P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-11 03:02:03 +02:00
Code Releases Activity

add confidence intervals (fixed #70), remove combine_IR

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-20 16:08:01 +02:00
parent 85e2fbe4a3
commit aa2c0639d0
19 changed files with 248 additions and 144 deletions
Download Patch File Download Diff File Expand all files Collapse all files

7
man/count.Rd
View File

@ -36,8 +36,7 @@ count_df(
data,
translate_ab = "name",
language = get_AMR_locale(),
combine_SI = TRUE,
combine_IR = FALSE
combine_SI = TRUE
)
}
\arguments{
@ -51,9 +50,7 @@ count_df(
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\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}{a \link{logical} to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see argument \code{combine_SI}.}
\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), defaults to \code{TRUE}}
}
\value{
An \link{integer}