The R package ComTreeOpt is a Community Tree Optimizer using Open Tree of Life. It enhances the phylogenetic resolution of community trees for the analysis of phylogenetic diversity and dispersion measures.
For more complete usage instructions, please read the manual at:
https://github.com/iantrotter/ComTreeOpt/blob/master/MANUAL.md
You can install the latest version with the commands:
install.packages("devtools")
devtools::install_github("iantrotter/ComTreeOpt")library(ComTreeOpt)
?ComTreeOpt
data(FSN_species)
tree <- ComTreeOpt(FSN_species)
plot(tree, show.node.label=T)
data(EifelDataset_species)
tree <- ComTreeOpt(EifelDataset_species)
plot(tree, show.node.label=T)Please cite the package as:
Gastauer, M., Caldeira, C. F., Trotter, I. M., Ramos, S. J., & Meira-Neto, J. A. A. (2018). Optimizing Community Trees Using the Open Tree of Life Increases the Reliability of Phylogenetic Diversity and Dispersion Indices. Ecological Informatics 46, 192–98. https://doi.org/10.1016/j.ecoinf.2018.06.008.
Gastauer, M., & Meira-Neto, J. A. A. (2013a). Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2. Ecological Informatics, 15, 85–90.
Gastauer, M., & Meira-Neto, J. A. A. (2013b). Interactions, Environmental Sorting and Chance: Phylostructure of a Tropical Forest Assembly. Folia Geobotanica, 1–17.
Gastauer, M., & Meira Neto, J. A. A. (2017). Updated angiosperm family tree for analyzing phylogenetic diversity and community structure . Acta Botanica Brasilica . scielo
This package is free and open source software, licensed under GPL-2.