cdm_reference objects constructor

cdm_reference objects constructor

Usage

newCdmReference(tables, cdmName, cdmVersion = NULL, .softValidation = FALSE)

Arguments

tables

List of tables that are part of the OMOP Common Data Model reference.

cdmName

Name of the cdm object.

cdmVersion

Version of the cdm. Supported versions 5.3 and 5.4.

.softValidation

Whether to perform a soft validation of consistency. If set to FALSE, non overlapping observation periods are ensured.

Value

A cdm_reference object.

Examples

# \donttest{
library(omopgenerics)
library(dplyr, warn.conflicts = FALSE)

cdmTables <- list(
  "person" = tibble(
    person_id = 1, gender_concept_id = 0, year_of_birth = 1990,
    race_concept_id = 0, ethnicity_concept_id = 0
  ) |>
    newCdmTable(newLocalSource(), "person"),
  "observation_period" = tibble(
    observation_period_id = 1, person_id = 1,
    observation_period_start_date = as.Date("2000-01-01"),
    observation_period_end_date = as.Date("2023-12-31"),
    period_type_concept_id = 0
  ) |>
    newCdmTable(newLocalSource(), "observation_period")
)
cdm <- newCdmReference(tables = cdmTables, cdmName = "mock")
#> Warning: ! 5 column in person do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> Warning: ! 3 column in observation_period do not match expected column type:
#> • `observation_period_id` is numeric but expected integer
#> • `person_id` is numeric but expected integer
#> • `period_type_concept_id` is numeric but expected integer

cdm
#> 
#> ── # OMOP CDM reference (local) of mock ────────────────────────────────────────
#> • omop tables: person, observation_period
#> • cohort tables: -
#> • achilles tables: -
#> • other tables: -
# }