Package index • CDMConnector

CDM Object

Create or transform a CDM reference object. These accept and return cdm objects.

assert_tables() assertTables(): Assert that tables exist in a cdm object

assert_write_schema() assertWriteSchema(): Assert that cdm has a writable schema

cdmCon(): Get underlying database connection

cdmDisconnect() cdm_disconnect(): Disconnect the connection of the cdm object

cdmFlatten() cdm_flatten(): Flatten a cdm into a single observation table

cdmName() cdm_name(): Get the CDM name

cdmSample() cdm_sample(): Subset a cdm object to a random sample of individuals

cdmSubset() cdm_subset(): Subset a cdm object to a set of persons

cdmSubsetCohort() cdm_subset_cohort(): Subset a cdm to the individuals in one or more cohorts

cdmWriteSchema(): Get cdm write schema

cdm_from_con() cdmFromCon(): Create a CDM reference object from a database connection

cdm_from_environment(): Create a CDM object from a pre-defined set of environment variables

cdm_from_files() cdmFromFiles(): Create a CDM reference from a folder containing parquet, csv, or feather files

cdm_from_tables(): Create a cdm object from local tables

cdm_select_tbl(): Select a subset of tables in a cdm reference object

copy_cdm_to() copyCdmTo(): Copy a cdm object from one database to another

dbSource(): Create a source for a cdm in a database.

snapshot(): Extract CDM metadata

stow(): Collect a list of lazy queries and save the results as files

tbl_group() tblGroup(): CDM table selection helper

validate_cdm() validateCdm(): Validation report for a CDM

version(): Get the CDM version

Cohort Creation and Transformation

A cohort is a set of person-days representing the time during which people in a CDM exhibited some observable characteristics. Cohorts are often the foundation of downstream analyses.

cohortAttrition() cohort_attrition(): Get attrition table from a cohort_table object

cohortSet() cohort_set(): Get cohort settings from a cohort_table object

cohort_count(): Get cohort counts from a generated_cohort_set object.

cohort_erafy() cohortErafy(): Collapse cohort records within a certain number of days

cohort_union() cohortUnion(): Union all cohorts in a cohort set with cohorts in a second cohort set

generateCohortSet() generate_cohort_set() experimental: Generate a cohort set on a cdm object

generateConceptCohortSet() generate_concept_cohort_set(): Create a new generated cohort set from a list of concept sets

intersect_cohorts() intersectCohorts(): Intersect all cohorts in a single cohort table

new_generated_cohort_set() newGeneratedCohortSet() superseded: Constructor for cohort_table objects

read_cohort_set() readCohortSet(): Read a set of cohort definitions into R

recordCohortAttrition() record_cohort_attrition(): Add attrition reason to a cohort_table object

union_cohorts() unionCohorts(): Union all cohorts in a single cohort table

dbplyr workarounds

Functions that can be used in cross database dplyr pipelines

appendPermanent() append_permanent(): Run a dplyr query and add the result set to an existing

asDate() as_date(): as.Date dbplyr translation wrapper

computeQuery() compute_query(): Execute dplyr query and save result in remote database

dateadd(): Add days or years to a date in a dplyr query

datediff(): Compute the difference between two days

datepart(): Extract the day, month or year of a date in a dplyr pipeline

inSchema() in_schema(): Helper for working with compound schemas

summarise_quantile() summarize_quantile() summariseQuantile() summarizeQuantile(): Quantile calculation using dbplyr

uniqueTableName() unique_table_name(): Create a unique table name for temp tables

DBI connection

Functions that accept DBI connections and are useful in cross database DBI code

dbms(): Get the database management system (dbms) from a cdm_reference or DBI connection

list_tables() listTables(): List tables in a schema

Eunomia example CDM

Easily create and use example CDMs in a duckdb database

downloadEunomiaData() download_eunomia_data(): Download Eunomia data files

eunomiaDir() eunomia_dir(): Create a copy of an example OMOP CDM dataset

eunomia_is_available() eunomiaIsAvailable(): Has the Eunomia dataset been cached?

exampleDatasets() example_datasets(): List the available example CDM datasets

requireEunomia() require_eunomia(): Require eunomia to be available. The function makes sure that you can later create a eunomia database with eunomiaDir().

Benchmarking

Run benchmarking of simple queries against your CDM reference

benchmarkCDMConnector(): Run benchmark of tasks using CDMConnector