estimateCompetingRiskSurvival {CohortSurvival} | R Documentation |
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,
targetCohortId = NULL,
outcomeCohortTable,
outcomeCohortId = NULL,
outcomeDateVariable = "cohort_start_date",
outcomeWashout = Inf,
competingOutcomeCohortTable,
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,
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 |
competingOutcomeCohortTable |
The competing outcome cohort table of interest. |
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. |
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
cdm <- mockMGUS2cdm()
surv <- estimateCompetingRiskSurvival(
cdm = cdm,
targetCohortTable = "mgus_diagnosis",
targetCohortId = 1,
outcomeCohortTable = "progression",
outcomeCohortId = 1,
competingOutcomeCohortTable = "death_cohort",
competingOutcomeCohortId = 1,
eventGap = 7
)