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fix first isolate

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dr. M.S. (Matthijs) Berends
2023-02-10 13:13:17 +01:00
parent 1a0dc4bf46
commit 70a7ba0206
13 changed files with 222 additions and 56 deletions
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8
man/first_isolate.Rd
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@ -52,7 +52,7 @@ filter_first_isolate(
\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 IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (such as test codes for screening). In that case \code{testcodes_exclude} will be ignored.}
@ -168,7 +168,7 @@ The default method is phenotype-based (using \code{type = "points"}) and episode
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
example_isolates[first_isolate(), ]
example_isolates[first_isolate(info = TRUE), ]
\donttest{
# get all first Gram-negatives
example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
@ -176,7 +176,7 @@ example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
if (require("dplyr")) {
# filter on first isolates using dplyr:
example_isolates \%>\%
filter(first_isolate())
filter(first_isolate(info = TRUE))
}
if (require("dplyr")) {
# short-hand version:
@ -187,7 +187,7 @@ if (require("dplyr")) {
# flag the first isolates per group:
example_isolates \%>\%
group_by(ward) \%>\%
mutate(first = first_isolate()) \%>\%
mutate(first = first_isolate(info = TRUE)) \%>\%
select(ward, date, patient, mo, first)
}
}