EDCimport

Import data from EDC softwares

https://github.com/danchaltiel/edcimport

Science Score: 26.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
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Academic publication links
○
Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (16.7%) to scientific vocabulary

Keywords from Contributors

interpretability standardization hack

Last synced: 10 months ago · JSON representation

Repository

Import data from EDC softwares

Basic Info

Host: GitHub
Owner: DanChaltiel
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://danchaltiel.github.io/EDCimport/
Size: 21.4 MB

Statistics

Stars: 0
Watchers: 2
Forks: 1
Open Issues: 10
Releases: 0

Created over 4 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Codemeta

EDCimport

Introduction 📦

The EDCimport package is designed to simplify the import and management of Electronic Data Capture (EDC) exports, particularly in clinical research settings. It is an opinionated framework, providing multiple streamlined tools for importing, cleaning, and checking your datasets.

[!WARNING] This package is experimental and under active development. Backward compatibility is not a priority for the moment. For reproducibility, use renv to set the package version.

Installation 🛠️

``` r

Install last version available on CRAN

install.packages("EDCimport")

Install development version on Github

pak::pak("DanChaltiel/EDCimport@v0.6.0.9002") ```

[!WARNING] The documentation pertains to the dev version, not the one on CRAN.

Features 🚀

Load the data

Use one of read_all_sas(), read_all_xpt(), read_all_csv(), or read_trialmaster(), depending on the type of files in your export directory. You can then load your datasets into the global environment with load_database().

r library(EDCimport) db = read_all_sas("path/to/my/files/folder") print(db) load_database(db) #this also removes `db` to save some RAM mean(dataset1$column5)

Database management tools

EDCimport includes a set of useful tools that help with using the imported database. See References for the complete list.

Database summary

edc_lookup() returns a dataframe containing the number of rows, columns, patients, and the CRF name of each dataset.

Search the whole database

find_keyword() runs a global search of the database for a given keyword (or regex).

For instance, say you are looking for the "date of ECG" but don't know where it is, you can run find_keyword("date") or find_keyword("ecg").

It won't look into the actual data, though, as this would take too much computing power.

Get the last news date of each subject

lastnews_table() finds the last date of each subject throughout the whole database and inform on the date original dataset and column. It has arguments to avoid selecting irrelevant dates.

This is very useful to get the actual followup time when fitting survival analyses.

Data checking system

edc_data_warn() throws a warning if an inconsistency is found in a dataset. The interface allows to perform multiple checks and get a report as a CSV file.

Join helpers

As the primary key is almost always the Subject ID, join helpers were added to reduce code clutter. Currently, only edc_left_join(), edc_right_join(), and edc_full_join() are supported.

Shiny browser

edc_viewer() runs a shiny application that browses the whole database. The HTML interface is quicker and less cluttered than it would be in RStudio. It also allows filtering by Subject ID.

Swimmer Plot

edc_swimmerplot() creates a swimmer plot of all date variables of the whole database. This is very useful to find inconsistencies and outliers, especially with the plotly interactive output.

Owner

Name: Dan Chaltiel
Login: DanChaltiel
Kind: user
Location: France
Company: @gustaveroussy

Twitter: DanChaltiel
Repositories: 4
Profile: https://github.com/DanChaltiel

Data analyst (PharmD, PhD) and programming enthusiast. I love to code in R (tidyverse FTW!) but also in Kotlin/Java (Android), Python, PHP, JS, Arduino...

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GitHub Events

Total

Create event: 77
Release event: 1
Issues event: 56
Delete event: 3
Issue comment event: 5
Push event: 233
Pull request event: 9

Last Year

Create event: 77
Release event: 1
Issues event: 56
Delete event: 3
Issue comment event: 5
Push event: 233
Pull request event: 9

Committers

Last synced: about 1 year ago

All Time

Total Commits: 957
Total Committers: 2
Avg Commits per committer: 478.5
Development Distribution Score (DDS): 0.185

Past Year

Commits: 633
Committers: 2
Avg Commits per committer: 316.5
Development Distribution Score (DDS): 0.172

Top Committers

Name	Email	Commits
Dan Chaltiel	1****l	780
github-actions	4****]	177

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 92
Total pull requests: 6
Average time to close issues: about 1 month
Average time to close pull requests: 9 days
Total issue authors: 4
Total pull request authors: 1
Average comments per issue: 0.25
Average comments per pull request: 0.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 35
Pull requests: 6
Average time to close issues: 14 days
Average time to close pull requests: 9 days
Issue authors: 3
Pull request authors: 1
Average comments per issue: 0.09
Average comments per pull request: 0.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

DanChaltiel (95)
Lpierott (2)
NusaibahIbr (1)
BaptisteArchambaud (1)

Pull Request Authors

DanChaltiel (8)

Top Labels

Issue Labels

enhancement (27) feature (21) bug (19) improvement (13) internal (7) documentation (4) Questionning (3) Feature request (2) question (1) Test (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 336 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 8
Total maintainers: 1

cran.r-project.org: EDCimport

Import Data from EDC Software

Homepage: https://github.com/DanChaltiel/EDCimport
Documentation: http://cran.r-project.org/web/packages/EDCimport/EDCimport.pdf
License: GPL-3
Latest release: 0.6.0
published 12 months ago

Versions: 8
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 336 Last month

Rankings

Forks count: 21.9%

Dependent packages count: 29.8%

Stargazers count: 35.2%

Dependent repos count: 35.5%

Average: 38.8%

Downloads: 71.5%

Maintainers (1)

dan.chaltiel@gmail.com

Last synced: 10 months ago

Dependencies

.github/workflows/check-standard.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 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/update_version.yaml actions

EndBug/add-and-commit v7.5.0 composite
actions/checkout v2 composite
r-lib/actions/setup-r v2 composite

DESCRIPTION cran

R >= 3.1.0 depends
cli * imports
dplyr * imports
forcats * imports
glue * imports
haven * imports
labelled * imports
purrr * imports
readr * imports
rlang * imports
stringr * imports
tibble * imports
tidyr * imports
callr * suggests
covr * suggests
crosstable * suggests
knitr * suggests
testthat >= 3.0.0 suggests
withr * suggests

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action v4.4.1 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