Summarise Database Characteristics for OMOP CDM

Usage

databaseCharacteristics(
  cdm,
  omopTableName = c("person", "visit_occurrence", "visit_detail", "condition_occurrence",
    "drug_exposure", "procedure_occurrence", "device_exposure", "measurement",
    "observation", "death"),
  sample = NULL,
  sex = FALSE,
  ageGroup = NULL,
  dateRange = NULL,
  interval = "overall",
  conceptIdCounts = FALSE,
  ...
)

Arguments

cdm: A cdm_reference object representing the Common Data Model (CDM) reference.
omopTableName: A character vector specifying the OMOP tables from the CDM to include in the analysis. If "person" is present, it will only be used for missing value summarisation.
sample: Either an integer or a character string. If an integer (n > 0), the function will first sample n distinct person_ids from the person table and then subset the input tables to those subjects. If a character string, it must be the name of a cohort in the cdm; in this case, the input tables are subset to subjects (subject_id) belonging to that cohort. Use NULL to disable subsetting (default value).
sex: Logical; whether to stratify results by sex (TRUE) or not (FALSE).
ageGroup: A list of age groups to stratify the results by. Each element represents a specific age range.
dateRange: A vector of two dates defining the desired study period. Only the start_date column of the OMOP table is checked to ensure it falls within this range. If dateRange is NULL, no restriction is applied.
interval: Time interval to stratify by. It can either be "years", "quarters", "months" or "overall".
conceptIdCounts: Logical; whether to summarise concept ID counts (TRUE) or not (FALSE).
...: additional arguments passed to the OmopSketch functions that are used internally.

Value

A summarised_result object containing the results of the characterisation.

Examples

# \donttest{
library(OmopSketch)

cdm <- mockOmopSketch(numberIndividuals = 100)

result <- databaseCharacteristics(
  cdm = cdm,
  omopTableName = c("drug_exposure", "condition_occurrence"),
  sex = TRUE, ageGroup = list(c(0, 50), c(51, 100)), interval = "years", conceptIdCounts = FALSE
)
#> The characterisation will focus on the following OMOP tables: drug_exposure and
#> condition_occurrence
#> → Getting cdm snapshot
#> → Getting population characteristics
#> ℹ Building new trimmed cohort
#> Adding demographics information
#> Creating initial cohort
#> Trim sex
#> ✔ Cohort trimmed
#> ℹ Building new trimmed cohort
#> Adding demographics information
#> Creating initial cohort
#> Trim sex
#> Trim age
#> ✔ Cohort trimmed
#> ℹ adding demographics columns
#> ℹ summarising data
#> ℹ summarising cohort general_population
#> ℹ summarising cohort age_group_0_50
#> ℹ summarising cohort age_group_51_100
#> ✔ summariseCharacteristics finished!
#> → Summarising clinical records
#> ℹ Adding variables of interest to drug_exposure.
#> ℹ Summarising records per person in drug_exposure.
#> ℹ Summarising subjects not in person table in drug_exposure.
#> ℹ Summarising records in observation in drug_exposure.
#> ℹ Summarising records with start before birth date in drug_exposure.
#> ℹ Summarising records with end date before start date in drug_exposure.
#> ℹ Summarising domains in drug_exposure.
#> ℹ Summarising standard concepts in drug_exposure.
#> ℹ Summarising source vocabularies in drug_exposure.
#> ℹ Summarising concept types in drug_exposure.
#> ℹ Summarising missing data in drug_exposure.
#> ℹ Adding variables of interest to condition_occurrence.
#> ℹ Summarising records per person in condition_occurrence.
#> ℹ Summarising subjects not in person table in condition_occurrence.
#> ℹ Summarising records in observation in condition_occurrence.
#> ℹ Summarising records with start before birth date in condition_occurrence.
#> ℹ Summarising records with end date before start date in condition_occurrence.
#> ℹ Summarising domains in condition_occurrence.
#> ℹ Summarising standard concepts in condition_occurrence.
#> ℹ Summarising source vocabularies in condition_occurrence.
#> ℹ Summarising concept types in condition_occurrence.
#> ℹ Summarising missing data in condition_occurrence.
#> → Summarising observation period
#> Warning: These columns contain missing values, which are not permitted:
#> "period_type_concept_id"
#> → Summarising trends: records, subjects, person-days, age and sex
#> → The number of person-days is not computed for event tables
#> ☺ Database characterisation finished. Code ran in 0 min and 57 sec
#> ℹ 1 table created: "og_011_1761918734".

PatientProfiles::mockDisconnect(cdm)
#> Warning: `mockDisconnect()` was deprecated in PatientProfiles 1.4.3.
# }