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, the created new columns (field) will be collapsed to a character vector separated by `;` to account for multiple values per person.
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)
library(omopgenerics, warn.conflicts = TRUE)
library(dplyr, warn.conflicts = TRUE)

cdm <- mockPatientProfiles(source = "duckdb")

concept <- 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_
) |>
  mutate(concept_name = paste0("concept: ", .data$concept_id))
cdm <- insertTable(cdm, "concept", concept)

cdm$cohort1 |>
  addConceptIntersectField(
    conceptSet = list("acetaminophen" = 1125315),
    field = "drug_type_concept_id"
  )
#> Warning: ! `codelist` casted to integers.
#> # Source:   table<og_071_1757798507> [?? x 5]
#> # Database: DuckDB 1.3.3-dev231 [unknown@Linux 6.11.0-1018-azure:R 4.5.1/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    2          2 1958-12-30        1959-08-13     
#>  2                    3          4 1923-08-12        1927-07-17     
#>  3                    2          3 1941-01-02        1941-10-30     
#>  4                    2          5 1926-04-05        1935-12-06     
#>  5                    1          8 1985-10-20        1992-01-16     
#>  6                    2          9 1925-11-26        1952-08-02     
#>  7                    2          6 1941-12-23        1949-02-18     
#>  8                    2         10 1930-10-30        1945-08-03     
#>  9                    3          7 1929-06-16        1944-07-01     
#> 10                    1          1 1930-07-27        1938-12-12     
#> # ℹ 1 more variable: drug_type_concept_id_acetaminophen_0_to_inf <chr>

# }