P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 23:21:56 +02:00
Code Releases Activity

keyab automatic

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-12-10 15:14:29 +01:00
parent 9478ab71be
commit 5ab7eb07bc
4 changed files with 37 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
man/first_isolate.Rd
View File

@ -21,7 +21,7 @@ first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}}
\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive)}
\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
@ -31,7 +31,7 @@ first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
\item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)}
\item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation.}
\item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use \code{col_keyantibiotics = FALSE} to prevent this.}
\item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again}