CDMConnector1.6.1 package

Connect to an OMOP Common Data Model

appendPermanent

Run a dplyr query and add the result set to an existing

asDate

as.Date dbplyr translation wrapper

assert_tables

Assert that tables exist in a cdm object

assert_write_schema

Assert that cdm has a writable schema

benchmarkCDMConnector

Run benchmark of tasks using CDMConnector

cdm_from_con

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

Create a CDM reference from a folder containing parquet, csv, or feath...

cdm_from_tables

Create a cdm object from local tables

cdm_select_tbl

Select a subset of tables in a cdm reference object

cdmCon

Get underlying database connection

CDMConnector-package

CDMConnector: Connect to an OMOP Common Data Model

cdmDisconnect

Disconnect the connection of the cdm object

cdmFlatten

Flatten a cdm into a single observation table

cdmName

Get the CDM name

cdmSample

Subset a cdm object to a random sample of individuals

cdmSubset

Subset a cdm object to a set of persons

cdmSubsetCohort

Subset a cdm to the individuals in one or more cohorts

cdmWriteSchema

Get cdm write schema

cohort_count

Get cohort counts from a generated_cohort_set object.

cohort_erafy

Collapse cohort records within a certain number of days

cohort_union

Union all cohorts in a cohort set with cohorts in a second cohort set

cohortAttrition

Get attrition table from a cohort_table object

cohortSet

Get cohort settings from a cohort_table object

computeQuery

Execute dplyr query and save result in remote database

copy_cdm_to

Copy a cdm object from one database to another

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

dbms

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

dbSource

Create a source for a cdm in a database.

downloadEunomiaData

Download Eunomia data files

eunomia_is_available

Has the Eunomia dataset been cached?

eunomiaDir

Create a copy of an example OMOP CDM dataset

exampleDatasets

List the available example CDM datasets

generateCohortSet

Generate a cohort set on a cdm object

generateConceptCohortSet

Create a new generated cohort set from a list of concept sets

inSchema

Helper for working with compound schemas

intersect_cohorts

Intersect all cohorts in a single cohort table

list_tables

List tables in a schema

new_generated_cohort_set

Constructor for cohort_table objects

pipe

Pipe operator

read_cohort_set

Read a set of cohort definitions into R

recordCohortAttrition

Add attrition reason to a cohort_table object

reexports

Objects exported from other packages

requireEunomia

Require eunomia to be available. The function makes sure that you can ...

snapshot

Extract CDM metadata

stow

Collect a list of lazy queries and save the results as files

summarise_quantile

Quantile calculation using dbplyr

tbl_group

CDM table selection helper

union_cohorts

Union all cohorts in a single cohort table

uniqueTableName

Create a unique table name for temp tables

validate_cdm

Validation report for a CDM

version

Get the CDM version

Provides tools for working with observational health data in the Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax. Common data model database table references are stored in a single compound object along with metadata.

  • Maintainer: Adam Black
  • License: Apache License (>= 2)
  • Last published: 2024-11-29