R script to perform a biogeographical regionalisation of the Adriatic Sea based on phylogenetic beta diversity

R function to perform a biogeographical regionalisation based on phylogenetic beta diversity<br>#<br># Date 13 January 2015<br># Copyright: Hattab et al, 2015<br># License: GPL-3<br>This R code provides a computational framework to perform a biogeographical regionalisation based on phylogenetic beta diversity. For this purpose, we will use two data sets: -Distribution_Data.csv: a csv file with 1323 observations (sites located on the Adreatic Sea) on 161 binary variables (species).<br>-Phylogenetic_Data.trd: a phylogenetic tree of 363 Mediterranean teleost species (see Meynard et al., 2012 for details: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036443). Two external functions are also required: -beta_pd_decompo.r: R function to quantify phylogenetic beta diversity (PBD) and its 'true' turnover and phylogenetic diversity (PD)<br> components based on the UniFrac and PhyloSor indices.<br>-A2R.r: R function for generating colored dendrograms which you can download here http://addictedtor.free.fr/packages/A2R/lastVersion/R/code.R.<br><br>For more details about this topic you can read the original article:<br>Tarek H, Albouy C, Ben Rais Lasram F, Le Loc'h F, Guilhaumon F, Leprieur F,(submited to Journal of Biogeography). A biogeographic regionalisation of coastal Mediterranean fishes. 1.Put all the documents in a single folder (this becomes your working directory) 2. Install the necessary packages in R (see first part of the script) 3. Define the working directory in the script (setwd(“C:/…/”), as indicated in the script) 4. Run the script in R