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teal.modules.clinical

Provides teal modules for the standard clinical trials outputs

https://github.com/insightsengineering/teal.modules.clinical

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 (11.9%) to scientific vocabulary

Keywords

clinical-trials modules nest outputs r shiny

Keywords from Contributors

general-purpose rna-seq statistical-engineering cdisc
Last synced: 6 months ago · JSON representation

Repository

Provides teal modules for the standard clinical trials outputs

Basic Info
Statistics
  • Stars: 39
  • Watchers: 24
  • Forks: 19
  • Open Issues: 106
  • Releases: 17
Topics
clinical-trials modules nest outputs r shiny
Created over 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Security

README.md

teal.modules.clinical

CRAN Version Total Downloads Last Month Downloads Last Week Downloads

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GitHub commit activity GitHub contributors GitHub last commit GitHub pull requests GitHub repo size GitHub language count Project Status: Active -- The project has reached a stable, usable state and is being actively developed. Current Version Open Issues <!-- end badges -->

This package contains a set of standard teal modules to be used with CDISC data in order to generate many of the standard outputs used in clinical trials.

These modules include, but are not limited to:

  • Data visualizations:
    • Forest plots (tm_g_forest_rsp()/tm_g_forest_tte())
    • Line plots (tm_g_lineplot())
    • Kaplan-Meier plots (tm_g_km())
    • ...
  • Statistical model fits:
    • MMRM (tm_a_mmrm())
    • Logistic regression (tm_t_logistic())
    • Cox regression (tm_t_coxreg())
    • ...
  • Summary tables:
    • Unique patients (tm_t_summary())
    • Exposure across patients (tm_t_exposure())
    • Change from baseline for parameters (tm_t_summary_by())
    • ...
  • Patient-level profile modules:
    • Table of basic information about chosen patient (tm_t_pp_basic_info())
    • Plot of patient vitals over time (tm_g_pp_vitals())
    • General timeline for individual patients (tm_g_pp_patient_timeline())
    • ...

Most modules in the package are implemented using functions from the R package tern in order to produce their output.

Please see the Teal Gallery and TLG Catalog for examples of shiny apps created using modules from this package.

Installation

r install.packages('teal.modules.clinical')

