Collect population incidence estimates

Usage

estimateIncidence(
  cdm,
  denominatorTable,
  outcomeTable,
  denominatorCohortId = NULL,
  outcomeCohortId = NULL,
  interval = "years",
  completeDatabaseIntervals = TRUE,
  outcomeWashout = Inf,
  repeatedEvents = FALSE,
  minCellCount = 5,
  strata = list(),
  includeOverallStrata = TRUE,
  returnParticipants = FALSE
)

Arguments

cdm: A CDM reference object
denominatorTable: A cohort table with a set of denominator cohorts (for example, created using the generateDenominatorCohortSet() function).
outcomeTable: A cohort table in the cdm reference containing a set of outcome cohorts.
denominatorCohortId: The cohort definition ids of the denominator cohorts of interest. If NULL all cohorts will be considered in the analysis.
outcomeCohortId: The cohort definition ids of the outcome cohorts of interest. If NULL all cohorts will be considered in the analysis.
interval: Time intervals over which incidence is estimated. Can be "weeks", "months", "quarters", "years", or "overall". ISO weeks will be used for weeks. Calendar months, quarters, or years can be used, or an overall estimate for the entire time period observed (from earliest cohort start to last cohort end) can also be estimated. If more than one option is chosen then results will be estimated for each chosen interval.
completeDatabaseIntervals: TRUE/ FALSE. Where TRUE, incidence will only be estimated for those intervals where the denominator cohort captures all the interval.
outcomeWashout: The number of days used for a 'washout' period between the end of one outcome and an individual starting to contribute time at risk. If Inf, no time can be contributed after an event has occurred (whether during the study period or if occurring beforehand).
repeatedEvents: TRUE/ FALSE. If TRUE, an individual will be able to contribute multiple events during the study period (time while they are present in an outcome cohort and any subsequent washout will be excluded). If FALSE, an individual will only contribute time up to their first event during the study period.
minCellCount: The minimum number of events to reported, below which results will be obscured. If 0, all results will be reported.
strata: Variables added to the denominator cohort table for which to stratify estimates.
includeOverallStrata: Whether to include an overall result as well as strata specific results (when strata has been specified).
returnParticipants: Either TRUE or FALSE. If TRUE references to participants from the analysis will be returned allowing for further analysis. Note, if using permanent tables and returnParticipants is TRUE, one table per analysis will be kept in the cdm write schema.

Value

Incidence estimates

Examples

# \donttest{
cdm <- mockIncidencePrevalenceRef(sampleSize = 1000)
cdm <- generateDenominatorCohortSet(
  cdm = cdm, name = "denominator",
  cohortDateRange = c(as.Date("2008-01-01"), as.Date("2018-01-01"))
)
#> ℹ Creating denominator cohorts
#> ✔ Cohorts created in 0 min and 2 sec
inc <- estimateIncidence(
  cdm = cdm,
  denominatorTable = "denominator",
  outcomeTable = "outcome"
)
#> Getting incidence for analysis 1 of 1
#> Overall time taken: 0 mins and 1 secs
# }