04_PGLS

This file contains 5 files, sufficient to re-do all of our PGLS analyses. 'bootstrap_rates.txt' contains the results of the ML r8s analysis and all 1000 subsequent bootstrap analyses. 'growth_forms.csv' contains information on the growth forms of species in each family. 'PGLS_analyses.r' is an R script which you can use to re-run all of our PGLS analyses. To use it you will need to change the line at the top that starts 'setwd' to point to the folder on your computer that contains all of the input files here. You'll also need to download R, and the packages listed at the top of the file. 'R8S_trees.txt' is a file of the 1001 trees from R8S. These are used in the PGLS analyses to correct for nonindepdence. The first tree is the ML tree, the rest are bootstrap trees. 'raw_data_sister_pairs.csv' is a csv file of the raw data. It's included here so that the R script will run without additional hassle. But it's identical to the file described in the '02_sister_pairs' section above.本数据集包含5个配套文件，可完整复现我们所有的PGLS（系统发育广义最小二乘，Phylogenetic Generalized Least Squares）分析。`bootstrap_rates.txt` 存储了最大似然（Maximum Likelihood，ML）r8s分析的结果，以及后续全部1000次自举分析的结果。`growth_forms.csv` 记录了各物种类群下物种的生长型信息。`PGLS_analyses.r` 为R脚本文件，可用于复现我们所有的PGLS分析。使用该脚本前，需将顶部以`setwd`开头的行修改为指向本地计算机上存放全部输入文件的文件夹路径；同时需提前安装R语言及脚本顶部列出的相关依赖包。`R8S_trees.txt` 存储了来自R8S软件的1001棵进化树，用于PGLS分析中校正数据的非独立性问题。其中第一棵为最大似然树，其余均为自举进化树。`raw_data_sister_pairs.csv` 为原始数据CSV文件，随本数据集提供以确保R脚本可无额外障碍运行。该文件与前文"02_sister_pairs"章节中描述的文件完全一致。