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.