riskmetric

Metrics to evaluate the risk of R packages

https://github.com/pharmar/riskmetric

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
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DOI references
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Academic publication links
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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 (16.3%) to scientific vocabulary

Keywords from Contributors

cdisc

Last synced: 9 months ago · JSON representation

Repository

Metrics to evaluate the risk of R packages

Basic Info

Host: GitHub
Owner: pharmaR
License: other
Language: R
Default Branch: master
Homepage: https://pharmar.github.io/riskmetric/
Size: 3.8 MB

Statistics

Stars: 170
Watchers: 14
Forks: 35
Open Issues: 131
Releases: 5

Created over 7 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog License

riskmetric

riskmetric is a collection of risk metrics to evaluate the quality of R packages.

This package is in experimentation. Final considerations about design are being considered, but core concepts are considered final.

Background

The risk of using an R package is evaluated based on a number of metrics meant to evaluate development best practices, code documentation, community engagement and development sustainability. We hope to provide a framework to quantify risk by assessing these metrics. This package serves as a starting point for exploring the heterogeneity of code quality, and begin a broader conversation about the validation of R packages. Primarily, this effort aims to provide some context for validation within regulated industries.

We separate three steps in the workflow to assess the risk of an R package using riskmetric:

Finding a source for package information (installed package or CRAN/git source) pkg_ref()
Assessing the package under validation criteria pkg_assess()
Scoring assessment criteria pkg_score()

The results will be assembled in a dataset of validation criteria containing an overall risk score for each package as shown in the example below.

Installation

You can install riskmetric from CRAN with:

r install.packages("riskmetric")

Or from GitHub using devtools with:

r devtools::install_github("pharmaR/riskmetric")

