Function reference • amstel

All functions

achilles(): Runs ACHILLES on AmsterdamUMCdb converted to the OMOP CDM

alter_system_settings(): Alters PostgreSQL System settings.

apply_corrections(): Apply corrections

catalogue_export(): Run EHDEN CatalogueExport

cdm_inspection(): Runs EHDEN CdmInspection to check the OMOP-CDM instance before submission to EHDEN

cloud_auth(): Small wrapper for authentication https://github.com/ropensci/googleLanguageR. Allows authentication using Google Cloud API credentials in default user folder'

connect(): Connect to database

create_cdm_indices(): Create Indices on Common Data Model Tables.

create_cdm_tables(): Create Common Data Model tables

create_cohort_tables(): Create the Common Data Model Results Cohort Tables

create_config(): Creates amstel configuration file

create_data_tables(): Create the Common Data Model Clinical Data tables

create_environment(): Creates a new database environment (database schemes) for AmsterdamUMCdb and the CDM data and results schemes for testing and/or example purposes.

create_vocabulary_tables(): Create the Common Data Model Vocabulary tables

create_webapi_tables(): Create OHDSI WebAPI tables

data_quality_dashboard(): Shows the OHDSI Data Quality Dashboard

download_drivers(): Downloads JDBC drivers

drop_data_tables(): Drop CDM Data Tables.

drop_vocabulary_tables(): Drop Vocabulary Tables.

etl(): Runs the main ETL steps for converting AmsterdamUMCdb to the OMOP CDM

execute_dqd_checks(): Evaluate Data Quality of AmsterdamUMCdb OMOP CDM after ETL.

extract_concepts(): Extract concepts

get_config(): Gets the configuration for working with the amstel package. Reads the config.yaml file from the user config folder or creates a new file if the configuration file is missing.

get_server_tablename(): Get case-sensitive table name on server

has_adb_environment(): Checks whether the AmsterdamUMCdb environment is available for running example code

has_cdm_environment(): Checks whether the CDM environment is available for running example code

has_example_environment(): Checks whether an example environment can be used

index_data_tables(): Create Indices on Common Data Model clinical data tables.

index_vocabulary_tables(): Create Indices on Common Data Model vocabulary tables.

load_concepts(): Load concepts

load_data_tables(): Load CDM Standardized Clinical Data Tables.

load_source_to_concept_map(): Load source_to_concept_map table from Usagi mapping Files.

load_source_to_value_map(): Load source_to_value_map table from SQL file.

load_usagi_concepts(): Load Usagi Concepts

load_vocabulary_tables(): Load Vocabulary Tables From CSV Files.

migrate_source_to_value_map(): Migrates the source_to_concept_map data to the new source_to_value_map table

read_vocabulary(): Read vocabulary

save_concepts(): Save Concepts

show_dqd_log(): Show Data Quality Dashboard log

swap_usagi_counts(): Swap counts

translate(): Small wrapper for translating using googleLanguageR.

translate_concepts(): Translate concepts