
It creates column to indicate the date overlap information between a table and a concept
Source:R/addConceptIntersect.R
addConceptIntersectDate.Rd
It creates column to indicate the date overlap information between a table and a concept
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.
- targetDate
Event date to use for the intersection.
- order
last or first date to use for date/days calculations.
- 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.
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` casted to integers.
#> # Source: table<og_051_1757798500> [?? 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 3 6 1958-10-23 1964-02-11
#> 2 1 7 1931-05-18 1957-09-03
#> 3 1 5 1949-10-04 1951-10-06
#> 4 2 8 1966-03-29 1970-05-20
#> 5 3 10 1923-03-21 1928-04-24
#> 6 3 2 1961-10-22 1964-02-03
#> 7 2 1 1959-04-06 1974-03-25
#> 8 3 4 1915-04-26 1932-08-19
#> 9 3 3 1987-10-06 1993-09-06
#> 10 2 9 1949-10-02 1950-05-06
#> # ℹ 1 more variable: acetaminophen_0_to_inf <date>
# }