Add survival information to a cohort table

Add survival information to a cohort table

Usage

addCohortSurvival(
  x,
  cdm,
  outcomeCohortTable,
  outcomeCohortId = 1,
  outcomeDateVariable = "cohort_start_date",
  outcomeWashout = Inf,
  censorOnCohortExit = FALSE,
  censorOnDate = NULL,
  followUpDays = Inf,
  name = NULL
)

Arguments

x

cohort table to add survival information

cdm

CDM reference

outcomeCohortTable

The outcome cohort table of interest.

outcomeCohortId

ID of event cohorts to include. Only one outcome (and so one ID) can be considered. It can either be a cohort_definition_id value or a cohort_name.

outcomeDateVariable

Variable containing date of outcome event

outcomeWashout

Washout time in days for the outcome. If an individual has an outcome during the washout period, status and time will be set to NA

censorOnCohortExit

If TRUE, an individual's follow up will be censored at their cohort exit

censorOnDate

if not NULL, an individual's follow up will be censored at the given date

followUpDays

Number of days to follow up individuals (lower bound 1, upper bound Inf)

name

Name of the new table, if NULL a temporary table is returned.

Value

Two additional columns will be added to x. The "time" column will contain number of days to censoring. The "status" column will indicate whether the patient had the event (value: 1), or did not have the event (value: 0)

Examples

# \donttest{

cdm <- mockMGUS2cdm()
#> Creating a new cdm
#> Uploading table person (1384 rows) - [1/7]
#> Uploading table observation_period (1384 rows) - [2/7]
#> Uploading table visit_occurrence (1 rows) - [3/7]
#> Uploading table death_cohort (963 rows) - [4/7]
#> Uploading table mgus_diagnosis (1384 rows) - [5/7]
#> Uploading table progression (115 rows) - [6/7]
#> Uploading table progression_type (230 rows) - [7/7]
cdm$mgus_diagnosis <- cdm$mgus_diagnosis |>
  addCohortSurvival(
    cdm = cdm,
    outcomeCohortTable = "death_cohort",
    outcomeCohortId = 1
  )
  # }