P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-02 19:44:04 +02:00
Code Releases Activity

(v1.6.0.9021) join functions update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-05-12 18:15:03 +02:00
parent 3319fbae58
commit 29dbfa2f49
119 changed files with 973 additions and 1040 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
man/key_antimicrobials.Rd
View File

@@ -45,15 +45,15 @@ antimicrobials_equal(
\item{antifungal}{names of antifungal agents for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.}
\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
\item{...}{ignored, only in place to allow future extensions}
\item{y, z}{character vectors to compare}
\item{y, z}{\link{character} vectors to compare}
\item{type}{type to determine weighed isolates; can be \code{"keyantimicrobials"} or \code{"points"}, see \emph{Details}}
\item{ignore_I}{logical to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}
\item{ignore_I}{\link{logical} to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}
\item{points_threshold}{minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
}
@@ -63,7 +63,7 @@ These functions can be used to determine first weighted isolates by considering
\details{
The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}.
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a character vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a character vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
Please see the \code{\link[=first_isolate]{first_isolate()}} function how these important functions enable the 'phenotype-based' method for determination of first isolates.
@@ -133,7 +133,7 @@ antimicrobials_equal(strainA, strainB, type = "keyantimicrobials")
# TRUE, because I is ignored (as well as missing values)
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE)
# FALSE, because I is not ignored and so the 4th character differs
# FALSE, because I is not ignored and so the 4th [character] differs
\donttest{
if (require("dplyr")) {