Diversification of bird lineages colonising urban habitats

<strong>This repository accompanies the manuscript "Bird lineages colonising urban habitats have diversified at high rates across deep time"</strong> The scripts of analyses are those with the <em>Rscript</em> extension. The data used for analyses and results are in the files with the <em>Rdata</em> extension, and can be loaded into R using the <em>load</em> function. <em>all.data.Rdata</em> - All data sets used. <em>passerine.all.tre</em> - The complete tree of passerines used. <em>extincton_rate_tables.csv</em> <em>speciation_rate_tables.csv</em> <em>transition_rates_tables.csv</em> - 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. <em>model_comparison_tables.csv</em> - Model comparison tables with each of the trimmed-tree analyses and those with the complete tree of passerines. <em>top_ML_hisse_models.Rdata</em> - Top model outputs from HiSSE. <em>hisse_script_reps.Rscript</em> <em>hisse_script_reps_fulltree.Rscript</em> - Scripts used for performing BiSSE and HiSSE analyses. <em>quasse_results.csv</em> <em>quasse_results.Rdata</em> - Results of QuaSSE analyses.