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crmPack

Object-Oriented Implementation of CRM Designs

https://github.com/openpharma/crmPack

Science Score: 49.0%

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
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 29 committers (3.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (19.4%) to scientific vocabulary

Keywords from Contributors

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

Repository

Object-Oriented Implementation of CRM Designs

Basic Info
Statistics
  • Stars: 21
  • Watchers: 10
  • Forks: 11
  • Open Issues: 106
  • Releases: 0
Created over 7 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Codeowners

README.Rmd 

---
output: github_document
---




# `crmPack` 


[![CRAN status](https://www.r-pkg.org/badges/version/crmPack)](https://CRAN.R-project.org/package=crmPack)
[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/license/apache-2-0)
[![Check 🛠](https://github.com/openpharma/crmPack/actions/workflows/check.yaml/badge.svg)](https://github.com/openpharma/crmPack/actions/workflows/check.yaml)
[![Test Coverage](https://raw.githubusercontent.com/openpharma/crmPack/_xml_coverage_reports/data/main/badge.svg)](https://raw.githubusercontent.com/openpharma/crmPack/_xml_coverage_reports/data/main/badge.svg)



 crmPack-logo 


```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

The goal of `crmPack` is to implement a wide range of model-based dose
escalation designs, ranging from classical and modern continual
reassessment methods (CRMs) based on dose-limiting toxicity endpoints to
dual-endpoint designs taking into account a biomarker/efficacy outcome. The
focus is on Bayesian inference, making it very easy to setup a new design
with your own JAGS code. However, it is also possible to implement 3+3
designs for comparison or models with non-Bayesian estimation. The whole
package is written in a modular form in the S4 class system, making it very
flexible for adaptation to new models, escalation or stopping rules.

## Installation

You can install the development version of `crmPack` from GitHub with:

```{r gh-installation, eval = FALSE}
devtools::install_github("openpharma/crmPack")
```

You can install the stable release version of `crmPack` from CRAN with:

