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

Usage

addConceptIntersectFlag(
  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

The original table (x) with one added column per intersection with the desired conceptSet in a specific window. One column will be created for each combination of window and conceptSet. The value of the column can either be: 1 to indicate presence of the intersection, 0 to indicate no intersection or NA if the individual is not in observation at any time of the window.

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 |>
  addConceptIntersectFlag(conceptSet = list("acetaminophen" = 1125315))
#> Warning: ! `codelist` casted to integers.
#> # Source:   table<og_097_1775495271> [?? x 5]
#> # Database: DuckDB 1.5.1 [unknown@Linux 6.17.0-1008-azure:R 4.5.3/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    1          4 1958-09-09        1981-10-18     
#>  2                    2          6 2014-02-11        2016-02-11     
#>  3                    2         10 1966-03-04        1970-12-07     
#>  4                    1          5 1965-09-27        1973-09-01     
#>  5                    3          8 1958-12-18        1962-10-05     
#>  6                    1          7 1947-10-01        1950-09-11     
#>  7                    1          1 1999-09-13        2000-01-27     
#>  8                    2          3 1952-02-08        1957-10-15     
#>  9                    1          2 1975-10-19        1976-04-27     
#> 10                    3          9 1975-01-12        1987-06-18     
#> # ℹ 1 more variable: acetaminophen_0_to_inf <dbl>

# }