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REDCapTidieR

REDCapTidieR: Extracting complex REDCap databases into tidy tables - Published in JOSS (2024)

https://github.com/chop-cgtinformatics/redcaptidier

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 10 committers (30.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

r redcap redcap-api tidy-data
Last synced: 6 months ago · JSON representation

Repository

Makes it easy to read REDCap Projects into R

Basic Info
Statistics
  • Stars: 39
  • Watchers: 4
  • Forks: 11
  • Open Issues: 15
  • Releases: 17
Topics
r redcap redcap-api tidy-data
Created over 3 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# REDCapTidieR 


[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-greeen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![R-CMD-check](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/workflows/R-CMD-check.yaml)
[![CRAN status](https://www.r-pkg.org/badges/version/REDCapTidieR)](https://CRAN.R-project.org/package=REDCapTidieR)
[![](https://cranlogs.r-pkg.org/badges/REDCapTidieR)](https://cran.r-project.org/package=REDCapTidieR)
[![](https://cranlogs.r-pkg.org/badges/grand-total/REDCapTidieR)](https://cran.r-project.org/package=REDCapTidieR)
[![Codecov test coverage](https://codecov.io/gh/CHOP-CGTInformatics/REDCapTidieR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/CHOP-CGTInformatics/REDCapTidieR?branch=main)
[![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/6845/badge)](https://bestpractices.coreinfrastructure.org/projects/6845)


The REDCapTidieR package provides an elegant way to [import](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#import) data from a [REDCap](https://projectredcap.org/) [project](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#project) into an R environment. It builds upon the [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package to query the [REDCap API](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#redcap-api) and then transforms the returned data into a set of [tidy](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tidy) [tibbles](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tibble).

REDCapTidieR is especially useful for dealing with complex REDCap projects that are [longitudinal](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#longitudinal-project) or include [repeating](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#repeating) [instruments](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#instrument) or both.

## Installation

The release version can be installed from [CRAN](https://cran.r-project.org/package=REDCapTidieR).

```r
install.packages("REDCapTidieR")
```

You can install the development version of REDCapTidieR from [GitHub](https://github.com/CHOP-CGTInformatics/REDCapTidieR):

```r
devtools::install_github("CHOP-CGTInformatics/REDCapTidieR")
```

## Usage

Use `read_redcap()` together with `bind_tibbles()` to import data from all instruments into your environment.

![Demonstration of using the `read_redcap()` and `bind_tibbles()` functions](man/figures/redcaptidier-demo.gif)

REDCapTidieR supports labelled data using the [labelled](https://larmarange.github.io/labelled/) package, and it can generate statistical summaries using the [skimr](https://docs.ropensci.org/skimr/) package. 

Read the [Getting Started vignette](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/REDCapTidieR.html) to learn more.

In addition, you can easily create collaborator-friendly Excel files using the `write_redcap_xlsx()` function:

```{r, eval=FALSE}
redcap_uri <- "https://my.institution.edu/redcap/api/"
token <- "123456789ABCDEF123456789ABCDEF04"

my_redcap_data <- read_redcap(redcap_uri, token)
write_redcap_xlsx(my_redcap_data, file = "my_redcap_data.xlsx")
```

![Sample REDCapTidieR .xlsx output using `write_redcap_xlsx()`](man/figures/write_xlsx_default.png)

To learn more about how to work with and customize the output, read the [Exporting to Excel vignette](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/export_to_xlsx.html).

## Collaboration

We invite you to give feedback and collaborate with us! If you are familiar with GitHub and R packages, please feel free to submit a [pull request](https://github.com/CHOP-CGTInformatics/REDCapTidieR/pulls). Please do let us know if REDCapTidieR fails for whatever reason with your database and submit a bug report by creating a GitHub [issue](https://github.com/CHOP-CGTInformatics/REDCapTidieR/issues).

Please note that this project is released with a [Contributor Code of Conduct](https://github.com/CHOP-CGTInformatics/REDCapTidieR/blob/main/CONDUCT.md). By participating you agree to abide by its terms.

We'd like to thank the following folks for their advice and code contributions: [Will Beasley](https://github.com/wibeasley) and [Paul Wildenhain](https://github.com/pwildenhain).

