Connect to an OMOP Common Data Model


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Documentation for package ‘CDMConnector’ version 0.5.1

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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
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
cdm_flatten Flatten a cdm into a single observation table
cdm_from_con Create a CDM reference object from a database connection
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_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 GeneratedCohortSet object
cohortCount Get cohort counts from a GeneratedCohortSet object
cohortSet Get cohort settings from a GeneratedCohortSet object
cohort_attrition Get attrition table from a GeneratedCohortSet object
cohort_count Get cohort counts from a GeneratedCohortSet object
cohort_set Get cohort settings from a GeneratedCohortSet object
collect.cdm_reference Bring a remote CDM reference into R
computePermanent Run a dplyr query and store the result in a permanent table
computeQuery Execute dplyr query and save result in remote database
compute_permanent Run a dplyr query and store the result in a permanent table
compute_query Execute dplyr query and save result in remote database
dateadd Add days or years to a date in a dplyr query
datediff Compute the difference between two days
dbms Get the database management system (dbms) from a cdm_reference or DBI connection
downloadEunomiaData Download Eunomia data files
download_eunomia_data Download Eunomia data files
dropTable Drop tables from write_schema of a cdm object
drop_table Drop tables from write_schema of a cdm object
eunomiaDir Create a copy of a Eunomia dataset
eunomiaIsAvailable Has the Eunomia dataset been cached?
eunomia_dir Create a new Eunomia CDM
eunomia_is_available Has the Eunomia dataset been cached?
generateCohortSet Generate a cohort set on a cdm object
generate_cohort_set Generate a cohort set on a cdm object
listTables List tables in a schema
list_tables List tables in a schema
newGeneratedCohortSet Low level constructor for GeneratedCohortSet objects for package developers
new_generated_cohort_set Low level constructor for GeneratedCohortSet objects for package developers
print.cdm_reference Print a CDM reference object
readCohortSet Read a set of cohort definitions into R
read_cohort_set Read a set of cohort definitions into R
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
validateCdm Validation report for a CDM
validate_cdm Validation report for a CDM
version Get the CDM version