Creates mock cdm object for testing

Creates a mock cdm with two default synthetic cohorts, one is the index cohort and the other one is the marker cohort. However the users could specify them should they wish.

Usage

mockCohortSymmetry(
  seed = 1,
  indexCohort = NULL,
  markerCohort = NULL,
  con = DBI::dbConnect(duckdb::duckdb(), ":memory:"),
  schema = "main"
)

Arguments

seed

The seed to be inputted.

indexCohort

The tibble of your index cohort. Default is NULL, which means the default indexCohort is being used.

markerCohort

The tibble of your marker cohort. Default is NULL, which means the default markerCohort is being used.

con

Connection detail.

schema

Name of your write schema.

Value

A mock cdm object contains your index and marker cohort

Examples

# \donttest{
library(CohortSymmetry)
cdm <- mockCohortSymmetry()
#> Warning: ! 9 column in cdm_source do not match expected column type:
#> • `cdm_source_abbreviation` is logical but expected character
#> • `cdm_holder` is logical but expected character
#> • `source_description` is logical but expected character
#> • `source_documentation_reference` is logical but expected character
#> • `cdm_etl_reference` is logical but expected character
#> • `source_release_date` is logical but expected date
#> • `cdm_release_date` is logical but expected date
#> • `cdm_version` is numeric but expected character
#> • `vocabulary_version` is logical but expected character
#> Warning: ! 3 column in concept do not match expected column type:
#> • `concept_id` is numeric but expected integer
#> • `valid_start_date` is character but expected date
#> • `valid_end_date` is character but expected date
#> Warning: ! 1 column in vocabulary do not match expected column type:
#> • `vocabulary_concept_id` is numeric but expected integer
#> Warning: ! 5 column in concept_relationship do not match expected column type:
#> • `concept_id_1` is numeric but expected integer
#> • `concept_id_2` is numeric but expected integer
#> • `valid_start_date` is logical but expected date
#> • `valid_end_date` is logical but expected date
#> • `invalid_reason` is logical but expected character
#> Warning: ! 2 column in concept_synonym do not match expected column type:
#> • `concept_id` is numeric but expected integer
#> • `language_concept_id` is numeric but expected integer
#> Warning: ! 4 column in concept_ancestor do not match expected column type:
#> • `ancestor_concept_id` is numeric but expected integer
#> • `descendant_concept_id` is numeric but expected integer
#> • `min_levels_of_separation` is numeric but expected integer
#> • `max_levels_of_separation` is numeric but expected integer
#> Warning: ! 9 column in drug_strength do not match expected column type:
#> • `drug_concept_id` is numeric but expected integer
#> • `ingredient_concept_id` is numeric but expected integer
#> • `amount_unit_concept_id` is numeric but expected integer
#> • `numerator_unit_concept_id` is numeric but expected integer
#> • `denominator_value` is logical but expected numeric
#> • `denominator_unit_concept_id` is numeric but expected integer
#> • `box_size` is numeric but expected integer
#> • `valid_start_date` is character but expected date
#> • `valid_end_date` is character but expected date
#> Warning: There are observation period end dates after the current date: 2024-10-30
#> ℹ The latest max observation period end date found is 2026-10-26
#> Warning: There are observation period end dates after the current date: 2024-10-30
#> ℹ The latest max observation period end date found is 2026-10-26
cdm
#> 
#> ── # OMOP CDM reference (duckdb) of mock database ──────────────────────────────
#> • omop tables: person, observation_period, cdm_source, concept, vocabulary,
#> concept_relationship, concept_synonym, concept_ancestor, drug_strength
#> • cohort tables: cohort_1, cohort_2
#> • achilles tables: -
#> • other tables: -
CDMConnector::cdmDisconnect(cdm = cdm)
# }