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

本R代码提供了一套基于系统发育β多样性（phylogenetic beta diversity）开展生物地理分区的计算框架。为此，我们将使用两类数据集：
- Distribution_Data.csv：该CSV文件包含1323条观测记录（对应亚得里亚海海域的采样位点），涵盖161个二元变量（代表物种）。
- Phylogenetic_Data.trd：包含363种地中海硬骨鱼的系统发育树，详细信息参见Meynard等人2012年的研究：http://www.plosone.org/article/info%3Adoi%2F10.1371/journal.pone.0036443。

此外还需两个外部R函数：
- beta_pd_decompo.r：用于量化系统发育β多样性（PBD）及其基于UniFrac和PhyloSor指数的「真实」周转组分与系统发育多样性（PD）组分的R函数。
- A2R.r：用于生成彩色聚类树的R函数，可在此处下载：http://addictedtor.free.fr/packages/A2R/lastVersion/R/code.R。

如需了解该主题的更多细节，可参阅原创研究论文：Hattab, T., Albouy, C., Ben Rais Lasram, F., Le Loc'h, F., Guilhaumon, F., Leprieur, F. (2015), 《地中海沿岸鱼类的生物地理分区》，《生物地理学杂志》(Journal of Biogeography)。doi: 10.1111/jbi.12505

操作步骤如下：
1. 将所有文件置于同一文件夹中，该文件夹即作为你的工作目录
2. 在R中安装所需的扩展包，详见脚本的第一部分
3. 按照脚本指示，在脚本中通过setwd(“C:/…/”)命令指定工作目录
4. 在R环境中运行该脚本