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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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16
R/get_episode.R
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@@ -29,7 +29,7 @@
#' Determine (New) Episodes for Patients
#'
#' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns values `TRUE`/`FALSE` for where [get_episode()] returns 1, and is thus equal to `get_episode(...) == 1`.
#' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns `TRUE` for every new [get_episode()] index, and is thus equal to `!duplicated(get_episode(...))`.
#' @param x vector of dates (class `Date` or `POSIXt`), will be sorted internally to determine episodes
#' @param episode_days required episode length in days, can also be less than a day or `Inf`, see *Details*
#' @param ... ignored, only in place to allow future extensions
@@ -83,7 +83,8 @@
#' patient,
#' new_index = get_episode(date, 60),
#' new_logical = is_new_episode(date, 60)
#' )
#' ) %>%
#' arrange(patient, ward, date)
#' }
#'
#' if (require("dplyr")) {
@@ -109,12 +110,7 @@
get_episode <- function(x, episode_days, ...) {
meet_criteria(x, allow_class = c("Date", "POSIXt"), allow_NA = TRUE)
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
exec_episode(
x = x,
episode_days = episode_days,
... = ...
)
exec_episode(x, episode_days, ...)
}
#' @rdname get_episode
@@ -122,10 +118,10 @@ get_episode <- function(x, episode_days, ...) {
is_new_episode <- function(x, episode_days, ...) {
meet_criteria(x, allow_class = c("Date", "POSIXt"), allow_NA = TRUE)
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
get_episode(x, episode_days, ...) == 1
!duplicated(exec_episode(x, episode_days, ...))
}
exec_episode <- function(x, type, episode_days, ...) {
exec_episode <- function(x, episode_days, ...) {
x <- as.double(as.POSIXct(x)) # as.POSIXct() required for Date classes
# since x is now in seconds, get seconds from episode_days as well