P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-02 18:24:09 +02:00
Code Releases Activity

(v1.2.0.9008) ab_class improvement

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-06-17 15:14:37 +02:00
parent c4d7412f36
commit ac12392da3
37 changed files with 619 additions and 362 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
man/proportion.Rd
View File

@@ -83,7 +83,7 @@ The function \code{\link[=resistance]{resistance()}} is equal to the function \c
\strong{Remember that you should filter your table to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set.
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{count()}][AMR::count()] functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[AMR:count]{count()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
The function \code{\link[=proportion_df]{proportion_df()}} takes any variable from \code{data} that has an \code{\link{rsi}} class (created with \code{\link[=as.rsi]{as.rsi()}}) and calculates the proportions R, I and S. It also supports grouped variables. The function \code{\link[=rsi_df]{rsi_df()}} works exactly like \code{\link[=proportion_df]{proportion_df()}}, but adds the number of isolates.
}