R: Connect to an OMOP Common Data Model

# Connect to an OMOP Common Data Model

## Documentation for package ‘CDMConnector’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

appendPermanent | Run a dplyr query and add the result set to an existing
append_permanent | Run a dplyr query and add the result set to an existing
asDate | as.Date dbplyr translation wrapper
assertTables | Assert that tables exist in a cdm object
assertWriteSchema | Assert that cdm has a writable schema
assert_tables | Assert that tables exist in a cdm object
assert_write_schema | Assert that cdm has a writable schema
as_date | as.Date dbplyr translation wrapper
benchmarkCDMConnector | Run benchmark of tasks using CDMConnector
cdmCon | Get underlying database connection
cdmDisconnect | Disconnect the connection of the cdm object
cdmFlatten | Flatten a cdm into a single observation table
cdmFromCon | Create a CDM reference object from a database connection
cdmFromFiles | Create a CDM reference from a folder containing parquet, csv, or feather files
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
cdm_disconnect | Disconnect the connection of the cdm object
cdm_flatten | Flatten a cdm into a single observation table
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 feather files
cdm_name | Get the CDM name
cdm_sample | Subset a cdm object to a random sample of individuals
cdm_select_tbl | Select a subset of tables in a cdm reference object
cdm_subset | Subset a cdm object to a set of persons
cdm_subset_cohort | Subset a cdm to the individuals in one or more cohorts
cohortAttrition | Get attrition table from a cohort_table object
cohortErafy | Collapse cohort records within a certain number of days
cohortSet | Get cohort settings from a cohort_table object
cohortUnion | Union all cohorts in a cohort set with cohorts in a second cohort set
cohort_attrition | Get attrition table from a cohort_table object
cohort_count | Get cohort counts from a generated_cohort_set object.
cohort_erafy | Collapse cohort records within a certain number of days
cohort_set | Get cohort settings from a cohort_table object
cohort_union | Union all cohorts in a cohort set with cohorts in a second cohort set
computeQuery | Execute dplyr query and save result in remote database
compute_query | Execute dplyr query and save result in remote database
copyCdmTo | Copy a cdm object from one database to another
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 connection
dbSource | Create a source for a cdm in a database.
downloadEunomiaData | Download Eunomia data files
download_eunomia_data | Download Eunomia data files
eunomiaDir | Create a copy of an example OMOP CDM dataset
eunomiaIsAvailable | Has the Eunomia dataset been cached?
eunomia_dir | Create a copy of an example OMOP CDM dataset
eunomia_is_available | Has the Eunomia dataset been cached?
exampleDatasets | List the available example CDM datasets
example_datasets | 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
generate_cohort_set | Generate a cohort set on a cdm object
generate_concept_cohort_set | Create a new generated cohort set from a list of concept sets
inSchema | Helper for working with compound schemas
intersectCohorts | Intersect all cohorts in a single cohort table
intersect_cohorts | Intersect all cohorts in a single cohort table
in_schema | Helper for working with compound schemas
listTables | List tables in a schema
list_tables | List tables in a schema
newGeneratedCohortSet | Constructor for cohort_table objects
new_generated_cohort_set | Constructor for cohort_table objects
readCohortSet | Read a set of cohort definitions into R
read_cohort_set | Read a set of cohort definitions into R
recordCohortAttrition | Add attrition reason to a cohort_table object
record_cohort_attrition | Add attrition reason to a cohort_table object
snapshot | Extract CDM metadata
stow | Collect a list of lazy queries and save the results as files
summariseQuantile | Quantile calculation using dbplyr
summarise_quantile | Quantile calculation using dbplyr
summarizeQuantile | Quantile calculation using dbplyr
summarize_quantile | Quantile calculation using dbplyr
tblGroup | CDM table selection helper
tbl_group | CDM table selection helper
unionCohorts | Union all cohorts in a single cohort table
union_cohorts | Union all cohorts in a single cohort table
uniqueTableName | Create a unique table name for temp tables
unique_table_name | Create a unique table name for temp tables
validateCdm | Validation report for a CDM
validate_cdm | Validation report for a CDM
version | Get the CDM version