It creates columns to indicate overlap information between a table and a concept

Usage

addConceptIntersect(
  x,
  conceptSet,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  window = list(c(0, Inf)),
  targetStartDate = "event_start_date",
  targetEndDate = "event_end_date",
  order = "first",
  value = c("flag", "count", "date", "days"),
  nameStyle = "{value}_{concept_name}_{window_name}"
)

Arguments

x: Table with individuals in the cdm.
conceptSet: Concept set list.
indexDate: Variable in x that contains the date to compute the intersection.
censorDate: whether to censor overlap events at a date column of x
window: window to consider events in.
targetStartDate: Event start date to use for the intersection.
targetEndDate: Event end date to use for the intersection.
order: last or first date to use for date/days calculations.
value: Choices between c("value", "flag", "days", "date").
nameStyle: naming of the added column or columns, should include required parameters.

Value

table with added columns with overlap information

Examples

# \donttest{
library(PatientProfiles)
cdm <- mockPatientProfiles()
 concept <- dplyr::tibble(
  concept_id = c(1125315),
  domain_id = "Drug",
  vocabulary_id = NA_character_,
  concept_class_id = "Ingredient",
  standard_concept = "S",
  concept_code = NA_character_,
  valid_start_date = as.Date("1900-01-01"),
  valid_end_date = as.Date("2099-01-01"),
  invalid_reason = NA_character_
 ) %>%
 dplyr::mutate(concept_name = paste0("concept: ", .data$concept_id))
 cdm <- CDMConnector::insertTable(cdm, "concept", concept)
result <- cdm$cohort1 %>%
 addConceptIntersect(
  conceptSet = list("acetaminophen"=1125315)
  ) %>%
 dplyr::collect()
#> Warning: `addConceptIntersect()` was deprecated in PatientProfiles 0.6.0.
#> please use the specific functions instead:
#> • addConceptIntersectFlag()
#> • addConceptIntersectCount()
#> • addConceptIntersectDate()
#> • addConceptIntersectDays()
 CDMConnector::cdmDisconnect(cdm = cdm)
 # }