estimateCompetingRiskSurvival: Estimate survival for a given event and competing risk of...

In CohortSurvival: Estimate Survival from Common Data Model Cohorts

Estimate survival for a given event and competing risk of interest using cohorts in the OMOP Common Data Model

Description

Estimate survival for a given event and competing risk of interest using cohorts in the OMOP Common Data Model

Usage

estimateCompetingRiskSurvival(
  cdm,
  targetCohortTable,
  outcomeCohortTable,
  competingOutcomeCohortTable,
  targetCohortId = NULL,
  outcomeCohortId = NULL,
  outcomeDateVariable = "cohort_start_date",
  outcomeWashout = Inf,
  competingOutcomeCohortId = NULL,
  competingOutcomeDateVariable = "cohort_start_date",
  competingOutcomeWashout = Inf,
  censorOnCohortExit = FALSE,
  censorOnDate = NULL,
  followUpDays = Inf,
  strata = NULL,
  eventGap = 30,
  estimateGap = 1,
  restrictedMeanFollowUp = NULL,
  minimumSurvivalDays = 1
)

Arguments

cdm	CDM reference
targetCohortTable	targetCohortTable
outcomeCohortTable	The outcome cohort table of interest.
competingOutcomeCohortTable	The competing outcome cohort table of interest.
targetCohortId	targetCohortId
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
competingOutcomeCohortId	ID of event cohorts to include. Only one competing 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
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)
strata	strata
eventGap	Days between time points for which to report survival events, which are grouped into the specified intervals.
estimateGap	Days between time points for which to report survival estimates. First day will be day zero with risk estimates provided for times up to the end of follow-up, with a gap in days equivalent to eventGap.
restrictedMeanFollowUp	number of days of follow-up to take into account when calculating restricted mean for all cohorts
minimumSurvivalDays	Minimum number of days required for the main cohort to have survived

Value

tibble with survival information for desired cohort, including: time, people at risk, survival probability, cumulative incidence, 95 CIs, strata and outcome. A tibble with the number of events is outputted as an attribute of the output

Examples

cdm <- mockMGUS2cdm()
surv <- estimateCompetingRiskSurvival(
  cdm = cdm,
  targetCohortTable = "mgus_diagnosis",
  targetCohortId = 1,
  outcomeCohortTable = "progression",
  outcomeCohortId = 1,
  competingOutcomeCohortTable = "death_cohort",
  competingOutcomeCohortId = 1,
  eventGap = 7
)

CohortSurvival documentation built on June 16, 2025, 5:10 p.m.