Connect to an OMOP Common Data Model


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Documentation for package ‘CDMConnector’ version 1.3.0

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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
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