P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 18:21:49 +02:00
Code Releases Activity

(v2.1.1.9078) 12 new formatting formats for antibiogram(), prepare for Bayesian WISCA

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-09-22 11:45:51 +02:00
parent 28bf91cbf5
commit 127892430d
8 changed files with 201 additions and 61 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
man/AMR-options.Rd
View File

@ -9,6 +9,7 @@ This is an overview of all the package-specific \code{\link[=options]{options()}
\section{Options}{
\itemize{
\item \code{AMR_antibiogram_formatting_type} \cr A \link{numeric} (1-12) to use in \code{\link[=antibiogram]{antibiogram()}}, to indicate which formatting type to use.
\item \code{AMR_breakpoint_type} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".
\item \code{AMR_cleaning_regex} \cr A \link[base:regex]{regular expression} (case-insensitive) to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to clean the user input. The default is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar".
\item \code{AMR_custom_ab} \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.