summariseLargeScaleCharacteristics {CohortCharacteristics}

This function is used to summarise the large scale characteristics of a cohort table

Description

This function is used to summarise the large scale characteristics of a cohort table

Usage

summariseLargeScaleCharacteristics(
  cohort,
  strata = list(),
  window = list(c(-Inf, -366), c(-365, -31), c(-30, -1), c(0, 0), c(1, 30), c(31, 365),
    c(366, Inf)),
  eventInWindow = NULL,
  episodeInWindow = NULL,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  includeSource = FALSE,
  minimumFrequency = 0.005,
  excludedCodes = c(0)
)

Arguments

cohort

The cohort to characterise.

strata

Stratification list.

window

Temporal windows that we want to characterize.

eventInWindow

Tables to characterise the events in the window. eventInWindow must be provided if episodeInWindow is not specified.

episodeInWindow

Tables to characterise the episodes in the window. episodeInWindow must be provided if eventInWindow is not specified.

indexDate

Variable in x that contains the date to compute the intersection.

censorDate

whether to censor overlap events at a specific date or a column date of x

includeSource

Whether to include source concepts.

minimumFrequency

Minimum frequency covariates to report.

excludedCodes

Codes excluded.

Value

The output of this function is a 'ResultSummary' containing the relevant information.

Examples

library(CohortCharacteristics)
cdm <- CohortCharacteristics::mockCohortCharacteristics()

concept <- dplyr::tibble(
  concept_id = c(1125315, 1503328, 1516978, 317009, 378253, 4266367),
  domain_id = NA_character_,
  vocabulary_id = NA_character_,
  concept_class_id = NA_character_,
  concept_code = NA_character_,
  valid_start_date = as.Date("1900-01-01"),
  valid_end_date = as.Date("2099-01-01")
) |>
  dplyr::mutate(concept_name = paste0("concept: ", .data$concept_id))
cdm <- CDMConnector::insertTable(cdm, "concept", concept)
results <- cdm$cohort2 |>
  summariseLargeScaleCharacteristics(
    episodeInWindow = c("condition_occurrence"),
    minimumFrequency = 0
  )
mockDisconnect(cdm = cdm)