Diversification of bird lineages colonising urban habitats

This repository accompanies the manuscript "Bird lineages colonising urban habitats have diversified at high rates across deep time"
The scripts of analyses are those with the Rscript extension. The data used for analyses and results are in the files with the Rdata extension, and can be loaded into R using the load function.

all.data.Rdata - All data sets used. passerine.all.tre - The complete tree of passerines used. extincton_rate_tables.csv speciation_rate_tables.csv transition_rates_tables.csv - Results from the best model out of the eight BiSSE and HiSSE assessed, and best replicate in each analysis. Each file contains two tables, one showing the results of the analyses with the trimmed tree of passerines, and another including the results with the full tree of passerines. model_comparison_tables.csv - Model comparison tables with each of the trimmed-tree analyses and those with the complete tree of passerines. top_ML_hisse_models.Rdata - Top model outputs from HiSSE. hisse_script_reps.Rscript hisse_script_reps_fulltree.Rscript - Scripts used for performing BiSSE and HiSSE analyses. quasse_results.csv quasse_results.Rdata - Results of QuaSSE analyses.

本仓库配套学术论文《拓殖城市生境的鸟类支系在漫长地质时间内以高速率发生分化》。分析脚本均为扩展名为.Rscript的文件。用于分析与结果生成的数据集存储于扩展名为.Rdata的文件中，可通过R语言的load函数加载至R运行环境。
all.data.Rdata：本研究使用的全部数据集；
passerine.all.tre：本研究使用的完整雀形目系统发育树；
extinction_rate_tables.csv、speciation_rate_tables.csv、transition_rates_tables.csv：本研究对8种BiSSE与HiSSE模型进行评估后选取的最优模型，以及各分析中的最优重复结果。每个文件包含两张数据表：其一对应基于修剪后雀形目系统发育树的分析结果，其二对应基于完整雀形目系统发育树的分析结果；
model_comparison_tables.csv：包含基于修剪后与完整雀形目系统发育树的所有分析的模型比较数据表；
top_ML_hisse_models.Rdata：HiSSE分析的最优最大似然模型输出结果；
hisse_script_reps.Rscript、hisse_script_reps_fulltree.Rscript：用于执行BiSSE与HiSSE分析的脚本文件；
quasse_results.csv、quasse_results.Rdata：QuaSSE分析的结果文件。