## Funding

This package was developed by the [Children's Hospital of Philadelphia](https://www.chop.edu) Cell and Gene Therapy Informatics Team to support the needs of the [Cellular Therapy and Transplant Section](https://www.chop.edu/centers-programs/cellular-therapy-and-transplant-section). The development was funded using the following sources:

-   *Stephan Kadauke Start-up funds.* Stephan Kadauke, PI, CHOP, 2018-2024

-   *CHOP-based GMP cell manufacturing (MFG) for CAR T clinical trials*. Stephan Grupp, PI; Stephan Kadauke, co-PI, CHOP, 2021-2023

Owner

  • Name: CHOP - CGT Informatics
  • Login: CHOP-CGTInformatics
  • Kind: organization

Open-source and public work for CHOP CGT Informatics

JOSS Publication

REDCapTidieR: Extracting complex REDCap databases into tidy tables
Published
February 17, 2024
DOI
Volume 9, Issue 94, Page 6277
Authors
Richard Hanna ORCID
Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
Ezra Porter ORCID
Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
Stephany Romero
Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
Paul Wildenhain
Division of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
William Beasley ORCID
Department of Pediatrics, The University of Oklahoma Health Sciences Center, College of Medicine, Oklahoma City, Oklahoma, USA
Stephan Kadauke ORCID
Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, Division of Transfusion Medicine, Children's Hospital of Philadelphia, Pennsylvania, Division of Pathology Informatics, Children's Hospital of Philadelphia, Pennsylvania
Editor
Michael Mahoney ORCID
Tags
REDCap data management
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 14
  • Release event: 5
  • Issues event: 13
  • Watch event: 4
  • Delete event: 10
  • Issue comment event: 50
  • Push event: 56
  • Pull request event: 17
  • Pull request review event: 24
  • Pull request review comment event: 16
  • Fork event: 2
Last Year
  • Create event: 14
  • Release event: 5
  • Issues event: 13
  • Watch event: 4
  • Delete event: 10
  • Issue comment event: 50
  • Push event: 56
  • Pull request event: 17
  • Pull request review event: 24
  • Pull request review comment event: 16
  • Fork event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 789
  • Total Committers: 10
  • Avg Commits per committer: 78.9
  • Development Distribution Score (DDS): 0.625
Past Year
  • Commits: 94
  • Committers: 6
  • Avg Commits per committer: 15.667
  • Development Distribution Score (DDS): 0.479
Top Committers
Name Email Commits
Richard Hanna r****1@g****m 296
Richard Hanna H****1@E****U 261
Ezra Porter 6****r 131
Stephan Kadauke K****S@E****U 90
Douglas Ezra Morrison d****n@u****u 5
Will Beasley w****y@h****m 2
olivroy o****1@h****m 1
Michael Mahoney m****8@g****m 1
Joseph Larmarange j****h@l****t 1
Elin Waring e****g@g****m 1
Committer Domains (Top 20 + Academic)
email.chop.edu: 2 larmarange.net: 1 ucdavis.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 84
  • Total pull requests: 100
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 21
  • Total pull request authors: 8
  • Average comments per issue: 3.0
  • Average comments per pull request: 1.79
  • Merged pull requests: 93
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 22
  • Average time to close issues: 13 days
  • Average time to close pull requests: 3 days
  • Issue authors: 7
  • Pull request authors: 5
  • Average comments per issue: 4.1
  • Average comments per pull request: 0.82
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rsh52 (36)
  • ezraporter (21)
  • skadauke (5)
  • pbilodeau94 (2)
  • RhysPeploe (2)
  • spgarbet (2)
  • larmarange (2)
  • higgi13425 (2)
  • d-morrison (2)
  • johnryan412 (1)
  • tschuler (1)
  • mike-caarg (1)
  • bcuer (1)
  • camcaan (1)
  • shannonpileggi (1)
Pull Request Authors
  • rsh52 (59)
  • ezraporter (39)
  • skadauke (10)
  • larmarange (2)
  • mikemahoney218 (2)
  • elinw (1)
  • d-morrison (1)
  • olivroy (1)
Top Labels
Issue Labels
enhancement (53) bug (29) backlog (14) documentation (3) refactor (2)
Pull Request Labels
enhancement (47) bug (34) documentation (22) joss (6)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 403 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 14
  • Total maintainers: 1
cran.r-project.org: REDCapTidieR

Extract 'REDCap' Databases into Tidy 'Tibble's

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 403 Last month
  • Docker Downloads: 21,613
Rankings
Forks count: 10.1%
Stargazers count: 11.6%
Average: 24.6%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Downloads: 35.9%
Maintainers (1)
richardshanna91@gmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • REDCapR >= 1.0.9000 imports
  • checkmate * imports
  • dplyr * imports
  • purrr * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • testthat >= 3.0.0 suggests
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  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
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  • r-lib/actions/setup-renv v2 composite
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  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
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.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite