Package: allofus 1.2.0

Rob Cavanaugh

allofus: Interface for 'All of Us' Researcher Workbench

Streamline use of the 'All of Us' Researcher Workbench (<https://www.researchallofus.org/data-tools/workbench/>)with tools to extract and manipulate data from the 'All of Us' database. Increase interoperability with the Observational Health Data Science and Informatics ('OHDSI') tool stack by decreasing reliance of 'All of Us' tools and allowing for cohort creation via 'Atlas'. Improve reproducible and transparent research using 'All of Us'.

Authors:Louisa Smith [aut, cph], Rob Cavanaugh [aut, cre, cph]

allofus_1.2.0.tar.gz
allofus_1.2.0.zip(r-4.7)allofus_1.2.0.zip(r-4.6)allofus_1.2.0.zip(r-4.5)
allofus_1.2.0.tgz(r-4.6-any)allofus_1.2.0.tgz(r-4.5-any)
allofus_1.2.0.tar.gz(r-4.7-any)allofus_1.2.0.tar.gz(r-4.6-any)
allofus_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
allofus/json (API)

# Install 'allofus' in R:
install.packages('allofus', repos = c('https://roux-ohdsi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/roux-ohdsi/allofus/issues

Pkgdown/docs site:https://roux-ohdsi.github.io

Datasets:

On CRAN:

Conda:

6.91 score 19 stars 53 scripts 749 downloads 19 exports 43 dependencies

Last updated from:0c79a0075d. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK160
source / vignettesOK232
linux-release-x86_64OK226
macos-release-arm64OK198
macos-oldrel-arm64OK193
windows-develOK138
windows-releaseOK102
windows-oldrelOK103
wasm-releaseOK169

Exports:%>%aou_atlas_cohortaou_bucket_to_workspaceaou_collectaou_computeaou_concept_setaou_connectaou_create_bucketaou_create_temp_tableaou_joinaou_ls_bucketaou_ls_workspaceaou_observation_periodaou_session_infoaou_sqlaou_surveyaou_tablesaou_workspace_to_bucketon_workbench

Dependencies:askpassbigrquerybitbit64blobbriocliclockcpp11curlDBIdbplyrdplyrfsgarglegenericsgluehttrjsonlitelifecyclemagrittrmimenanoparquetopensslpillarpkgconfigprettyunitspurrrR6rapidjsonrrappdirsrlangsessioninfostringistringrsystibbletidyrtidyselecttzdbutf8vctrswithr

Managing files on the workbench
Setting Up a Bucket | Listing Files | In Your Workspace | In Your Bucket | Transferring Files | From Workspace to Bucket | From Bucket to Workspace | Workflow Example | Important Considerations
Rendered fromworkspace.Rmdusingknitr::rmarkdown

Last update: 2026-07-02
Started: 2023-12-18

All of Us in R
The Basics | Installing and Loading allofus | Accessing Data | Connecting to the database | Accessing a table | Data manipulation on the database | The collect() Function | Data manipulation with multiple tables | aou_join() | Joins from different sources? | Viewing the Underlying SQL with show_query() | Running SQL code directly
Rendered fromallofus.Rmdusingknitr::rmarkdown

Last update: 2024-08-22
Started: 2023-12-18

Using ATLAS to create a cohort
Rendered fromatlas.Rmdusingknitr::rmarkdown

Last update: 2024-08-22
Started: 2023-12-18

Extracting All of Us survey and EHR data
Survey data | EHR data | Health history survey data
Rendered fromdata.Rmdusingknitr::rmarkdown

Last update: 2024-08-02
Started: 2023-12-18