This repository contains R codes that can be used to run BDTT on a community ecology dataset. BDTT decomposes community dissimilarities by time-slicing the phylogenetic tree of all members (e.g. 16S rDNA reads) present in all communities. It allows the user to detect at which time or phylogenetic scale an environmental factor of interest shapes the most community compositions. It has recently been applied to analyse the composition of mammalian communities around the world and the composition of gut bacterial communities within mammalian guts
The main function, called BDTT has three main arguments:
-- similarity_slices: a numerical vector giving the h heights at which the tree should be sliced
-- tree: a phylogeny in the phylo ape format, with tip labels matching the OTUS names in the OTU matrix (the row names of the sampleOTUs argument)
-- sampleOTUs: a matrix of n OTUS (row) by m samples (columns). The row names of sampleOTUs should correspond to your unique OTU names and match the tip labels of the phylogeny. Column names should be sample names.
You can find more information on how to use the function in the example and tutorials
The main function, called BDTT, returns an array of beta diversity values (h x b x m x m): m is the number of samples, h is the number of slices, and b is the number of beta-diversity metrics computed (3 so far: BrayCurtis, Jaccard and the true turnover component of Jaccard).
You can find more information on how to use the function in the example and tutorials
Groussin, M., Mazel, F., Sanders, J. G., Smillie, C. S., Lavergne, S., Thuiller, W., & Alm, E. J. (2017). Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nature communications, 8, 14319.
Mazel, F., Wüest, R. O., Lessard, J. P., Renaud, J., Ficetola, G. F., Lavergne, S., & Thuiller, W. (2017). Global patterns of β‐diversity along the phylogenetic time‐scale: The role of climate and plate tectonics. Global Ecology and Biogeography, 26(10), 1211-1221.
This code has been written by myself with inputs from M. Groussin and J. Roy. In this repository, we provide a file that contains functions needed to run BDTT and example and tutorials. If you have any questions, please contact either Mathieu Groussin (mgroussi@gmail.com) or myself (flo.mazel@gmail.com)