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dr. M.S. (Matthijs) Berends
2023-03-11 14:43:31 +01:00
parent 262598b8d7
commit 45e840c02f
4 changed files with 16 additions and 11 deletions
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8
R/get_episode.R
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@ -27,7 +27,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Determine (Clinical or Epidemic) Episodes
#' Determine Clinical or Epidemic Episodes
#'
#' These functions determine which items in a vector can be considered (the start of) a new episode. 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. Both absolute and relative episode determination are supported.
#' @param x vector of dates (class `Date` or `POSIXt`), will be sorted internally to determine episodes
@ -71,7 +71,7 @@
#'
#' The [get_episode()] function returns the index number of the episode, so all cases/patients/isolates in the first episode will have the number 1, all cases/patients/isolates in the second episode will have the number 2, etc.
#'
#' The [is_new_episode()] function returns `TRUE` for every new [get_episode()] index, and is thus equal to `!duplicated(get_episode(...))`.
#' The [is_new_episode()] function on the other hand, returns `TRUE` for every new [get_episode()] index.
#'
#' To specify, when setting `episode_days = 365` (using method 1 as explained above), this is how the two functions differ:
#'
@ -214,8 +214,8 @@ is_new_episode <- function(x, episode_days = NULL, case_free_days = NULL, ...) {
}
exec_episode <- function(x, episode_days, case_free_days, ...) {
stop_if((is.null(episode_days) && is.null(case_free_days)) || (!is.null(episode_days) && !is.null(case_free_days)),
"either `episode_days` or `case_free_days` must be set.",
stop_if_not(is.null(episode_days) || is.null(case_free_days),
"either argument `episode_days` or argument `case_free_days` must be set.",
call = -2
)