metalite.ae

An R package for standard adverse events analysis

https://github.com/merck/metalite.ae

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 (14.1%) to scientific vocabulary

Keywords

cdisc clinical-trials metadata r-package

Keywords from Contributors

biostatistics boundaries spending-functions ectd packaging-tool pharmaverse

Last synced: 6 months ago · JSON representation

Repository

An R package for standard adverse events analysis

Basic Info

Host: GitHub
Owner: Merck
License: gpl-3.0
Language: R
Default Branch: main
Homepage: http://merck.github.io/metalite.ae/
Size: 9.39 MB

Statistics

Stars: 21
Watchers: 4
Forks: 4
Open Issues: 6
Releases: 4

Topics

cdisc clinical-trials metadata r-package

Created almost 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License

metalite.ae

Installation

The easiest way to get metalite.ae is to install from CRAN:

r install.packages("metalite.ae")

Alternatively, to use a new feature or get a bug fix, you can install the development version of metalite.ae from GitHub:

```r

install.packages("remotes")

remotes::install_github("Merck/metalite.ae") ```

Overview

metalite.ae is an R package designed for the analysis of adverse events (AE) in clinical trials. It operates on ADaM datasets and adheres to the metalite structure. The R package streamlines the process of generating production-ready tables, listings, and figures as outlined in the AE summary chapter and the specific AE chapter of the R for Clinical Study Reports and Submission book. The package encompasses the following components:

AE summary

Specific AE analysis

AE listing

Highlighted features

Avoid duplicated input by using metadata structure.
- For example, define analysis population once to use in all adverse events analysis.
Consistent input and output in standard functions.
Streamlines mock table generation.

Example

r meta_ae_example() |> # Example AE data created using metalite prepare_ae_summary( population = "apat", # Select population by keywords observation = "wk12", # Select observation by keywords parameter = "any;rel;ser" # Select AE terms by keywords ) |> format_ae_summary() |> tlf_ae_summary( source = "Source: [CDISCpilot: adam-adsl; adae]", # Define data source path_outtable = "ae0summary.rtf" # Define output )

Additional tutorials

Owner

Name: Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc.
Login: Merck
Kind: organization
Location: Kenilworth, NJ

Website: http://www.merck.com
Repositories: 34
Profile: https://github.com/Merck

GitHub Events

Total

Create event: 12
Issues event: 6
Release event: 1
Watch event: 4
Delete event: 7
Member event: 2
Issue comment event: 4
Push event: 27
Pull request review event: 5
Pull request event: 13

Last Year

Create event: 12
Issues event: 6
Release event: 1
Watch event: 4
Delete event: 7
Member event: 2
Issue comment event: 4
Push event: 27
Pull request review event: 5
Pull request event: 13

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 206
Total Committers: 18
Avg Commits per committer: 11.444
Development Distribution Score (DDS): 0.743

Top Committers

Name	Email	Commits
Nan Xiao	me@n****e	53
Wang, Benjamin	b**g@m**m	43
Yilong Zhang	e**7@g**m	24
Yilong Zhang	y**g@m**m	24
LittleBeannie	y**o@m**m	11
ginnaram	m**y@m**m	10
Ruchit Patel	4**2@u**m	7
baekhow	h**k@m**m	7
Nepal, Sarad	s**l@m**m	7
wangben718	8**8@u**m	5
Venkatesh Burla	v**a@m**m	4
BrianLang	b**9@g**m	4
Howard Baek	5**k@u**m	2
Brian Lang	B**g@u**m	1
turnbach	m**h@m**m	1
Yilong Zhang	e**7@f**m	1
Brian M Lang	b**g@B**l	1
Nan Xiao	n**1@m**m	1

Committer Domains (Top 20 + Academic)

merck.com: 9 fb.com: 1 nanx.me: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 61
Total pull requests: 112
Average time to close issues: 4 months
Average time to close pull requests: 7 days
Total issue authors: 11
Total pull request authors: 17
Average comments per issue: 1.21
Average comments per pull request: 0.85
Merged pull requests: 102
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 10
Average time to close issues: N/A
Average time to close pull requests: 6 days
Issue authors: 3
Pull request authors: 6
Average comments per issue: 0.25
Average comments per pull request: 0.2
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

LittleBeannie (15)
elong0527 (11)
nanxstats (10)
wangben718 (10)
fb-elong (4)
BrianLang (3)
ginnaram13 (2)
MargheAnna (1)
ruchitpatel2002 (1)
jialuo-liu (1)
lovestat (1)

Pull Request Authors

wangben718 (31)
nanxstats (27)
elong0527 (10)
fukuhiro2023 (10)
jeetendersinghc (10)
ginnaram13 (7)
LittleBeannie (6)
lm3388 (6)
narendrakolisetty (5)
BrianLang (4)
srnep (4)
howardbaek (4)
ruchitpatel2002 (2)
wangchen46 (2)
fb-elong (1)

Top Labels

Issue Labels

independent test (11) bug (5) documentation (3) enhancement (2) release (1) future (1) question (1)

Pull Request Labels

bug (2)

Packages

Total packages: 1
Total downloads:
- cran 602 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 3
Total maintainers: 1

cran.r-project.org: metalite.ae

Adverse Events Analysis Using 'metalite'

Homepage: https://merck.github.io/metalite.ae/
Documentation: http://cran.r-project.org/web/packages/metalite.ae/metalite.ae.pdf
License: GPL-3
Latest release: 0.1.3
published over 1 year ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 602 Last month

Rankings

Forks count: 14.2%

Stargazers count: 16.5%

Dependent repos count: 23.9%

Average: 26.0%

Dependent packages count: 28.7%

Downloads: 46.7%

Maintainers (1)

yujie.zhao@merck.com

Last synced: 6 months ago

Dependencies

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

actions/checkout v2 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

JamesIves/github-pages-deploy-action 4.1.4 composite
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

R >= 4.1.0 depends
DescTools * imports
dplyr * imports
glue * imports
haven * imports
metalite * imports
r2rtf * imports
stats * imports
tidyr * imports
covr * suggests
kableExtra * suggests
knitr * suggests
readxl * suggests
rmarkdown * suggests
rprojroot * suggests
testthat >= 3.0.0 suggests

.github/workflows/style.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

metalite.ae

Science Score: 26.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

metalite.ae

Installation

install.packages("remotes")

Overview

AE summary

Specific AE analysis

AE listing

Highlighted features

Example

Owner

GitHub Events

Total

Last Year

Committers

All Time

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

cran.r-project.org: metalite.ae

Rankings

Maintainers (1)

Dependencies