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README.md

mulTree

Build Status codecov Project Status: Active - The project has reached a stable, usable state and is being actively developed. DOI

This package is based on the MCMCglmm package and runs a MCMCglmm analysis on multiple trees. This code has been used prior to this package release in Healy et. al. (2014). Please send me an email or a pull request if you find/have any issue using this package.

Check out the presentation of some aspects of the package.

Installing mulTree

## 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.

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:

## Install the missing packages
install.packages(c("MCMCglmm", "coda", "hdrcde", "snow", "ape", "corpcor", "curl"))

Vignettes

Patch notes (latest version)
  • 2018/05/08 - 1.3.4
    • Increased test coverage for all functions.
    • Improved optional arguments handling for mulTree (following Eldar Rakhimberdiev's contribution)
    • Converted patch_notes.md into NEWS.md (with the correct standard format).
    • Minor bug fix: the trees in data(lifespan) are now all ultrametric.
    • Complex formula management in mulTree and as.mulTree.
    • Added ask option to mulTree, whether to ask to overwrite files or not.
    • Minor changes (internal) and code coverage increased for SIDER release.

Previous patch notes and the next version ones can be seen here.

Authors

Thomas Guillerme and Kevin Healy

Contributors

Eldar Rakhimberdiev.

Citation

If you are using this package, please cite:

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

BibTeX, EndNote, DataCite, RefWorks

Related packages

SIDER R package

Used in

Click on the google logo for citations details.

11 publications have cited mulTree since 2014 (2.75 per year). The average cites for papers using mulTree is 9.9 (the median is 3; calculated on the 08/12/2018).

  • A Sadier, K Davies, L Yohe, K Yun, P Donat, BP Hedrick, E Dumont, L Davalos, S Rossiter, KE Sears (2018)Mixing models and stable isotopes as tools for research on feeding aquatic organisms. Cienc. Rural 48:7. DOI: 10.1590/0103-8478cr20160101

  • J Karagicheva, E Rakhimberdiev, A Saveliev, T Piersma (2018) Annual chronotypes functionally link life histories and life cycles in birds. Funct Ecol. 00:1–11. DOI: 10.1111/1365-2435.13181

  • A Sadier, K Davies, L Yohe, K Yun, P Donat, BP Hedrick, E Dumont, L Davalos, S Rossiter, KE Sears (2018)Evidence for multifactorial processes underlying phenotypic variation in bat visual opsins. bioRxiv 300301. DOI: 10.1101/300301

  • K Elspeth, TR Birkhead, JP Green (2017) Allopreening in birds is associated with parental cooperation over offspring care and stable pair bonds across years. Behavioral Ecology 28.4: 1142-1148. DOI: 10.1093/beheco/arx078

  • P Minias, R Włodarczyk, W Meissner (2017) Leukocyte profiles are associated with longevity and survival, but not migratory effort: A comparative analysis of shorebirds. Functional Ecology. DOI: 10.1111/1365-2435.12991.

  • NJ Clark, SM Clegg, K Sam, W Goulding, B Koane, K Wells (2017) Climate, host phylogeny and the connectivity of host communities govern regional parasite assembly. Diversity and Distributions. DOI: 10.1111/ddi.12661.

  • JS Gutiérrez, E Rakhimberdiev, T Piersma, DW Thieltges (2017) Migration and parasitism: habitat use, not migration distance, influences helminth species richness in Charadriiform birds. Journal of Biogeography. DOI: 10.1111/jbi.12956

  • G Zhang, Q Zhao, AP Møller, JJ Komdeur, X Lu (2017) Climate predicts which sex acts as helpers among cooperatively breeding bird species. Biology Letters 13:1. DOI: 10.1098/rsbl.2016.0863

  • K Healy, SBA Kelly, T Guillerme, R Inger, S Bearhop, AL Jackson (2017) SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness. Ecography DOI: 10.1111/ecog.03371

  • K Healy (2015) Eusociality but not fossoriality drives longevity in small mammals. Proceedings of the Royal Society B 282, 20142917. DOI: 10.1098/rspb.2014.2917

  • K Healy, T Guillerme, S Finlay, A Kane, SBA Kelly, D McClean, DJ Kelly, I Donohue, AL Jackson, N Cooper (2014) Ecology and mode-of-life explain lifespan variation in birds and mammals. Proceedings of the Royal Society B 281, 20140298. DOI:10.1098/rspb.2014.0298