P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-11 23:01:56 +02:00
Code Releases Activity

(v1.4.0.9032) auto-data guessing for functions

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-07 16:06:42 +01:00
parent fdf29e6c5b
commit 1bdb136b3a
38 changed files with 455 additions and 353 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
man/first_isolate.Rd
View File

@ -50,7 +50,7 @@ filter_first_weighted_isolate(
)
}
\arguments{
\item{x}{a \link{data.frame} containing isolates.}
\item{x}{a \link{data.frame} containing isolates. Can be omitted when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}.}
\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column with a date class}
@ -93,6 +93,8 @@ A \code{\link{logical}} vector
Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
}
\details{
These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} parameter can be omitted, please see \emph{Examples}.
The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names.
All isolates with a microbial ID of \code{NA} will be excluded as first isolate.
@ -107,7 +109,7 @@ The functions \code{\link[=filter_first_isolate]{filter_first_isolate()}} and \c
The function \code{\link[=filter_first_isolate]{filter_first_isolate()}} is essentially equal to either:\preformatted{ x[first_isolate(x, ...), ]
x \%>\% filter(first_isolate(x, ...))
x \%>\% filter(first_isolate(...))
}
The function \code{\link[=filter_first_weighted_isolate]{filter_first_weighted_isolate()}} is essentially equal to:\preformatted{ x \%>\%
@ -161,6 +163,8 @@ if (require("dplyr")) {
filter(first_isolate == TRUE)
# short-hand versions:
example_isolates \%>\%
filter(first_isolate())
example_isolates \%>\%
filter_first_isolate()