graphicalmcp

Graphical Multiple Comparison Procedures

https://github.com/openpharma/graphicalmcp

Last synced: 9 months ago · JSON representation

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Graphical Multiple Comparison Procedures

Basic Info

Host: GitHub
Owner: openpharma
License: apache-2.0
Language: R
Default Branch: main
Homepage: https://openpharma.github.io/graphicalMCP/
Size: 41 MB

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Stars: 19
Watchers: 4
Forks: 0
Open Issues: 18
Releases: 6

Created over 4 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog License Codemeta

README.Rmd

---
output: github_document
bibliography: "`r system.file('references.bib', package='graphicalMCP')`"
---



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```



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[![CRAN status](https://www.r-pkg.org/badges/version/graphicalMCP)](https://cran.r-project.org/package=graphicalMCP)
[![CRAN monthly downloads](https://cranlogs.r-pkg.org/badges/graphicalMCP)](https://cranlogs.r-pkg.org/badges/graphicalMCP)
[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/graphicalMCP)](https://cranlogs.r-pkg.org/badges/grand-total/graphicalMCP)




# graphicalMCP 

# Introduction

Graphical approaches for multiple comparison procedures (MCPs) are a general framework to control the family-wise error rate strongly at a pre-specified significance level $0<\alpha<1$. This approach includes many commonly used MCPs as special cases and is transparent in visualizing MCPs for better communications. `graphicalMCP` is designed to design and analyze graphical MCPs in a flexible, informative and efficient way.

# Installation

### Release

You can install the current release version from *CRAN* with:

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

### Development

You can install the current development version from *GitHub* with:

```{r github-installation, eval = FALSE}
# install.packages("pak")
pak::pak("openpharma/graphicalMCP")
```

# Documentation

- For basic usage instructions, see `vignette("graphicalMCP")`
- To become familiar with graphical MCP terminologies, see `vignette("glossary")`
- To learn examples of how to use `graphicalMCP`,
  - see `vignette("shortcut-testing")` for sequentially rejective graphical multiple comparison procedures based on Bonferroni tests
  - see `vignette("closed-testing")` for graphical multiple comparison procedures based on the closure principle using Bonferroni, Hochberg, parametric and Simes tests
  - see `vignette("graph-examples")` for common multiple comparison procedures illustrated using `graphicalMCP`
  - see `vignette("internal-validation")` for internal validation via power simulations for methods used in `graphicalMCP`
  - see `vignette("generate-closure")` for rationales to generate the closure and the weighting strategy of a graph
  - see `vignette("comparisons")` for comparisons to other R packages
- To view vignettes in R after properly installing `graphicalMCP`, we can build vignettes by `devtools::install(build_vignettes = TRUE)`, and then use `browseVignettes("graphicalMCP")` to view the full list of vignettes

# Related work

- Graphical MCPs - [gMCP](https://cran.r-project.org/package=gMCP)
- Lighter version of `gMCP` which removes the rJava dependency - [gMCPLite](https://cran.r-project.org/package=gMCPLite)
- Graphical MCPs with Simes tests - [lrstat](https://cran.r-project.org/package=lrstat)

Built upon these packages, we hope to implement graphical MCPs in a more general framework, with fewer dependencies and simpler S3 classes, and without losing computational efficiency.

# Acknowledgments

Along with the authors and contributors, thanks to the following people for their suggestions and inspirations on the package:

Frank Bretz, Willi Maurer, Ekkehard Glimm, Nan Chen, Jeremy Wildfire, Spencer Childress, Colleen McLaughlin, Matt Roumaya, Chelsea Dickens, Nan Xiao, Keaven Anderson, and Ron Yu

We owe a debt of gratitude to the authors of [gMCP](https://cran.r-project.org/package=gMCP) for their pioneering work, without which this package would not be nearly as extensive as it is.

Owner

Name: openpharma
Login: openpharma
Kind: organization

Website: openpharma.github.io
Repositories: 30
Profile: https://github.com/openpharma

Further precompetitive collaboration in life sciences

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cran.r-project.org: graphicalMCP

Graphical Multiple Comparison Procedures

Homepage: https://github.com/openpharma/graphicalMCP
Documentation: http://cran.r-project.org/web/packages/graphicalMCP/graphicalMCP.pdf
License: Apache License (≥ 2)
Latest release: 0.2.8
published about 1 year ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 564 Last month

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Stargazers count: 15.8%

Dependent packages count: 28.5%

Forks count: 28.8%

Dependent repos count: 35.2%

Average: 39.0%

Downloads: 86.7%

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dong.xi1@gilead.com

Last synced: 10 months ago

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graphicalmcp

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