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sdtmchecks

Analysis facing checks for SDTM data

https://github.com/pharmaverse/sdtmchecks

Science Score: 26.0%

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
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (20.5%) to scientific vocabulary

Keywords from Contributors

projection interactive serializer cycles packaging charts network-simulation shellcodes hacking autograding
Last synced: 9 months ago · JSON representation

Repository

Analysis facing checks for SDTM data

Basic Info
Statistics
  • Stars: 23
  • Watchers: 5
  • Forks: 8
  • Open Issues: 87
  • Releases: 2
Created almost 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)
```

# sdtmchecks


drawing


[![R-CMD-check](https://github.com/pharmaverse/sdtmchecks/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/pharmaverse/sdtmchecks/actions/workflows/R-CMD-check.yml) 
[![codecov](https://codecov.io/github/pharmaverse/sdtmchecks/branch/devel/graph/badge.svg)](https://app.codecov.io/github/pharmaverse/sdtmchecks) 
[![CRAN status](https://www.r-pkg.org/badges/version/sdtmchecks)](https://cran.r-project.org/package=sdtmchecks)
![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/sdtmchecks)

 

The sdtmchecks package contains functions to identify common data issues in SDTM data. These checks are intended to be **generalizable**, **actionable**, and **meaningful for analysis**.


## Installation

### CRAN

You can install {sdtmchecks} from [CRAN](https://cran.r-project.org/):

``` r
install.packages("sdtmchecks")
```
### Development version (devel branch)

The development version (based on the default *devel branch*) can be installed via:
``` r
install.packages("sdtmchecks", repos = "https://pharmaverse.r-universe.dev")  

```

Or, via [GitHub](https://github.com/) repo `pharmaverse/sdtmchecks@HEAD`:

``` r
# install.packages("devtools")
devtools::install_github("pharmaverse/sdtmchecks")

# Note that `ref = "devel"` is not needed since devel is the default branch

```



## Use the package

The [Get started page](https://pharmaverse.github.io/sdtmchecks/articles/sdtmchecks.html) walks you through how the package can be used. 


## Data checks in the package

To search available data check functions, please see [this search page](https://pharmaverse.github.io/sdtmchecks/articles/search_checks.html).

The main data check functions of the package are saved as R program files beginning with **"check_..."** and are referenced under the [Data Checks](https://pharmaverse.github.io/sdtmchecks/reference/index.html#data-checks) portion of the Reference page.


## SDTM version

This package aims to be SDTM version agnostic and does not require users to specify the version. 


## Contributing

This package has been developed internally at [Roche](https://www.roche.com/) since 2014. There may be areas where the checks expect Roche-specific SDTM implementation choices. Proposed additions or modifications should attempt to maintain generalizability for slightly different data standards across companies. For examples on how to do so and to learn more about contributing in general, please refer to the [Writing a New Check](https://pharmaverse.github.io/sdtmchecks/articles/write_a_check.html) page.  

If you have an idea for a new check but no time for development, please [open an issue](https://github.com/pharmaverse/sdtmchecks/issues).


## FAQs

The package [FAQs](https://pharmaverse.github.io/sdtmchecks/articles/faqs.html) may provide additional information you are looking for. If not, please feel free to post your question as [an issue](https://github.com/pharmaverse/sdtmchecks/issues).

Owner

  • Name: pharmaverse
  • Login: pharmaverse
  • Kind: organization
  • Location: Switzerland

GitHub Events

Total
  • Issues event: 5
  • Watch event: 2
  • Issue comment event: 4
  • Push event: 3
  • Pull request event: 5
  • Pull request review event: 2
  • Create event: 1
Last Year
  • Issues event: 5
  • Watch event: 2
  • Issue comment event: 4
  • Push event: 3
  • Pull request event: 5
  • Pull request review event: 2
  • Create event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 640
  • Total Committers: 16
  • Avg Commits per committer: 40.0
  • Development Distribution Score (DDS): 0.558
Past Year
  • Commits: 118
  • Committers: 9
  • Avg Commits per committer: 13.111
  • Development Distribution Score (DDS): 0.653
Top Committers
Name Email Commits
Bodach, Sara {MDBB~South San Francisco} b****a@g****m 283
harric17 h****l@g****m 196
sarabodach s****h 42
harriscw h****w 35
Wang, Laura {TBB~SOUTH SAN FRANCISCO} w****a@g****m 35
lomaxj1 j****x@r****m 17
Shuliar, Vladyslav {TDBP~WELWYN} v****r@r****m 7
Kimberly Fernandes k****s@r****m 6
Alcaraz, Josue {TBB~SOUTH SAN FRANCISCO} a****e@g****m 5
Ross Farrugia 8****a 4
vrakinav v****a@g****m 3
laywang142 l****2 2
Shah, Monarch {MDBU~South San Francisco} s****h@g****m 2
Mancini, Edoardo {MDBB~Welwyn} e****i@r****m 1
AlcJ123 A****3 1
dependabot[bot] 4****] 1
Committer Domains (Top 20 + Academic)
gene.com: 5 roche.com: 4

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 52
  • Total pull requests: 59
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 11 days
  • Total issue authors: 10
  • Total pull request authors: 7
  • Average comments per issue: 0.42
  • Average comments per pull request: 0.66
  • Merged pull requests: 52
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 3
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 1 month
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sarabodach (36)
  • harriscw (13)
  • manciniedoardo (2)
  • parmsam-pfizer (2)
  • rossfarrugia (2)
  • vbshuliar (2)
  • billdenney (2)
  • pawelru (1)
  • fernank8 (1)
  • jimrothstein (1)
  • monarch83 (1)
Pull Request Authors
  • harriscw (65)
  • sarabodach (31)
  • AlcJ123 (8)
  • jimrothstein (4)
  • vbshuliar (3)
  • manciniedoardo (1)
  • rossfarrugia (1)
  • monarch83 (1)
  • laywang142 (1)
  • fernank8 (1)
Top Labels
Issue Labels
documentation (18) dev (8) CI/CD (5) new check (5) update existing check (5) enhancement (2) good first issue (2) help wanted (1) question (1) bug (1)
Pull Request Labels
documentation (4) good first issue (2) update existing check (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 119 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: sdtmchecks

Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 119 Last month
Rankings
Dependent packages count: 28.5%
Dependent repos count: 35.2%
Average: 50.1%
Downloads: 86.7%
Maintainers (1)
harric17@gene.com
Last synced: 10 months ago

Dependencies

.github/workflows/R-CMD-check.yml actions
  • actions/checkout v3 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
  • tj-actions/branch-names v5.4 composite
.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
DESCRIPTION cran
  • dplyr * imports
  • openxlsx * imports
  • tidyselect * imports
  • knitr * suggests
  • rmarkdown * suggests
.github/workflows/document.yml actions
  • actions/checkout v3 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
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite