cdm_reference objects constructor
Arguments
- tables
List of tables that are part of the OMOP Common Data Model reference.
- cdmName
Name of the
<cdm_reference>object.- cdmVersion
Version of the OMOP Common Data Model. Supported versions are "5.3" and "5.4".
- .softValidation
Whether to perform a soft validation of consistency. If set to FALSE, non overlapping observation periods are ensured.
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 cast column in person as do not match the expected column type:
#> • `person_id` from numeric to integer
#> • `gender_concept_id` from numeric to integer
#> • `year_of_birth` from numeric to integer
#> • `race_concept_id` from numeric to integer
#> • `ethnicity_concept_id` from numeric to integer
#> Warning: ! 3 cast column in observation_period as do not match the expected column type:
#> • `observation_period_id` from numeric to integer
#> • `person_id` from numeric to integer
#> • `period_type_concept_id` from numeric to integer
cdm
#>
#> ── # OMOP CDM reference (local) of mock ────────────────────────────────────────
#> • omop tables: observation_period, person
#> • cohort tables: -
#> • achilles tables: -
#> • other tables: -
# }