https://github.com/tguillerme/multree

Performs MCMCglmm on multiple phylogenetic trees
https://github.com/tguillerme/multree

bayesian comparative-genomics mcmcglmm multiple-trees phylogenetics r

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Performs MCMCglmm on multiple phylogenetic trees

• Host: GitHub
• URL: https://github.com/tguillerme/multree
• Owner: TGuillerme
• Created: 2014-08-13T13:52:04.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2024-01-17T14:03:18.000Z (11 months ago)
• Last Synced: 2024-01-17T20:53:43.195Z (11 months ago)
• Topics: bayesian, comparative-genomics, mcmcglmm, multiple-trees, phylogenetics, r
• Language: R
• Size: 7.43 MB
• Stars: 12
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# `mulTree`

[![R-CMD-check](https://github.com/TGuillerme/mulTree/workflows/R-CMD-check/badge.svg)](https://github.com/TGuillerme/mulTree/actions)

[![codecov](https://codecov.io/gh/TGuillerme/mulTree/branch/release/graph/badge.svg)](https://codecov.io/gh/TGuillerme/mulTree)

[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12902.svg)](https://doi.org/10.5281/zenodo.12902)

This package is based on the [MCMCglmm](http://cran.r-project.org/web/packages/MCMCglmm/index.html) package

and runs a MCMCglmm analysis on multiple trees.

This code has been used prior to this package release in [Healy et. al. (2014)](http://rspb.royalsocietypublishing.org/content/281/1784/20140298.full.pdf?ijkey=gPt28ElSAYBvRhZ&keytype=ref).

Please send me an [email](mailto:[email protected]) or a pull request if you find/have any issue using this package.

 

Check out the [presentation](https://figshare.com/articles/Guillerme_BESMacro2016_pdf/3478922) of some aspects of the package.

## Installing mulTree

```r

## Installing the package

if(!require(devtools)) install.packages("devtools")

library(devtools)

install_github("TGuillerme/mulTree", ref = "release")

library(mulTree)

```

The following installs the latest released version (see patch notes below). For the piping hot development version (not recommended), replace the `ref="release"` option by `ref="master"`. If you're using the `master` branch, see the latest developement in the [patch note](https://github.com/TGuillerme/mulTree/blob/master/patch_notes.md).

#### Warning note:

If you're using a PC and the package doesn't install correctly, it might be due to the fact that dependencies are not installed correctly. You can fix buy downloading `R`'s latest version and installing the missing packages manualy:

```r

## Install the missing packages

install.packages(c("MCMCglmm", "coda", "hdrcde", "snow", "ape", "corpcor", "curl"))

```

#### Vignettes

*  The package manual [here (in .Rnw)](https://github.com/TGuillerme/mulTree/blob/master/doc/mulTree-manual.Rnw) or [here (in .pdf)](https://github.com/TGuillerme/mulTree/blob/master/doc/mulTree-manual.pdf).

*  An additional example of running simple phylogenetic models is [here](https://github.com/TGuillerme/mulTree/blob/master/doc/Vanilla_flavoured_phylogenetic_analyses.Rmd).

##### Patch notes (latest version)

* 2020-04-12 - 1.3.7

  * Updated package to R version 3.6.3

  * Updated package to `ape` version 5.3

    

Previous patch notes and the *next version* ones can be seen [here](https://github.com/TGuillerme/mulTree/blob/master/patch_notes.md).

Authors

-------

[Thomas Guillerme](http://tguillerme.github.io) and [Kevin Healy](http://healyke.github.io)

## Contributors

[Eldar Rakhimberdiev](https://github.com/eldarrak), [Hugo Gruson](https://github.com/Bisaloo).

Citation

-------

If you are using this package, please cite (if the DOI is in there, even better!):

* Guillerme, T. & Healy, K. (**2014**). mulTree: a package for running MCMCglmm analysis on multiple trees. ZENODO. 10.5281/zenodo.12902

    ###### [BibTeX](https://zenodo.org/record/12902/export/hx), [CSL](https://zenodo.org/record/12902/export/csl), [DataCite](https://zenodo.org/record/12902/export/dcite3), [Dublin core](https://zenodo.org/record/12902/export/xd), [Mendeley](https://www.mendeley.com/import/?url=https://zenodo.org/record/12902), [more...](https://zenodo.org/record/12902/#.XTpLtlBS8W8)

Related packages

-------

 

[`SIDER` R package](https://github.com/healyke/SIDER)

Used in

-------

Check out the papers that have cited `mulTree` since 2014 here (>50):