Fixed missing cdm_schema attribute in
cdm_reference when using remote databases (e.g., SQL
Server).
Implemented dynamic, unique schema names (prefixed with
cdm_testgenerator_) to prevent database
collisions.
Fixed patientsCDM() to ensure the correct remote CDM
reference is returned during the injection process.
Added regression tests to verify cdm_schema
attribute presence and CohortConstructor compatibility on
SQL Server.
Removed DARWIN_ prefix from environment variables to
run tests on SQL Server and Postgres.
Support for PostgreSQL as a DBMS in
patientsCDM()
Added RPostgres to Imports
Added skip_on_cran() to several tests to avoid
network dependencies during R CMD check
Updated .gitignore and
.Rbuildignore
Support other database types next to duckdb: sqlserver and databricks
Remove dependency on arrow
generateTestTables() creates the most common used
tables in the Excel sheet by default
readPatients.xl(),
that table then is pushed to “other tables” in the CDM reference using
patientsCDM().generateTestTable() creates an Excel file with
sheets that correspond to OMOP-CDM tables.
patientsCDM() now accepts cdmName as
argument to allow for custom cdm name.
getEmptyCDM() returns an empty cdm object.
readPatients() now has a parameter to select either
Excel or CSV files as an input.
readPatients.xl() and readPatients.csv
are also exported functions for convenience.
graphCohort() provides a visualisation of cohort
timelines.
JSONS are saved in the testthat/testCases folder as default for better test self-containment.
Tested with MIMIC database.