Alternatively, you might want to use the development version.

```r

install.packages("pak")

pak::pak("insightsengineering/teal.modules.clinical") ```

Usage

To understand how to use this package, please refer to the Getting Started article, which provides multiple examples of code implementation.

Playground

You can try out the package without installing it in the Shinylive:

Getting help

If you encounter a bug or have a feature request, please file an issue. For questions, discussions, and staying up to date, please use the teal channel in the pharmaverse slack workspace.

Acknowledgment

This package is the result of the joint efforts of many developers and stakeholders. We would like to thank everyone who has contributed so far!

Stargazers and Forkers

Stargazers over time

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Stargazers

Stargazers repo roster for

Forkers

Forkers repo roster for

Owner

  • Name: Roche/Genentech - Insights Engineering
  • Login: insightsengineering
  • Kind: organization
  • Location: Switzerland

Roche/Genentech - Insights Engineering

GitHub Events

Total
  • Create event: 101
  • Release event: 3
  • Issues event: 105
  • Watch event: 6
  • Delete event: 99
  • Issue comment event: 405
  • Push event: 1,422
  • Pull request review comment event: 239
  • Pull request event: 189
  • Pull request review event: 352
  • Fork event: 2
Last Year
  • Create event: 101
  • Release event: 3
  • Issues event: 105
  • Watch event: 6
  • Delete event: 99
  • Issue comment event: 405
  • Push event: 1,422
  • Pull request review comment event: 239
  • Pull request event: 189
  • Pull request review event: 352
  • Fork event: 2

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 2,025
  • Total Committers: 85
  • Avg Commits per committer: 23.824
  • Development Distribution Score (DDS): 0.84
Past Year
  • Commits: 144
  • Committers: 16
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.792
Top Committers
Name Email Commits
waddella a****l@r****m 323
Emily de la Rua 5****a 230
Rucki, Pawel {MDBB~Basel} p****i@r****m 78
Hallal, Mahmoud {MDBB~Basel} m****l@r****m 75
shajoezhu s****u 69
Pagacz, Konrad {FIEV~Warsaw} k****z@c****m 64
gogonzo g****o 54
Marcin 1****r 54
wangh107 w****7@g****m 49
Rosemary Li 4****7 45
Nikolas Burkoff n****f@r****m 42
Collin, Francois {FISV~Warsaw} f****n@c****m 40
Zhao, Junlue {MDBE~SOUTH SAN FRANCISCO} z****e@g****m 39
Wang, Heng {MDBB~South San Francisco} w****g@g****m 38
Stoilova, Jana {MDBB~Mississauga} j****a@r****m 36
Sundrelingam, Vaakesan {MDBA~Mississauga} v****m@r****m 34
Vedha Viyash 4****v 31
ruckip p****i@c****m 31
liaoc10 c****o@r****m 30
Abinaya Yogasekaram 7****m 28
rothem1 m****e@r****m 28
songy24 y****g@r****m 27
nikolas-burkoff n****f 25
André Veríssimo 2****o 24
Sebastian Wolf s****1@r****m 23
Nasinski, Maciej {FIEV~Warsaw} m****i@c****m 22
Insights Engineering Bot 6****t 22
Imanol Zubizarreta 8****i 22
J Zhao j****5@g****m 22
Melkiades M****s 21
and 55 more...
Committer Domains (Top 20 + Academic)
roche.com: 22 gene.com: 12 contractors.roche.com: 6 atorusresearch.com: 1 wangh107-9ehtd7.dhcp.gene.com: 1 tessella.com: 1 sebastian.wolf.sw1: 1 wangh107-9ehtd7.wifi.gene.com: 1 users.noreply.github.roche.com: 1 waddell.ch: 1 cybertronika.eu: 1 nala.roche.com: 1 businesspartner.roche.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 254
  • Total pull requests: 402
  • Average time to close issues: 2 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 46
  • Total pull request authors: 30
  • Average comments per issue: 1.4
  • Average comments per pull request: 2.29
  • Merged pull requests: 325
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 67
  • Pull requests: 202
  • Average time to close issues: 10 days
  • Average time to close pull requests: 3 days
  • Issue authors: 25
  • Pull request authors: 13
  • Average comments per issue: 1.03
  • Average comments per pull request: 2.36
  • Merged pull requests: 163
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cicdguy (59)
  • shajoezhu (51)
  • donyunardi (15)
  • edelarua (14)
  • m7pr (10)
  • jenko1979 (9)
  • llrs-roche (8)
  • pawelru (7)
  • vedhav (6)
  • anajens (6)
  • kartikeyakirar (6)
  • averissimo (5)
  • Mia-data (5)
  • chlebowa (4)
  • gogonzo (4)
Pull Request Authors
  • m7pr (75)
  • edelarua (65)
  • vedhav (60)
  • averissimo (52)
  • llrs-roche (36)
  • shajoezhu (19)
  • gogonzo (12)
  • pawelru (11)
  • ayogasekaram (10)
  • kartikeyakirar (9)
  • yli110-stat697 (8)
  • donyunardi (6)
  • kpagacz (4)
  • walkowif (4)
  • insights-engineering-bot (3)
Top Labels
Issue Labels
sme (111) core (74) enhancement (65) bug (56) question (17) priority (9) New (6) SP1 (6) blocked (5) documentation (4) discussion (4) low-priority (3) research (3) SP8 (3) good first issue (3) refactor (2) SP2 (2) refined (2) SP5 (2) release (2) migrate (1)
Pull Request Labels
core (261) sme (109) bug (6) enhancement (4) documentation (3) automation (3) blocked (2) devops (1) request changes (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 445 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: teal.modules.clinical

'teal' Modules for Standard Clinical Outputs

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 445 Last month
Rankings
Dependent packages count: 28.1%
Dependent repos count: 36.1%
Average: 49.7%
Downloads: 84.8%
Maintainers (1)
dawid.kaledkowski@roche.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6 depends
  • teal >= 0.12.0 depends
  • tern >= 0.7.10 depends
  • DT * imports
  • assertthat * imports
  • broom * imports
  • checkmate * imports
  • dplyr * imports
  • formatters >= 0.3.1 imports
  • ggplot2 * imports
  • ggrepel * imports
  • grid * imports
  • lifecycle * imports
  • logger >= 0.2.0 imports
  • magrittr * imports
  • methods * imports
  • rlang * imports
  • rmarkdown * imports
  • rtables >= 0.5.1 imports
  • scales * imports
  • shiny * imports
  • shinyWidgets * imports
  • shinyjs * imports
  • shinyvalidate * imports
  • stats * imports
  • styler * imports
  • teal.code >= 0.2.0 imports
  • teal.logger >= 0.1.1 imports
  • teal.reporter >= 0.1.1 imports
  • teal.transform >= 0.2.0 imports
  • teal.widgets >= 0.2.0 imports
  • tern.gee >= 0.0.0.9002 imports
  • tern.mmrm >= 0.2.2 imports
  • tidyr * imports
  • utils * imports
  • vistime * imports
  • forcats * suggests
  • knitr * suggests
  • nestcolor >= 0.1.0 suggests
  • scda >= 0.1.5 suggests
  • scda.2022 >= 0.1.3 suggests
  • teal.data >= 0.1.2 suggests
  • testthat >= 2.0 suggests