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revert back to pre-antibiogram

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-09 13:07:39 +01:00
parent aa48c6bf53
commit 1a0dc4bf46
53 changed files with 984 additions and 1996 deletions
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10
R/get_episode.R
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@ -109,7 +109,7 @@
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,
@ -127,10 +127,10 @@ is_new_episode <- function(x, episode_days, ...) {
exec_episode <- function(x, type, 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
episode_seconds <- episode_days * 60 * 60 * 24
if (length(x) == 1) { # this will also match 1 NA, which is fine
return(1)
} else if (length(x) == 2 && !all(is.na(x))) {
@ -140,7 +140,7 @@ exec_episode <- function(x, type, episode_days, ...) {
return(c(1, 1))
}
}
# we asked on StackOverflow:
# https://stackoverflow.com/questions/42122245/filter-one-row-every-year
run_episodes <- function(x, episode_seconds) {
@ -157,7 +157,7 @@ exec_episode <- function(x, type, episode_days, ...) {
}
indices
}
ord <- order(x)
out <- run_episodes(x[ord], episode_seconds)[order(ord)]
out[is.na(x) & ord != 1] <- NA # every NA expect for the first must remain NA