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# graphicalMCP <a href="https://openpharma.github.io/graphicalMCP/"><img src="man/figures/logo.png" align="right" height="139" /></a>

# 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
install.packages("graphicalMCP")
```

### Development

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

``` r
# 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.
