It adds a custom column (field) from the intersection with a certain table subsetted by concept id. In general it is used to add the first value of a certain measurement.

Usage

addConceptIntersectField(
  x,
  conceptSet,
  field,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  window = list(c(0, Inf)),
  targetDate = "event_start_date",
  order = "first",
  inObservation = TRUE,
  allowDuplicates = FALSE,
  nameStyle = "{field}_{concept_name}_{window_name}",
  name = NULL
)

Arguments

x: Table with individuals in the cdm.
conceptSet: Concept set list.
field: Column in the standard omop table that you want to add.
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.
targetDate: Event date to use for the intersection.
order: 'last' or 'first' to refer to which event consider if multiple events are present in the same window.
inObservation: If TRUE only records inside an observation period will be considered.
allowDuplicates: Whether to allow multiple records with same conceptSet, person_id and targetDate. If switched to TRUE, it can have a different and unpredictable behavior depending on the cdm_source.
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 the `field` value obtained from the intersection

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 |>
  addConceptIntersectField(
    conceptSet = list("acetaminophen" = 1125315),
    field = "drug_type_concept_id"
  )
#> Warning: ! `codelist` casted to integers.
#> # Source:   table<og_072_1740755690> [?? x 5]
#> # Database: DuckDB v1.2.0 [unknown@Linux 6.8.0-1021-azure:R 4.4.2/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    1          7 1968-06-16        1976-09-21     
#>  2                    2          6 1988-02-19        1998-02-14     
#>  3                    2         10 1956-12-14        1957-08-29     
#>  4                    1          8 1929-08-04        1935-12-22     
#>  5                    3          3 1923-01-15        1955-01-28     
#>  6                    3          4 1978-03-12        1979-09-05     
#>  7                    3          5 1958-04-10        1966-02-17     
#>  8                    3          2 1963-10-21        1977-05-08     
#>  9                    2          9 1937-05-15        1946-03-29     
#> 10                    2          1 1952-10-19        1971-07-29     
#> # ℹ 1 more variable: drug_type_concept_id_acetaminophen_0_to_inf <int>

mockDisconnect(cdm = cdm)
# }