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HADES development announcements

SqlRender 1.12.1 has been released. This contains two bugfixes for Snowflake.

DataQualityDashboard 2.1.1 has been released. This is the first release of the package which meets all HADES requirements, and hereafter DQD will be a part of HADES.

DataQualityDashboard is an OHDSI mainstay used to evaluate and expose data quality in an OMOP CDM instance. It’s an R package that includes an R shiny application which can be used to visualize and explore the results of its data quality evaluations.

The DQD runs a set of data quality checks against the OMOP CDM (it currently supports CDM versions 5.2, 5.3, and 5.4). These checks are highly configurable; they can be toggled off and on and their failure thresholds can be adjusted according to the user’s needs. The thousands of checks in the DQD are grouped into a smaller set of data quality “check types” which each represent a singular data quality idea. Each check type corresponds to a parameterized SQL query into which OMOP tables, fields, and concepts are substituted to create an individual data quality check.

The threshold files used to configure checks and their failure thresholds can be shared amongst institutions to facilitate consistent use of the DQD for network-level projects. Similarly, the results of a DQD run are portable and can be stored in json, csv, and/or a database table.

For a comprehensive overview of the DataQualityDashboard, please see the package website here. Questions and bug reports can be submitted on our issue tracker here. I’ll be on point as the package maintainer but send most credit to @clairblacketer @Frank and other DQ WG members for building the package and supporting the HADES submission :slight_smile:

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BigKnn 1.0.2 has been released. This adds support for the upcoming Andromeda release (using arrow instead of SQLite in the backend for improved speed).

SqlRender 1.13.0 has been released. This has some fixes for BigQuery, SQLite, and DuckDB.

ROhdsiWebApi 1.3.3 has been released. This is again just a minor update to pass R Check again.

Capr 2.0.0 has been released. This is a major update overhauling the user-interface of Capr. The intent of the overhaul is to improve the readability of the Capr code. For full details visit the package website. Below is a brief summary of some updates:

  • new handling of concept sets using cs(). Can build concept sets on the fly (requiring only a name and id) to use in a cohort definition. Improved functionality for handling descendants, mapped and excluded concepts. An example: cs(desecendants(201826L), name = "T2D")
  • new interface for specifying cohort logic via cohort(entry, attrition, exit, era). Stylistically definitions are to be layered as nested functions in order to convey the entire logic within one function. This change improves is intended to improve the readability of the Capr call.
  • maintain support for cohort templating
  • change end point of Capr to only produce the json structure for the cohort definition (either as a character string or saved file). It is suggested that the user deploys the json using the appropriate tools like CohortGenerator or CirceR, which are better suited to generating the cohort definition.

DatabaseConnector 6.1.0 has been released. This adds support for DuckDB, fixes some issues related to Java heap memory, and fixes some Snowflake issues (related to DATETIME).

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DataQualityDashboard 2.1.2 has been released. This release contains a bug fix for the cdmDataType check SQL.

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Andromeda 0.6.2 has been released (on github but not CRAN). This adds one function isAndromedaTable() that should work with both SQLite and Arrow andromeda tables.
Reminder, we are moving to a new backend for Andromeda based on Apache Arrow soon. If your package depends on Andromeda please test it using the Andromeda develop branch and report any issues in the Andromeda issue tracker. You may need to make some slight changes to your code such as using nrow instead of tally to get the number of rows in an Andromeda table.

SqlRender 1.13.1 has been released, with a single bugfix for Netezza.

DeepPatientLevelPrediction 1.1 has been released. This adds adds a number of bug fixes and some new features. The new features are:

  • An automatic learning rate finder has been implemented, used by setting learningRate="auto"
  • Training loop parameters are now handled by a new settings object and as a result more of the training loop parameters are customizable by the user
  • Custom metrics can be created by the user to use for early stopping and learning rate schedule.
  • Seeds have been added in various places, making the whole process more reproducible

Thanks to @lhjohn for his contributions to this release.

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DeepPatientLevelPrediction 1.1.1 has been released. One small bugfix when uploading to database.

Andromeda 0.6.3 has been release on Github and CRAN. This release add isAndromedaTable function that works with both the current andromeda tables (SQLite references) and the Andromeda v1.0 tables (Apache Arrow FileSystemDatasets). Reminder: If you depend on Andromeda please run R check with the development branch (v1.0) and report any issues on the issue tracker.

CohortGenerator v0.8.0 was released a few weeks ago (sorry for the delayed announcement). The release notes are here.

This release of CohortGenerator adds the ability to generate subsets of cohorts. So, for example, if you have a target cohort of new users of a drug, you can use CohortGenerator to define a subset definition to further subset that target based on a combination of demographic criteria, “limit” criteria (i.e. X days of prior observation) and even based on intersection with another cohort definition. Here is the Creating Cohort Subset Definitions vignette if you are interested in the details.

A big thanks to @jpegilbert who lead the development of this important new feature.

Capr v2.0.1 has been released. This is a patch release so no major changes. Updates include:

  • Additional vignettes and updated documentation
  • compile generic function to coerce Capr class to json structure
  • more informative cs print statement
  • other minor bug fixes

Please keep trying out Capr and posting issues! Feedback always welcome!

CohortDiagnostics version 3.2.0. There are no major api changes in this release so all existing scripts should maintain compatibility with this release.

The main changes are as follows:

  • Improved support for Subset operators by fixing some issues around concept sets
  • Added a database migration for existing results databases to support cohort definition sets with subsets
  • Almost all shiny code has been moved to the OhdsiShinyModules package - this is a single package to install and keep up to date
  • Some alterations to plots and tables in the DiagnosticsExplorer shiny app were changed as the ggiraph package was removed due to compatibility and installation issues on Linux environments. All plots now use ggplot2 and/or plotly
  • Support for easier publishing to Posit Connect/Rconnect and shinyapps.io (testing of shinyapps.io was limited as it was a paid service)

Please check the release notes for for details of changes.

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ResultModelManager v0.4.0 has been released.
This release adds some vignettes on usage as well as a QueryNamespace class that adds a wrapper around SqlRender functionality that allows execution of queries with fixed parameters from result model specifications.

See this guide on basic usage. The intention is that this will be useful for writing shiny apps and Quatro reports.

In addition, the function createResultsDataModel has been removed as it was added in error when migrating code.

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EvidenceSynthesis 0.4.1 has been released. The only change is the addition of a video vignette, which was also featured in the ESMARConf 2023 conference.

CohortDiagnostics version 3.2.1 . Has been released.
This is a hotfix that resolves an issue related to the cohort subsetting functionality.

Please check the release notes for for details of changes.

SqlRender 1.14.0 has been released. Contains some fixes for Spark, Oracle, Netezza, and PostgreSQL.