Package: CDMConnector 1.5.0

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_1.5.0.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'))

Peer review:

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

On CRAN:

11.02 score 12 stars 11 packages 306 scripts 1.3k downloads 102 exports 43 dependencies

Last updated 3 months agofrom:d35ff2c328. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-winOKOct 28 2024
R-4.5-linuxOKOct 28 2024
R-4.4-winOKOct 28 2024
R-4.4-macOKOct 28 2024
R-4.3-winOKOct 28 2024
R-4.3-macOKOct 28 2024

Exports:%>%append_permanentappendPermanentas_dateasDateassert_tablesassert_write_schemaassertTablesassertWriteSchemaattritionbenchmarkCDMConnectorbindcdm_disconnectcdm_flattencdm_from_concdm_from_environmentcdm_from_filescdm_from_tablescdm_namecdm_samplecdm_select_tblcdm_subsetcdm_subset_cohortcdmConcdmDisconnectcdmFlattencdmFromConcdmFromFilescdmFromTablescdmNamecdmSamplecdmSubsetcdmSubsetCohortcdmVersioncdmWriteSchemacohort_attritioncohort_countcohort_erafycohort_setcohort_unioncohortAttritioncohortCodelistcohortCountcohortErafycohortSetcohortUnioncomputecompute_querycomputeQuerycopy_cdm_tocopyCdmTodateadddatediffdatepartdbmsdbSourcedownload_eunomia_datadownloadEunomiaDatadropSourceTabledropTableeunomia_direunomia_is_availableeunomiaDireunomiaIsAvailableexample_datasetsexampleDatasetsgenerate_cohort_setgenerate_concept_cohort_setgenerateCohortSetgenerateConceptCohortSetin_schemainSchemainsertTableintersect_cohortsintersectCohortslist_tableslistSourceTableslistTablesnew_generated_cohort_setnewCohortTablenewGeneratedCohortSetread_cohort_setreadCohortSetreadSourceTablerecord_cohort_attritionrecordCohortAttritionsettingssnapshotstowsummarise_quantilesummariseQuantilesummarize_quantilesummarizeQuantiletbl_grouptblGroupunion_cohortsunionCohortsunique_table_nameuniqueTableNamevalidate_cdmvalidateCdmversion

Dependencies:backportsbitbit64blobcheckmateclicliprcpp11crayonDBIdbplyrdiffobjdplyrfansifsgenericsgluehmsjsonlitelifecyclemagrittromopgenericspillarpkgconfigprettyunitsprogresspurrrR6readrrematch2rlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwaldowithr

CDM reference backends

Rendered froma05_cdm_reference_backends.Rmdusingknitr::rmarkdownon Oct 28 2024.

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

CDMConnector and dbplyr

Rendered froma03_dbplyr.Rmdusingknitr::rmarkdownon Oct 28 2024.

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

DBI connection examples

Rendered froma04_DBI_connection_examples.Rmdusingknitr::rmarkdownon Oct 28 2024.

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

Getting Started

Rendered froma01_getting-started.Rmdusingknitr::rmarkdownon Oct 28 2024.

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

Using CDM attributes

Rendered froma06_using_cdm_attributes.Rmdusingknitr::rmarkdownon Oct 28 2024.

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

Working with cohorts

Rendered froma02_cohorts.Rmdusingknitr::rmarkdownon Oct 28 2024.

Last update: 2024-07-15
Started: 2024-01-22

Readme and manuals

Help Manual

Help pageTopics
Run a dplyr query and add the result set to an existingappendPermanent append_permanent
as.Date dbplyr translation wrapperasDate as_date
Assert that tables exist in a cdm objectassertTables assert_tables
Assert that cdm has a writable schemaassertWriteSchema assert_write_schema
Run benchmark of tasks using CDMConnectorbenchmarkCDMConnector
Create a CDM reference object from a database connectioncdmFromCon cdm_from_con
Create a CDM object from a pre-defined set of environment variablescdm_from_environment
Create a CDM reference from a folder containing parquet, csv, or feather filescdmFromFiles cdm_from_files
Create a cdm object from local tablescdm_from_tables
Select a subset of tables in a cdm reference objectcdm_select_tbl
Get underlying database connectioncdmCon
Disconnect the connection of the cdm objectcdmDisconnect cdm_disconnect
Flatten a cdm into a single observation tablecdmFlatten cdm_flatten
Get the CDM namecdmName cdm_name
Subset a cdm object to a random sample of individualscdmSample cdm_sample
Subset a cdm object to a set of personscdmSubset cdm_subset
Subset a cdm to the individuals in one or more cohortscdmSubsetCohort cdm_subset_cohort
Get cdm write schemacdmWriteSchema
Get cohort counts from a generated_cohort_set object.cohort_count
Collapse cohort records within a certain number of dayscohortErafy cohort_erafy
Union all cohorts in a cohort set with cohorts in a second cohort setcohortUnion cohort_union
Get attrition table from a cohort_table objectcohortAttrition cohort_attrition
Get cohort settings from a cohort_table objectcohortSet cohort_set
Execute dplyr query and save result in remote databasecomputeQuery compute_query
Copy a cdm object from one database to anothercopyCdmTo copy_cdm_to
Add days or years to a date in a dplyr querydateadd
Compute the difference between two daysdatediff
Extract the day, month or year of a date in a dplyr pipelinedatepart
Get the database management system (dbms) from a cdm_reference or DBI connectiondbms
Create a source for a cdm in a database.dbSource
Download Eunomia data filesdownloadEunomiaData download_eunomia_data
Has the Eunomia dataset been cached?eunomiaIsAvailable eunomia_is_available
Create a copy of an example OMOP CDM dataseteunomiaDir eunomia_dir
List the available example CDM datasetsexampleDatasets example_datasets
Generate a cohort set on a cdm objectgenerateCohortSet generate_cohort_set
Create a new generated cohort set from a list of concept setsgenerateConceptCohortSet generate_concept_cohort_set
Helper for working with compound schemasinSchema in_schema
Intersect all cohorts in a single cohort tableintersectCohorts intersect_cohorts
List tables in a schemalistTables list_tables
Constructor for cohort_table objectsnewGeneratedCohortSet new_generated_cohort_set
Read a set of cohort definitions into RreadCohortSet read_cohort_set
Add attrition reason to a cohort_table objectrecordCohortAttrition record_cohort_attrition
Extract CDM metadatasnapshot
Collect a list of lazy queries and save the results as filesstow
Quantile calculation using dbplyrsummariseQuantile summarise_quantile summarizeQuantile summarize_quantile
CDM table selection helpertblGroup tbl_group
Union all cohorts in a single cohort tableunionCohorts union_cohorts
Create a unique table name for temp tablesuniqueTableName unique_table_name
Validation report for a CDMvalidateCdm validate_cdm
Get the CDM versionversion