- Inject cohort schema and table into
createCohortBasedCovariateSettings
(#181) - Provide hook to optimize cohort SQL construction (#179)
- Fixes broken links in R6 class documentation (#183)
- Eliminated the dependencies for
keyring
,renv
andtargets
(#135) - Centralized all modules into the Strategus package (#29, #45, #51, #140)
- Strategus execution provides a summary of the execution time (#4) and continues after an error (#64, #141)
- Modules provide functions for creating their results data model (#43) and to upload results.
- Allow modules to obtain the full set of OMOP CDM metadata collected (#20, #154)
- Adds the
cdm_holder
attribute to the database_id hash calculation (#48) - Moves the
incremental
setting to the execution settings vs. the module settings (#155) - Adds threading options via execution settings (#151)
- Select subset of modules to execute from analysis specification (#169)
- Ensure release of Strategus has Python dependencies (#22) and OHDSI Shiny App dependencies (#78). See StrategusStudyRepoTemplate for more details.
- Document the results data model for HADES modules (#143)
- Make negative control outcome shared resource optional (#153)
- Export results data model specification file for PatientLevelPrediction (#165)
- Provide option to skip modules (#87)
- Central log file for execution (#132)
- Create function to collect all results into a single ZIP file for sharing (#46)
- Install latest modules (#125)
- Update SelfControlledCaseSeries Module to v0.4.1
- Add functions for developers to help with renv.lock file validation (#69)
- Use renv project profiles for modules (#94)
- Convert relative paths to absolute path before passing to a module (#99)
- Address missing package dependencies in modules (#99)
- Throw informative error message when connection detail reference not set in keyring (#100)
- Validate execution settings (#101)
- Pass temp emulation schema properly (#76)
- Remove local library package dependencies (#96)
- Adds an initial implementation for uploading results to a results database (#72)
- Robust handling of connection details via keyring (#74)
- Ensures uniqueness of all CDM tables when gathering database metadata (#82)
tempEmulationSchema
added to execution settings and passed properly to modules (#82)- Adding logging to module initialization to detect
renv
restore errors (#82) - Adopt HADES-wide lock file in latest versions of all modules (#83)
- Use renv >= v1.0.0 for all modules and Strategus (#83)
- Add GitHub unit tests for HADES adopted version (currently v4.2.3) and the latest R versions for all modules and Strategus. (#83)
- Ensure all Strategus GitHub unit tests run on all operating systems and available OHDSI test database platforms (#83)
- Use CDM v5.4 schemas for all unit tests (#85)
- Allow for passing
renv
configuration options when running Strategus (#88) - Adds SQL for test cohorts to package (#1)
- Update SCCS module reference
inst/testdata/analysisSpecification.json
- Required metadata tables check fails with DatabaseConnector < 6.0 (#61)
- Update module references and add script to run Strategus on Eunomia in
extras/ExecuteStrategusOnEunomia.R
(#66)
- Add DB Platform Tests (#53)
- Add error handling for missing/empty tables (#54)
- Remove uniqueness check for module table prefix (#55)
- Breaking change: removed function
createExecutionSettings()
and replaced with 2 new functions:createCdmExecutionSettings()
andcreateResultsExecutionSettings()
. (#19) - Added Vignettes (#23)
- Provide better support for
keyring
to handle named/locked keyrings (#24) - Add function to list HADES modules (#30)
- Fixes from testing (#36)
- Enforce module structure for proper use with renv (#37)
- Support CDM 5.4 source table format (#41)
- Add unit tests (#47)
- Updates renv to 0.15.5
- Call renv::use() for each module
Initial version