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

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). -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) components based on the UniFrac and PhyloSor indices. -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: Hattab, T., Albouy, C., Ben Rais Lasram, F., Le Loc'h, F., Guilhaumon, F., Leprieur, F. (2015), A biogeographical regionalization of coastal Mediterranean fishes. Journal of Biogeography. doi: 10.1111/jbi.12505 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