Example

Scrape metadata locally or remotely, then assess that metadata and score it to estimate risk. For each package, derive a composite measure of risk, or a collection of individual scores which can be easily used to generate validation reports.

```r library(dplyr) library(riskmetric)

pkgref(c("riskmetric", "utils", "tools")) %>% pkgassess() %>% pkg_score() ```

The `{riskassessment}` application

riskassessment is a full-fledged R package containing a shiny front-end that augments the utility of riskmetric. The application's goal is to provide a central hub for an organization to review and assess the risk of R packages, providing handy tools and guide rails along the way. The app uses a local database to store & display:

all riskmetric metrics, including package risk scores over time
organization-wide metric weighting, plus rules to automate org decisions (whether to endorse/ prohibit the pkg)
package-level user dialogue on the perceived risk, to facilitate communication & notes

To learn more about riskassessment, please browse the user guide or consider taking the demo app for a spin.

Get Involved

We have a bi-weekly sprint meeting for developers to discuss the progress.

Contact eric.milliman@biogen.com to be added to the meeting.
Project Planning Meeting Structure
Milestone

riskmetric is centrally a community project. Comfort with a quantification of risk comes via consensus, and for that this project is dependent on close community engagement. There are plenty of ways to help:

Share the package
File issues when you encounter bugs
Weigh in on proposed metrics, or suggest a new one
Help us devise the best way to summarize risk into a single score
Help us keep documentation up to date
Contribute code to tackle the metric backlog

Owner

Name: pharmaR
Login: pharmaR
Kind: organization

Repositories: 6
Profile: https://github.com/pharmaR

GitHub Events

Total

Create event: 7
Release event: 1
Issues event: 26
Watch event: 10
Delete event: 4
Issue comment event: 39
Push event: 35
Pull request review comment event: 4
Pull request review event: 18
Pull request event: 17
Fork event: 4

Last Year

Create event: 7
Release event: 1
Issues event: 26
Watch event: 10
Delete event: 4
Issue comment event: 39
Push event: 35
Pull request review comment event: 4
Pull request review event: 18
Pull request event: 17
Fork event: 4

Committers

Last synced: over 2 years ago

All Time

Total Commits: 407
Total Committers: 21
Avg Commits per committer: 19.381
Development Distribution Score (DDS): 0.703

Past Year

Commits: 52
Committers: 6
Avg Commits per committer: 8.667
Development Distribution Score (DDS): 0.558

Top Committers

Name	Email	Commits
dgkf	1****f	121
Eric Milliman	e**n@b**m	38
elimillera	e**a@g**m	36
Yilong Zhang	y**g@m**m	32
Eric Milliman	e**4@g**m	28
Marly Gotti	m**i@g**m	27
Kevin	k**n@g**t	20
yilong zhang	e**7@g**m	16
Eli Miller	E**a@g**m	16
Sam Parmar	1****r	15
Marly Gotti	m**r@b**m	12
Yilong Zhang	z**o@c**m	12
Eric Milliman	e****5	9
Wang, Sheng-Wei [JRDUS]	s**9@I**m	6
jmanitz	j**z@e**m	5
James J. Kim	j**m@p**m	4
mpadge	m**m@e**m	4
Eli Miller	E**r@A**m	3
Elio Campitelli	e**i@g**m	1
Martin R. Smith	1****9	1
AARON-CLARK	c**s@g**m	1

Committer Domains (Top 20 + Academic)

biogen.com: 2 atorusresearch.com: 1 email.com: 1 pfizer.com: 1 emdserono.com: 1 its.jnj.com: 1 ctchpcpe001.merck.com: 1 gmx.net: 1 merck.com: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 140
Total pull requests: 66
Average time to close issues: 8 months
Average time to close pull requests: 2 months
Total issue authors: 44
Total pull request authors: 22
Average comments per issue: 1.49
Average comments per pull request: 2.11
Merged pull requests: 48
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 22
Pull requests: 21
Average time to close issues: 9 days
Average time to close pull requests: 5 days
Issue authors: 8
Pull request authors: 7
Average comments per issue: 0.23
Average comments per pull request: 1.67
Merged pull requests: 13
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

dgkf (22)
emilliman5 (18)
elong0527 (15)
fh-kpikhart (8)
parmsam-pfizer (8)
AARON-CLARK (7)
llrs-roche (5)
elimillera (4)
nicolekjones (3)
paulie-of-punskas (3)
thebioengineer (3)
Edward-Gillian (2)
pawelru (2)
rabiibouhestine (2)
wiligl (2)

Pull Request Authors

emilliman5 (15)
elimillera (10)
llrs-roche (8)
parmsam-pfizer (7)
rabiibouhestine (6)
fh-kpikhart (4)
narayanan-iyer-pfizer (4)
olivroy (2)
kimjj93 (2)
Gotfrid (2)
jthompson-arcus (2)
dgkf (2)
thisisnic (2)
AKlebus (2)
ghost (1)

Top Labels

Issue Labels

Enhancement (22) Metric Proposal (21) Bug (18) Discussion (17) Difficulty: Low (11) Difficulty: Medium (11) Strategy (8) High Priority (7) Cohort Metric (7) Difficulty: High (4) remotes ☐ (4) Package Integration (3) Hacktoberfest (3) source ☐ (2) Duplicate/Redundant (1) source ☑️ (1) remotes ☑️ (1) status: awaiting dev planning (1)

Pull Request Labels

Enhancement (3) Bug (1)

Packages

Total packages: 4
Total downloads:
- cran 349 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 20
Total maintainers: 1

proxy.golang.org: github.com/pharmaR/riskmetric

Documentation: https://pkg.go.dev/github.com/pharmaR/riskmetric#section-documentation
License: other
Latest release: v0.2.5
published over 1 year ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 10 months ago

proxy.golang.org: github.com/pharmar/riskmetric

Documentation: https://pkg.go.dev/github.com/pharmar/riskmetric#section-documentation
License: other
Latest release: v0.2.5
published over 1 year ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 10 months ago

cran.r-project.org: riskmetric

Risk Metrics to Evaluating R Packages

Homepage: https://pharmar.github.io/riskmetric/
Documentation: http://cran.r-project.org/web/packages/riskmetric/riskmetric.pdf
License: MIT + file LICENSE
Latest release: 0.2.5
published over 1 year ago

Versions: 9
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 349 Last month

Rankings

Stargazers count: 2.8%

Forks count: 3.2%

Average: 19.6%

Dependent repos count: 23.8%

Dependent packages count: 28.7%

Downloads: 39.5%

Maintainers (1)

eli.miller@atorusresearch.com

Last synced: 10 months ago

conda-forge.org: r-riskmetric

Homepage: https://pharmar.github.io/riskmetric/, https://github.com/pharmaR/riskmetric
License: MIT
Latest release: 0.1.2
published almost 4 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Stargazers count: 29.0%

Average: 32.2%

Forks count: 35.4%

Last synced: 10 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
actions/upload-artifact main 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/pkgdown.yaml actions

actions/checkout 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/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

DESCRIPTION cran

BiocManager * imports
backports * imports
covr * imports
cranlogs * imports
curl * imports
devtools * imports
httr * imports
memoise * imports
pillar * imports
pkgload * imports
qpdf * imports
tibble * imports
tools * imports
urltools * imports
utils * imports
vctrs * imports
xml2 * imports
dplyr * suggests
jsonlite * suggests
knitr * suggests
magrittr * suggests
rmarkdown * suggests
testthat * suggests
webmockr * suggests
withr * suggests

tests/testthat/test_packages/pkgsourcebad/DESCRIPTION cran

R >= 3.1.2 depends
testthat * suggests

tests/testthat/test_packages/pkgsourcegood/DESCRIPTION cran

R >= 3.1.2 depends
testthat * suggests

tests/testthat/test_packages/secondLib/secondLibPkg/DESCRIPTION cran

R >= 3.1.2 depends
testthat * suggests

riskmetric

Science Score: 26.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

riskmetric

Background

Installation

Example

The {riskassessment} application

Get Involved

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/pharmaR/riskmetric

Rankings

proxy.golang.org: github.com/pharmar/riskmetric

Rankings

cran.r-project.org: riskmetric

Rankings

Maintainers (1)

conda-forge.org: r-riskmetric

Rankings

Dependencies

The `{riskassessment}` application