README.md

In allofus: Interface for 'All of Us' Researcher Workbench

allofus R Package

The goal of the allofus R package is to streamline the use of R within the All of Us Researcher Workbench.

The allofus R package is a not affiliated with or endorsed by the All of Us Research Program.

The allofus package helps researchers query the database and build transparent and reproducible analysed pipeline. The package allows researchers to easily use other database packages, such as dbplyr and DBI, with the All of Us database. The package also includes functions to help researchers manage storage in their workspace and bucket, as well as take advantage of tools developed for OMOP CDM data.

Installation

Install the released version of allofus from CRAN:

install.packages("allofus")

Install the development version from Github:

install.packages("pak")
pak::pak("roux-ohdsi/allofus")

On the new RStudio interface on the workbench, you will need to manually specify the CRAN mirror to be able to download any recently updated packages.

# specify the mirror directly
install.packages("allofus", repos = "https://cloud.r-project.org")

# OR set the mirror as an option at the top of your script
options(repos = c(CRAN = "https://cloud.r-project.org"))

# Github development versions may requires using the remotes package
install.packages("remotes")
remotes::install_github("roux-ohdsi/allofus", repos = "https://cloud.r-project.org")

Use

Read through the getting started vignette to learn how to use the package.

Citation

Please cite the allofus package as:

Smith L, Cavanaugh R (2023). allofus: Interface for ‘All of Us’ Researcher Workbench. doi:10.5281/zenodo.10420610, https://roux-ohdsi.github.io/allofus/.

or with

citation("allofus")

Bugs

Please leave us comments, requests, and report bugs using the “Issues” tab on github located here: https://github.com/roux-ohdsi/allofus/issues.

allofus documentation built on July 4, 2024, 9:09 a.m.