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.
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
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