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

Usage

estimateSingleEventSurvival(
  cdm,
  targetCohortTable,
  targetCohortId = NULL,
  outcomeCohortTable,
  outcomeCohortId = NULL,
  outcomeDateVariable = "cohort_start_date",
  outcomeWashout = Inf,
  censorOnCohortExit = FALSE,
  censorOnDate = NULL,
  followUpDays = Inf,
  strata = NULL,
  eventGap = 30,
  estimateGap = 1,
  restrictedMeanFollowUp = NULL,
  minimumSurvivalDays = 1,
  minCellCount = 5,
  returnParticipants = FALSE
)

Arguments

cdm: CDM reference
targetCohortTable: targetCohortTable
targetCohortId: targetCohortId
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
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.
returnParticipants: Either TRUE or FALSE. If TRUE, references to participants from the analysis will be returned allowing for further analysis.

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 <- estimateSingleEventSurvival(
  cdm = cdm,
  targetCohortTable = "mgus_diagnosis",
  targetCohortId = 1,
  outcomeCohortTable = "death_cohort",
  outcomeCohortId = 1,
  eventGap = 7
)
#> - Getting survival for target cohort 'mgus_diagnosis' and outcome cohort
#> 'death_cohort'
#> Getting overall estimates
# }