It creates column to indicate the count overlap information between a table and a concept

Usage

addConceptIntersectCount(
  x,
  conceptSet,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  window = list(c(0, Inf)),
  targetStartDate = "event_start_date",
  targetEndDate = "event_end_date",
  inObservation = TRUE,
  nameStyle = "{concept_name}_{window_name}",
  name = NULL
)

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.
inObservation: If TRUE only records inside an observation period will be considered.
nameStyle: naming of the added column or columns, should include required parameters.
name: Name of the new table, if NULL a temporary table is returned.

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)

cdm$cohort1 |>
  addConceptIntersectCount(conceptSet = list("acetaminophen" = 1125315))
#> Warning: ! `codelist` contains numeric values, they are casted to integers.
#> # Source:   table<og_045_1734613797> [?? x 5]
#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    3          8 1947-04-05        1963-12-09     
#>  2                    3          3 1978-03-12        2004-08-10     
#>  3                    3         10 1948-06-03        1948-06-15     
#>  4                    2          2 1928-08-04        1931-10-26     
#>  5                    2          5 1915-02-28        1923-06-06     
#>  6                    1          6 1924-09-21        1931-05-01     
#>  7                    2          9 1914-10-01        1926-03-23     
#>  8                    2          7 1997-11-09        1998-11-12     
#>  9                    2          1 1917-11-19        1942-07-09     
#> 10                    1          4 1997-06-13        1999-04-12     
#> # ℹ 1 more variable: acetaminophen_0_to_inf <dbl>

mockDisconnect(cdm = cdm)
# }