allofus 1.3.0

The package now supports All of Us workbench 2.0. In particular, environment variables are resolved on package load. aou_create_bucket() can now be used to create a workspace bucket, as it is no longer automatic.

In addition, this version fixes aou_create_temp_table() on workbench 2.0, where the resulting table could not be joined to a CDR table. The workbench 2.0 CDR lives in a single BigQuery region (us-central1), but a query built entirely from local data references no CDR table, so BigQuery had nothing to infer a location from and ran it in the US multi-region instead. Queries are now run with the CDR as the default dataset, which pins them to the CDR’s region.

allofus 1.2.0

• The allofus R package now has a peer-reviewed publication in the Journal of the American Medical Informatics Association (JAMIA) under the Special Issue: Focus Issue on Returning Value to Communities from the All of Us Research Program through Innovative Approaches for Data Use, Analysis, Dissemination, and Research Capacity Building. The citation is:

  • Smith LH, Cavanaugh R (2024). “allofus: An R Package to Facilitate Use of the All of Us Researcher Workbench.” Journal of the American Medical Informatics Association, ocae198. doi:10.1093/jamia/ocae198.

  • preprint: https://doi.org/10.1101/2024.04.10.24305611

• Fixed with aou_sql() and aou_atlas_cohort() to clarify that a connection is necessary when collect = FALSE.

• updated documentation on installing allofus on the RStudio Workbench and reference to community workspace

• fixed links in vignettes

• Updated DOI throughout documentation

allofus 1.1.0

• added new features including creation of temporary tables using aou_compute() and aou_create_temp_table() and a new aou_collect() function which accomodates bit64 integers when needed.

• simplified aou_observation_period() function to look at earliest and latest clinical events rather than strictly implementing OHDSI conventions per expert advice

• all functions with the option to collect data locally default to collect = FALSE

• minor big fixes, improved error messages, and improved documentation