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