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,
  minCellCount = 5
)

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
minCellCount: The minimum number of events to reported, below which results will be obscured. If 0, all results will be reported.

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

# \donttest{
cdm <- mockMGUS2cdm()
surv <- estimateCompetingRiskSurvival(
  cdm = cdm,
  targetCohortTable = "mgus_diagnosis",
  targetCohortId = 1,
  outcomeCohortTable = "progression",
  outcomeCohortId = 1,
  competingOutcomeCohortTable = "death_cohort",
  competingOutcomeCohortId = 1,
  eventGap = 7
)
#> - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort
#> 'progression' with competing outcome cohort 'death_cohort'
#> Getting overall estimates
# }