Package: CDMConnector 1.6.0

Adam Black

CDMConnector: Connect to an OMOP Common Data Model

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.

Authors:Adam Black [aut, cre], Artem Gorbachev [aut], Edward Burn [aut], Marti Catala Sabate [aut]

CDMConnector_1.6.0.tar.gz
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CDMConnector.pdf |CDMConnector.html✨
CDMConnector/json (API)
NEWS

# Install 'CDMConnector' in R:

install.packages('CDMConnector', repos = c('https://darwin-eu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/darwin-eu/cdmconnector/issues

On CRAN:

11.12 score 12 stars 11 packages 310 scripts 1.4k downloads 104 exports 42 dependencies

Last updated 12 days agofrom:af064fce69. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 13 2024
R-4.5-win	OK	Nov 13 2024
R-4.5-linux	OK	Nov 13 2024
R-4.4-win	OK	Nov 13 2024
R-4.4-mac	OK	Nov 13 2024
R-4.3-win	OK	Nov 13 2024
R-4.3-mac	OK	Nov 13 2024

Exports:%>%append_permanent appendPermanent as_date asDate assert_tables assert_write_schema assertTables assertWriteSchema attrition benchmarkCDMConnector bind cdm_disconnect cdm_flatten cdm_from_con cdm_from_environment cdm_from_files cdm_from_tables cdm_name cdm_sample cdm_select_tbl cdm_subset cdm_subset_cohort cdmCon cdmDisconnect cdmFlatten cdmFromCon cdmFromFiles cdmFromTables cdmName cdmSample cdmSubset cdmSubsetCohort cdmVersion cdmWriteSchema cohort_attrition cohort_count cohort_erafy cohort_set cohort_union cohortAttrition cohortCodelist cohortCount cohortErafy cohortSet cohortUnion compute compute_query computeQuery copy_cdm_to copyCdmTo dateadd datediff datepart dbms dbSource download_eunomia_data downloadEunomiaData dropSourceTable dropTable eunomia_dir eunomia_is_available eunomiaDir eunomiaIsAvailable example_datasets exampleDatasets generate_cohort_set generate_concept_cohort_set generateCohortSet generateConceptCohortSet in_schema inSchema insertTable intersect_cohorts intersectCohorts list_tables listSourceTables listTables new_generated_cohort_set newCohortTable newGeneratedCohortSet read_cohort_set readCohortSet readSourceTable record_cohort_attrition recordCohortAttrition require_eunomia requireEunomia settings snapshot stow summarise_quantile summariseQuantile summarize_quantile summarizeQuantile tbl_group tblGroup union_cohorts unionCohorts unique_table_name uniqueTableName validate_cdm validateCdm version

Dependencies:backports bit bit64 blob checkmate cli clipr cpp11 crayon DBI dbplyr diffobj dplyr fansi fs generics glue hms jsonlite lifecycle magrittr omopgenerics pillar pkgconfig prettyunits progress purrr R6 readr rlang snakecase stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs vroom waldo withr

CDM reference backends

Rendered froma05_cdm_reference_backends.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-01-23
Started: 2023-03-06

CDMConnector and dbplyr

Rendered froma03_dbplyr.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-04-02
Started: 2023-03-06

DBI connection examples

Rendered froma04_DBI_connection_examples.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2023-11-09
Started: 2023-03-06

Getting Started

Rendered froma01_getting-started.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-11-06
Started: 2023-03-06

Using CDM attributes

Rendered froma06_using_cdm_attributes.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-05-03
Started: 2023-08-01

Working with cohorts

Rendered froma02_cohorts.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-11-13
Started: 2024-01-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Run a dplyr query and add the result set to an existing	appendPermanent append_permanent
as.Date dbplyr translation wrapper	asDate as_date
Assert that tables exist in a cdm object	assertTables assert_tables
Assert that cdm has a writable schema	assertWriteSchema assert_write_schema
Run benchmark of tasks using CDMConnector	benchmarkCDMConnector
Create a CDM reference object from a database connection	cdmFromCon cdm_from_con
Create a CDM object from a pre-defined set of environment variables	cdm_from_environment
Create a CDM reference from a folder containing parquet, csv, or feather files	cdmFromFiles cdm_from_files
Create a cdm object from local tables	cdm_from_tables
Select a subset of tables in a cdm reference object	cdm_select_tbl
Get underlying database connection	cdmCon
Disconnect the connection of the cdm object	cdmDisconnect cdm_disconnect
Flatten a cdm into a single observation table	cdmFlatten cdm_flatten
Get the CDM name	cdmName cdm_name
Subset a cdm object to a random sample of individuals	cdmSample cdm_sample
Subset a cdm object to a set of persons	cdmSubset cdm_subset
Subset a cdm to the individuals in one or more cohorts	cdmSubsetCohort cdm_subset_cohort
Get cdm write schema	cdmWriteSchema
Get cohort counts from a generated_cohort_set object.	cohort_count
Collapse cohort records within a certain number of days	cohortErafy cohort_erafy
Union all cohorts in a cohort set with cohorts in a second cohort set	cohortUnion cohort_union
Get attrition table from a cohort_table object	cohortAttrition cohort_attrition
Get cohort settings from a cohort_table object	cohortSet cohort_set
Execute dplyr query and save result in remote database	computeQuery compute_query
Copy a cdm object from one database to another	copyCdmTo copy_cdm_to
Add days or years to a date in a dplyr query	dateadd
Compute the difference between two days	datediff
Extract the day, month or year of a date in a dplyr pipeline	datepart
Get the database management system (dbms) from a cdm_reference or DBI connection	dbms
Create a source for a cdm in a database.	dbSource
Download Eunomia data files	downloadEunomiaData download_eunomia_data
Has the Eunomia dataset been cached?	eunomiaIsAvailable eunomia_is_available
Create a copy of an example OMOP CDM dataset	eunomiaDir eunomia_dir
List the available example CDM datasets	exampleDatasets example_datasets
Generate a cohort set on a cdm object	generateCohortSet generate_cohort_set
Create a new generated cohort set from a list of concept sets	generateConceptCohortSet generate_concept_cohort_set
Helper for working with compound schemas	inSchema in_schema
Intersect all cohorts in a single cohort table	intersectCohorts intersect_cohorts
List tables in a schema	listTables list_tables
Constructor for cohort_table objects	newGeneratedCohortSet new_generated_cohort_set
Read a set of cohort definitions into R	readCohortSet read_cohort_set
Add attrition reason to a cohort_table object	recordCohortAttrition record_cohort_attrition
Require eunomia to be available. The function makes sure that you can later create a eunomia database with 'eunomiaDir()'.	requireEunomia require_eunomia
Extract CDM metadata	snapshot
Collect a list of lazy queries and save the results as files	stow
Quantile calculation using dbplyr	summariseQuantile summarise_quantile summarizeQuantile summarize_quantile
CDM table selection helper	tblGroup tbl_group
Union all cohorts in a single cohort table	unionCohorts union_cohorts
Create a unique table name for temp tables	uniqueTableName unique_table_name
Validation report for a CDM	validateCdm validate_cdm
Get the CDM version	version