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(v0.7.1.9088) bug_drug improvement

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dr. M.S. (Matthijs) Berends
2019-09-25 15:43:22 +02:00
parent 04cd0d25db
commit 99d0fe76dd
19 changed files with 603 additions and 186 deletions
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21
man/bug_drug_combinations.Rd
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@ -11,9 +11,12 @@
bug_drug_combinations(x, col_mo = NULL, minimum = 30,
FUN = mo_shortname, ...)
\method{format}{bug_drug_combinations}(x, combine_IR = FALSE,
add_ab_group = TRUE, decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","), ...)
\method{format}{bug_drug_combinations}(x,
translate_ab = "name (ab, atc)", language = get_locale(),
minimum = 30, combine_SI = TRUE, combine_IR = FALSE,
add_ab_group = TRUE, remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark ==
",", ".", ","), ...)
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
@ -24,12 +27,20 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
\item{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link{mo_shortname}}}
\item{...}{argumments passed on to \code{FUN}}
\item{...}{arguments passed on to \code{FUN}}
\item{translate_ab}{a character of length 1 containing column names of the \code{\link{antibiotics}} data set}
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\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 parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion 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{add_ab_group}{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 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.}
@ -38,7 +49,7 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
decimal point.}
}
\description{
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a publicable/printable format, see Examples.
}
\details{
The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.