
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\item{warnings}{give warning about missing antibiotic columns, they will anyway be ignored}
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\item{...}{other parameters passed on to function}
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\item{y, z}{characters to compare}
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\item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see Details}
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\item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details}
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\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details}
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\item{info}{print progress}
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}
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\description{
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These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first \emph{weighted} isolates.
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}
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\details{
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The function \code{\link[=key_antibiotics]{key_antibiotics()}} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link[=first_isolate]{first_isolate()}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link[=first_isolate]{first_isolate()}}). Without key antibiotic comparison it would not.
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At default, the antibiotics that are used for \strong{Gram-positive bacteria} are:
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\itemize{
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\item Amoxicillin
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\item Amoxicillin/clavulanic acid
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\item Cefuroxime
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\item Piperacillin/tazobactam
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\item Ciprofloxacin
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\item Trimethoprim/sulfamethoxazole
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\item Vancomycin
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\item Teicoplanin
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\item Tetracycline
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\item Erythromycin
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\item Oxacillin
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\item Rifampin
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}
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At default the antibiotics that are used for \strong{Gram-negative bacteria} are:
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\itemize{
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\item Amoxicillin
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\item Amoxicillin/clavulanic acid
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\item Cefuroxime
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\item Piperacillin/tazobactam
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\item Ciprofloxacin
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\item Trimethoprim/sulfamethoxazole
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\item Gentamicin
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\item Tobramycin
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\item Colistin
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\item Cefotaxime
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\item Ceftazidime
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\item Meropenem
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}
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The function \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}} checks the characters returned by \code{\link[=key_antibiotics]{key_antibiotics()}} for equality, and returns a \code{\link{logical}} vector.
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}
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\section{Key antibiotics}{
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There are two ways to determine whether isolates can be included as first \emph{weighted} isolates which will give generally the same results:
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\enumerate{
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\item Using \code{type = "keyantibiotics"} and parameter \code{ignore_I}
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Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the \code{\link[=key_antibiotics]{key_antibiotics()}} function.
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\item Using \code{type = "points"} and parameter \code{points_threshold}
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A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which default to \code{2}, an isolate will be (re)selected as a first weighted isolate.
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}
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\examples{
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# `example_isolates` is a dataset available in the AMR package.
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# See ?example_isolates.
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library(dplyr)
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# set key antibiotics to a new variable
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my_patients <- example_isolates \%>\%
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mutate(keyab = key_antibiotics(.)) \%>\%
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mutate(
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# now calculate first isolates
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first_regular = first_isolate(., col_keyantibiotics = FALSE),
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# and first WEIGHTED isolates
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first_weighted = first_isolate(., col_keyantibiotics = "keyab")
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)
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# Check the difference, in this data set it results in 7\% more isolates:
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sum(my_patients$first_regular, na.rm = TRUE)
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sum(my_patients$first_weighted, na.rm = TRUE)
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# output of the `key_antibiotics` function could be like this:
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strainA <- "SSSRR.S.R..S"
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strainB <- "SSSIRSSSRSSS"
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key_antibiotics_equal(strainA, strainB)
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# TRUE, because I is ignored (as well as missing values)
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key_antibiotics_equal(strainA, strainB, ignore_I = FALSE)
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# FALSE, because I is not ignored and so the 4th value differs
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}
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\seealso{
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\code{\link[=first_isolate]{first_isolate()}}
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}
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