```{r cran-installation, eval = FALSE}
install.packages("crmPack")
```

## Examples

The package vignettes provide information on various aspects of CRM trial design, implementation, simulation and analysis:

* [Trial definition](https://openpharma.github.io/crmPack/main/articles/trial_definition.html)
* [Trial analysis](https://openpharma.github.io/crmPack/main/articles/trial_analysis.html)
* [Sanity checking](https://openpharma.github.io/crmPack/main/articles/trial_sanity_checks.html)
* [Simulation of operating characteristics](https://openpharma.github.io/crmPack/main/articles/trial_simulation.html)
* [Ordinal CRM models](https://openpharma.github.io/crmPack/main/articles/ordinal-crm.html)
* [Extending `crmPack`](https://openpharma.github.io/crmPack/main/articles/parallel_computing_with_extensions.html)
* [Tidy `crmPack` data](https://openpharma.github.io/crmPack/main/articles/tidy_method.html)
* [Describing `crmPack` objects in Markdown and Quarto documents](https://openpharma.github.io/crmPack/main/articles/knit_print.html)
* [Migration from the old crmPack](https://openpharma.github.io/crmPack/main/articles/migration_from_the_old_crmPack.html)
* Sabanes Bove et al (2019)  Model-based Dose Escalation Designs in R with `crmPack`. JSS 89:10 [DOI 10.18637/jss.v089.i10](https://www.jstatsoft.org/article/view/v089i10)

Owner

  • Name: openpharma
  • Login: openpharma
  • Kind: organization

Further precompetitive collaboration in life sciences

GitHub Events

Total
  • Issues event: 4
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 18
  • Pull request event: 4
  • Pull request review event: 2
  • Create event: 2
Last Year
  • Issues event: 4
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 18
  • Pull request event: 4
  • Pull request review event: 2
  • Create event: 2

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 889
  • Total Committers: 29
  • Avg Commits per committer: 30.655
  • Development Distribution Score (DDS): 0.652
Past Year
  • Commits: 105
  • Committers: 11
  • Avg Commits per committer: 9.545
  • Development Distribution Score (DDS): 0.39
Top Committers
Name Email Commits
Wojciech 1****h 309
Daniel Sabanes Bove d****e@r****m 185
Winnie Yeung w****1@l****k 114
John Kirkpatrick 1****e 73
Daniel Sabanes Bove d****e 38
GIUSEPPE PALERMO g****o@r****m 35
Oliver Boix 9****5 24
Yeung y****3@e****m 21
pengguanya g****4@g****m 13
Thomas Jaki j****s@g****m 12
John Kirkpatrick 5****e 7
Daniel Sabanes Bove s****d@r****m 7
Daniel Sabanes Bove d****e@g****t 6
dimitriskontosBAY 9****Y 6
Dinakar 2****y 5
Clara Beck 9****r 5
winnie yeung w****g 4
dimitris.kontos 9****Y 4
Marlene 1****g 3
Doug Kelkhoff 1****f 3
Dinakar 2****9 3
Palermo p****g@e****m 2
Prerana Chandratre 8****7 2
TJaki 5****i 2
Burak Kürsad Günhan b****n@g****m 2
Phillip Crout 3****4 1
reikoch 8****h 1
Chao Cheng 4****4@q****m 1
Chao Cheng c****o@z****m 1
Committer Domains (Top 20 + Academic)
roche.com: 3 emea.roche.com: 2 zaiming.com: 1 qq.com: 1 gmx.net: 1 lancaster.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 52
  • Total pull requests: 54
  • Average time to close issues: 29 days
  • Average time to close pull requests: 23 days
  • Total issue authors: 7
  • Total pull request authors: 8
  • Average comments per issue: 1.17
  • Average comments per pull request: 3.09
  • Merged pull requests: 50
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 2
  • Pull requests: 4
  • Average time to close issues: about 5 hours
  • Average time to close pull requests: 36 minutes
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • danielinteractive (37)
  • Puzzled-Face (16)
  • wwojciech (10)
  • 0liver0815 (3)
  • PuzzledFace-Astellas (2)
  • jfiksel (1)
  • dimitriskontosBAY (1)
  • pengguanya (1)
  • fenguoerbian (1)
  • gunhanb (1)
Pull Request Authors
  • wwojciech (37)
  • Puzzled-Face (20)
  • danielinteractive (7)
  • PuzzledFace-Astellas (4)
  • cicdguy (3)
  • TJaki (2)
  • pengguanya (2)
  • gravesti (1)
  • 0liver0815 (1)
  • fenguoerbian (1)
  • JiawenZhuxm (1)
  • renovate[bot] (1)
Top Labels
Issue Labels
cleanup (39) enhancement (15) documentation (7) CRAN (6) high priority (3) bug (3) question (2) discussion (1) design (1) SP8 (1) good first issue (1) invalid (1)
Pull Request Labels
cleanup (32) enhancement (5) documentation (3) CRAN (1) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 474 last-month
  • Total docker downloads: 43,390
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 16
  • Total maintainers: 1
cran.r-project.org: crmPack

Object-Oriented Implementation of CRM Designs

  • Versions: 16
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 474 Last month
  • Docker Downloads: 43,390
Rankings
Forks count: 9.1%
Stargazers count: 14.6%
Average: 22.2%
Downloads: 22.3%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
daniel.sabanes_bove@rconis.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.0 depends
  • ggplot2 >= 2.0.0 depends
  • graphics * depends
  • GenSA * imports
  • checkmate * imports
  • futile.logger * imports
  • grid * imports
  • gridExtra * imports
  • kableExtra * imports
  • lifecycle * imports
  • magrittr * imports
  • methods * imports
  • mvtnorm * imports
  • parallel * imports
  • parallelly * imports
  • rjags * imports
  • survival * imports
  • tibble * imports
  • tools * imports
  • utils * imports
  • dplyr * suggests
  • ggmcmc * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • stringr * suggests
  • testthat >= 3.0.0 suggests
  • tidyr * suggests
  • vdiffr * suggests