Calculates death from SoS data

Source: R/create_deathvar.R

[Experimental]

Calculates cause-specific death (and optionally time to death) from codes in the Cause of Death Registry.

create_deathvar(
  cohortdata,
  indexdate,
  deathdate,
  censdate,
  calctimetodeath = FALSE,
  name,
  orsakkod,
  orsakvar = ULORSAK,
  valsclass = "num",
  meta_reg = "Cause of Death",
  meta_pos,
  warnings = TRUE
)

Arguments

cohortdata

Data containing the cohort.

indexdate

Index date for the patient (usually date of admission or discharge entered into SwedeHF). Must be given if calctimetodeath = TRUE.

deathdate

Vector of death dates.

censdate

Vector of dates. Deaths are allowed up until this day (usually date of death or end follow-up).

calctimetodeath

Should time to death be calculated? Default is FALSE.

name

Name of resulting variable (prefix is sos_out_death).

orsakkod

String of icd codes as a regular expression defining the cause specific death. Should preferably start with blank space " ".

orsakvar

Column where diakod is found. All codes should preferably start with blank space " ". Default is ULORSAK.

valsclass

optional argument specifying the class of the comorbidities/outcomes. Allowed values are "num" (numeric: 1, 0), "char" (character: "Yes", "No"), "fac" (factor: "Yes", "No"). Default is "num".

meta_reg

Optional argument specifying registries used. Printed in metadatatable. Default is "Cause of Death".

meta_pos

Optional argument specifying positions used to search for deaths. Printed in metadatatable.

warnings

Should warnings be printed. Default is FALSE.

Value

dataset with column containing cause-specifc death. Also dataset metaout that writes directly to global enviroment with information on constructed variables.

Examples


dors_data <- prep_sosdata(dors_data, registry = "dors", impute = FALSE)
rs_data <- dplyr::left_join(rs_data, dors_data, by = "id")

rs_data <- create_deathvar(
  cohortdata = rs_data,
  name = "cv",
  orsakkod = " I"
)