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HADES development announcements

Andromeda 0.6.0 has been released on github and CRAN. This version add methods for getting and setting the names of tables in Andromeda objects as well as the column names of an Andromeda table. This should allow all interaction with Andromeda objects to be done without the need for RSQLite.

CohortGenerator v0.3.0 has been released on GitHub. This version adds a method for retrieving a cohort definition set from a CSV settings file as is normally done in OHDSI study packages.

CohortDiagnostics version 2.2.1 has been released. This includes a number of bug fixes that occur following a recently released version of tidyr.

ParallelLogger 3.0.0 has been released. This version switches to the new condition handling system introduced in R 4, which should be more stable than the legacy system. A nice additional benefit is that now all message() calls are automatically logged (at the ‘INFO’ level), in addition to the warning() and stop() calls that were already logged in previous versions. So message() is now equivalent to ParallelLogger::logInfo().

This does mean a minimum R version of 4.0.0 is now required for HADES.

CohortDiagnostics version 2.2.2 has been released. This includes a hot fix for a bug introduced in the last release.

DatabaseConnector 5.0.2 has been released. This includes several minor improvements and bugfixes. Perhaps the most important one is that there’s now a separate vignette about setting up a connection to your database that I recommend we reference in the instructions for all OHDSI study packages.

SqlRender 1.9.0 has been released. Most important change is further support for Spark.


CohortGenerator v0.4.0 has been released. There is a breaking change in the defaults for saving/getting a cohortDefinitionSet to/from the file system to support the new approach for storing cohorts in study packages.

PatientLevelPrediction v5.0.4 has been released.

There are breaking changes in runPlp and the setModel functions.

  • New interface for running predictions (via settings objects)
  • Models are now saved as json files when possible
  • Added flexibility with customization possible for feature engineering/selection, split design and under/over sampling
  • Deep learning has been moved to a new package (see DeepPatientLevelPrediction)
  • Ensemble learning has been moved to a new package (see EnsemblePatientLevelPrediction)

See NEWS.md for complete release notes.

Hydra v0.3.0 has been released. This release includes:

  • A new skeleton for CohortDiagnostics
  • All skeletons now use renv for managing R package dependencies
  • Added unit tests for Hydra

Please see the NEWS.md for complete release notes.

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EnsemblePatientLevelPrediction v0.0.2 has been released.

This is a new package that includes additional functionality that uses PatientLevelPrediction to enable users to develop and validate ensemble models.

  • Currently the package enables users to develop stacker ensembles and fusion ensembles
  • Performance evaluation is implemented per base model and for the ensemble

See NEWS.md for complete release notes.

Capr v1.0.3 has been released.

  • Fixed bug in conceptSetExpression S4 object that created same guid.
  • Added function to create a cohort data frame format that fits into CohortGenerator and CohortDiagnostics pipeline

Please review NEWS.md for all release notes.

CohortDiagnostics v3.0.0 has been Released. This includes a number of breaking changes including:

  • Movement to an sqlite backend as default for the DiagnosticsExplorer shiny app
  • The runCohortDiagnostics function has now been completely replaced with an executeDiagnostics function
  • The CohortGenerator OHDSI package is now required to generate all cohorts

Please see our usage guide for executing the package.

Please review the NEWS.md for complete release notes.

Andromeda 0.6.1 has been released. This is a patch release to accommodate changes in dependencies.

SelfControlledCaseSeries 3.3.0 has been released. Most important change is in our new time-trend stability diagnostic, which now uses a max ratio to avoid signaling problems just because the data are big.

CohortGenerator v0.5.0 has been released. This minor release provides the ability to export cohort statistics to a data frame and adds some utility methods for reading/writing CSV files to enforce HADES standards.

CohortDiagnostics v3.0.1 has been released. This is a hotfix that mainly includes bug fixes (including one that will require an upgrade to CohortGenerator v0.5.0.

Please review the NEWS.md for complete release notes.

ParallelLogger 3.0.1 has been released. Most important changes are some fixes when loading and saving to JSON.

DatabaseConnector 5.0.3 has been released. This contains some minor bugfixes.

DatabaseConnector 5.0.4 has been released. This has just one tiny bugfix that was essential for Strategus.