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calculate LOS based on time to last measurement of e.g. heart rate #6

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calculate LOS based on time to last measurement of e.g. heart rate #6

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19 changes: 16 additions & 3 deletions R/gen.R
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Original file line number Diff line number Diff line change
Expand Up @@ -163,15 +163,28 @@ gen_los.icu <- function(dt, var.name="los.icu",
icu.dod.date="NIHR_HIC_ICU_0042",
icu.dod.time="NIHR_HIC_ICU_0043",
id.name="id",
sim=TRUE) {
sim=TRUE,
sim.var="NIHR_HIC_ICU_0108") {
'
Generate ICU length of stay (hours)
If sim: do so "simply", using time to last measurement, optionally (if sim.var is not NULL) to last sim.var measurement (default HR)
Else: use admission and discharge time, or admission and date/time of death, depending on discharge status.
'

if (sim) {
# check id and time available
assert_that(all(sapply(c(id.name, "time"), function(x) x %in% names(dt))))
dt[, (var.name) := max(time, na.rm=TRUE), by=id.name]
if (is.null(sim.var)){
# just take max time from any record (WARNING: measurements can be recorded after discharge)
dt[, (var.name) := max(time, na.rm=TRUE), by=id.name]
} else {
# time is taken from between first and last measurement of sim.var (by default, heart rate)
assert_that(sim.var %in% names(dt))
dt[!is.na(get(sim.var)), (var.name) := max(time) - min(time), by=id.name]
# need to record var.name even when sim.var is NA
# WARNING: if a patient never has a recorded sim.var, this will produce NA for their LOS
dt[, (var.name) := mean(get(var.name), na.rm=TRUE), by=id.name]
}
} else {
# if alive on discharge, use 0412 for discharge time
dt[get(icu.dis)=='A', (var.name) := time_length(ymd_hms(get(icu.dc.ts)) - ymd_hms(get(icu.in.ts)), unit='hours')]
Expand All @@ -181,7 +194,7 @@ gen_los.icu <- function(dt, var.name="los.icu",
# need to check BSDTP, then use either DOD/TOD (as above) or DDBSD/TDBSD
}
}

#' @export
gen_los.hosp <- function(dt, var.name="los.hosp",
hosp.in.dt="NIHR_HIC_ICU_0032",
Expand Down