Add competing risk survival information to a cohort table
addCompetingRiskCohortSurvival.Rd
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()
crsurvivaldata <- cdm$mgus_diagnosis %>%
addCompetingRiskCohortSurvival(
cdm = cdm,
outcomeCohortTable = "progression",
outcomeCohortId = 1,
competingOutcomeCohortTable = "death_cohort",
competingOutcomeCohortId = 1
)
# }