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

Usage

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

Arguments

x: A table containing individuals in a CDM reference.
conceptSet: A named list of concept sets.
indexDate: Name of a date column in x, or a single date to use for all rows, used as the reference date.
censorDate: Date or name of a date column in x on which to censor follow-up. If NULL, no censoring is applied.
window: Window or windows of time relative to indexDate to consider.
targetDate: Name or names of date columns in the target tables to use for the intersection.
order: Which record to use when multiple records occur in a window: "first" or "last".
inObservation: If TRUE, only records that occur during an observation period are considered.
nameStyle: Naming pattern for the added column or columns. It should include the required formatting variables. If more than one tableName is provided, it must include {table_name}.
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)
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 |>
  addConceptIntersectDate(conceptSet = list("acetaminophen" = 1125315))
#> Warning: ! `codelist` cast to integers.
#> # A query:  ?? x 5
#> # Database: DuckDB 1.5.4 [unknown@Linux 6.17.0-1020-azure:R 4.6.1/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    1          9 1951-08-30        1952-02-18     
#>  2                    1          6 1967-11-29        1977-06-16     
#>  3                    2          1 1958-10-17        1973-07-23     
#>  4                    2          5 1981-05-13        1983-07-18     
#>  5                    1          3 1932-01-04        1932-11-28     
#>  6                    3          8 1904-06-08        1927-08-15     
#>  7                    2          2 1962-11-17        1964-09-24     
#>  8                    3         10 1930-04-29        1942-09-13     
#>  9                    2          7 1961-02-23        1965-04-15     
#> 10                    1          4 1951-06-14        1951-07-30     
#> # ℹ 1 more variable: acetaminophen_0_to_inf <date>

# }