Connect to an OMOP Common Data Model
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Documentation for package ‘CDMConnector’ version 1.6.0
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| 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_from_tables | Create a cdm object from local tables |
| 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 |
| requireEunomia | Require eunomia to be available. The function makes sure that you can later create a eunomia database with 'eunomiaDir()'. |
| require_eunomia | Require eunomia to be available. The function makes sure that you can later create a eunomia database with 'eunomiaDir()'. |
| 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 |