generic 1d variable definitions for cchic (depends on ccfun library)

cchic-common1d.R

#  ==================================
#  = Define generic study variables =
#  ==================================
find_NHIC("shortName", "dead")

# Mortality
gen_mortality(wdt, "mort.icu", "NIHR_HIC_ICU_0097")
table(unique(wdt[,.(id,mort.icu)])$mort.icu)

gen_mortality(wdt, "mort.hosp", "NIHR_HIC_ICU_0095")
table(unique(wdt[,.(id,mort.hosp)])$mort.hosp)

# Sex
names(wdt)
lookfor(NIHR_HIC_ICU_0093, wdt)
wdt[tolower(NIHR_HIC_ICU_0093) == "m", `:=`(male, TRUE)]
wdt[tolower(NIHR_HIC_ICU_0093) == "f", `:=`(male, FALSE)]
table(wdt$male)

# Age
# - [ ] TODO(2016-11-30): fix, convert back to calc when AGE is replaced with DoB
# gen_age(wdt, sim=!cconfig$IDHS)
# wdt[, .(NIHR_HIC_ICU_0411, NIHR_HIC_ICU_0033)]
# gen_age(wdt, sim=FALSE)
wdt[, AGE:= as.double(AGE)]
summary(wdt$AGE)

# Unit LOS
find_NHIC("shortName","dt_icu_admit")
find_NHIC("shortName","dt_icu_dc")

library(lubridate)
wdt[, los.icu := ymd_hms(NIHR_HIC_ICU_0412)-ymd_hms(NIHR_HIC_ICU_0411)]
# summary(as.numeric(wdt$los.icu)/(60*24))

wdt[, los.icu.pre := as.Date(ymd_hms(NIHR_HIC_ICU_0412))-ymd(NIHR_HIC_ICU_0032)]
wdt[, los.icu.post := ymd(NIHR_HIC_ICU_0406)-as.Date(ymd_hms(NIHR_HIC_ICU_0412))]

# Hospital LOS
find_NHIC("shortName","dt_hosp_admit")
find_NHIC("shortName","dt_hosp_dc")

wdt[, los.hosp := ymd(NIHR_HIC_ICU_0406)-ymd(NIHR_HIC_ICU_0032)]
wdt[,.(NIHR_HIC_ICU_0032, NIHR_HIC_ICU_0406, los.hosp)]

# Report los.hosp in days
summary(as.numeric(wdt$los.hosp))


# Admission category
find_NHIC("shortName", "adm_type")
find_NHIC("shortName", "loca_in")

gen_admx.cat(wdt)
table(unique(wdt[,.(id,adm.cat)])$adm.cat)

# Diagnostic coding
find_NHIC("shortName", "diag_admx1")
wdt <- parse.icnarc.code(wdt, "NIHR_HIC_ICU_0399")
wdt[, lapply(.SD, head, 1), by=id, .SDcols=c("condition", "dc.2")][order(dc.2)]
table(unique(wdt[,.(id,dc.2)])$dc.2)

#  ========================
#  = Past medical history =
#  ========================
find_NHIC("shortName", "pmhx")
find_NHIC("shortName", "pmhx_depend")
# Remove dependency prior to admission from PMHx
f <- function(y,v) grepl(v, y)
which_NHIC("shortName", "pmhx", f)
pmhx.cols <- setdiff(which_NHIC("shortName", "pmhx", f), c("NIHR_HIC_ICU_0055", "pmhx.sum"))
pmhx.cols
sapply(pmhx.cols, function(x) x %in% names(wdt))

gen_pmhx.sum(wdt, pmhx.cols)
table(unique(wdt[,.(id,pmhx.sum)])$pmhx.sum)