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(v3.0.1.9059) Fix WISCA in vignette

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dr. M.S. (Matthijs) Berends
2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
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42
man/first_isolate.Rd
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@@ -5,18 +5,38 @@
\alias{filter_first_isolate}
\title{Determine First Isolates}
\usage{
first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, col_testcode = NULL, col_specimen = NULL,
col_icu = NULL, col_keyantimicrobials = NULL, episode_days = 365,
testcodes_exclude = NULL, icu_exclude = FALSE, specimen_group = NULL,
type = "points", method = c("phenotype-based", "episode-based",
"patient-based", "isolate-based"), ignore_I = TRUE, points_threshold = 2,
info = interactive(), include_unknown = FALSE,
include_untested_sir = TRUE, ...)
first_isolate(
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
col_testcode = NULL,
col_specimen = NULL,
col_icu = NULL,
col_keyantimicrobials = NULL,
episode_days = 365,
testcodes_exclude = NULL,
icu_exclude = FALSE,
specimen_group = NULL,
type = "points",
method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
ignore_I = TRUE,
points_threshold = 2,
info = interactive(),
include_unknown = FALSE,
include_untested_sir = TRUE,
...
)
filter_first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, episode_days = 365, method = c("phenotype-based",
"episode-based", "patient-based", "isolate-based"), ...)
filter_first_isolate(
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
episode_days = 365,
method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
...
)
}
\arguments{
\item{x}{A \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.}