Add competing risk survival information to a cohort table

Usage

addCompetingRiskCohortSurvival(
  x,
  cdm,
  outcomeCohortTable,
  outcomeCohortId = 1,
  outcomeDateVariable = "cohort_start_date",
  outcomeWashout = Inf,
  outcomeCensorOnCohortExit = FALSE,
  outcomeCensorOnDate = NULL,
  outcomeFollowUpDays = Inf,
  competingOutcomeCohortTable,
  competingOutcomeCohortId = 1,
  competingOutcomeDateVariable = "cohort_start_date",
  competingOutcomeWashout = Inf,
  competingOutcomeCensorOnCohortExit = FALSE,
  competingOutcomeCensorOnDate = NULL,
  competingOutcomeFollowUpDays = Inf
)

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.
outcomeDateVariable: Variable containing date of outcome event
outcomeWashout: Washout time in days for the outcome
outcomeCensorOnCohortExit: If TRUE, an individual's follow up will be censored at their cohort exit
outcomeCensorOnDate: if not NULL, an individual's follow up will be censored at the given date
outcomeFollowUpDays: Number of days to follow up individuals (lower bound 1, upper bound Inf)
competingOutcomeCohortTable: The outcome cohort table of interest.
competingOutcomeCohortId: ID of event cohorts to include. Only one outcome (and so one ID) can be considered.
competingOutcomeDateVariable: Variable containing date of competing outcome event
competingOutcomeWashout: Washout time in days for the competing outcome
competingOutcomeCensorOnCohortExit: If TRUE, an individual's follow up will be censored at their cohort exit
competingOutcomeCensorOnDate: if not NULL, an individual's follow up will be censored at the given date
competingOutcomeFollowUpDays: Number of days to follow up individuals (lower bound 1, upper bound Inf)

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 outcome event (value: 1), competing event (value:2) or did not have the event/is censored (value: 0)

Examples

# \donttest{

cdm <- mockMGUS2cdm()
#> ■■■■■■■■■■■■■■■■■■■■■■■■■         80% | ETA:  1s
crsurvivaldata <- cdm$mgus_diagnosis %>%
  addCompetingRiskCohortSurvival(
    cdm = cdm,
    outcomeCohortTable = "progression",
    outcomeCohortId = 1,
    competingOutcomeCohortTable = "death_cohort",
    competingOutcomeCohortId = 1
  )
  # }