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(v1.6.0.9021) join functions update

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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
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12
man/bug_drug_combinations.Rd
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@ -29,23 +29,23 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
\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{FUN}{function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link[=mo_shortname]{mo_shortname()}}}
\item{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link[=mo_shortname]{mo_shortname()}}}
\item{...}{arguments passed on to \code{FUN}}
\item{translate_ab}{character of length 1 containing column names of the \link{antibiotics} data set}
\item{translate_ab}{a \link{character} of length 1 containing column names of the \link{antibiotics} data set}
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
\item{combine_SI}{a \link{logical} to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
\item{combine_IR}{logical to indicate whether values R and I should be summed}
\item{combine_IR}{a \link{logical} to indicate whether values R and I should be summed}
\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
\item{add_ab_group}{a \link{logical} to indicate where the group of the antimicrobials must be included as a first column}
\item{remove_intrinsic_resistant}{logical to indicate that rows and columns with 100\% resistance for all tested antimicrobials must be removed from the table}
\item{remove_intrinsic_resistant}{\link{logical} to indicate that rows and columns with 100\% resistance for all tested antimicrobials must be removed from the table}
\item{decimal.mark}{the character to be used to indicate the numeric
decimal point.}