Package index • gaiaCore

All functions

addDataSource(): Append a well-formatted data_source record to the backbone.data_source table in PostGIS

appendAttrIndexRecord(): Append a attr_index record to the attrIndexTable object

appendGeomIndexRecord(): Append a geom_index record to the geomIndexTable object

assignGeomIdToAttr(): Join a column of geom_X record identifiers to a staged attr_X table

checkTableExists(): Check if a table exists in a database

checkVariableExists(): Check if a variable exists in an attr_X table

createAttrInstanceTable(): Create an empty instance of the attr_template in a given schema in PostGIS

createOccurrencePrimaryKeys() createOccurrenceForeignKeys() createDdl() createPrimaryKeys() createForeignKeys(): Create the OHDSI-SQL Common Data Model DDL code

createExposure(): Create an exposure_occurrence (exposure) table from a variable source id

createGeomInstanceTable(): Create an empty instance of the geom_template in a given schema in PostGIS

createGeomTableIndexes(): Create indexes on a geom_* table

createIndices(): Create and populate backbone.geom_index and backbone.attr_index from registered sources in backbone.data_source

createNameString(): Sanitize and create table name from source values

createOccurrenceDdl(): Create the OHDSI-SQL Common Data Model DDL code

createSchemaString(): Create the schema and sanitize source values

geocodeAddresses(): Geocode a table with addresses

getAttrIndexRecord(): Get a single record from the backbone.attr_index table

getAttrIndexTable(): Get the backbone.attr_index table

getAttrNameFromVariableSourceId(): Get the name of a variable_source's attr dependency

getAttrOfGeomIndexId(): Get foreign key for attr_of_geom_index_id

getAttrTemplate(): Get the attr_template table

getCohortAddresses(): Get Cohort Addresses

getDataSourceRecord(): Get a single record from the backbone.data_source table

getDataSourceTable(): Get the entire backbone.data_source table

getGeomIdMap(): Create a mapping table between identifiers and values for a given geom_X

getGeomIndexRecord(): Get a record from the backbone.geom_index table from it's corresponding UUID in backbone.data_source table

getGeomIndexTable(): Get the backbone.geom_index table

getGeomNameFromVariableSourceId(): Get the name of a variable_source's geom dependency

getGeomTemplate(): Get the geom_template table

getLocationAddresses(): Get Location Table Addresses

getStaged(): Download and import data from a web-hosted source

getVariableSourceRecord(): Get a single record from the backbone.variable_source table

getVariableSourceSummaryTable(): Get the Variable Source Summary table

getVariableSourceTable(): Get the backbone.variable_source table

importAttrIndexTable(): Import the attr_index table to PostGIS

importAttrTable(): Import a well-formatted attribute table into an empty instance of attr_X in PostGIS

importCohortTable(): Import a geocoded cohort table to gaiaDB

importGeomIndexTable(): Import the geom_index table to PostGIS

importGeomTable(): Import a well-formatted geometry table into an empty instance of geom_X in PostGIS

importLocationTable(): Import a geocoded cohort table to gaiaDB

initializeDatabase(): Initialize gaiaDB

insertPostgisGeometry(): Connect to the Postgis database and insert a geometry table

loadGeometry(): Loads a geometry from a registered source into PostGIS as geom_X

loadVariable(): Loads a variable from a registered source into PostGIS as attr_X

readFromTar(): Unrar and read contents of a rar file into R memory

readFromZip(): Unzip and read contents of a zipfile into R memory

readStorageConfig(): Read config.yml file from inst

setSridWgs84(): Set the SRID on the geom_wgs84 column in PostGIS gaiaDB

setup_offline_storage(): Configure offline storage

splitAddresses(): Split a table of addresses based on presence of coordinates

standardizeStaged(): Create a standardized version of the staged data that was imported from source

writeOccurrencePrimaryKeys() writeOccurrenceForeignKeys() writeOccurrenceIndex() writeDdl() writePrimaryKeys() writeForeignKeys(): Write gaiaDB DDL script

writeOccurrenceDdl(): Write DDL script