Taxon Sampling And Inferred Community Phylogenies: R Replication Code And Data.

1 ) Code for simulating community phylogenies: community_simulations_creation.R [taxon].gene [taxon].phy [taxon].RAxML_bestTree.tre [taxon].Simulate.A.Community.pl [taxon].Simulate.B.Community.pl [taxon].Simulate.C.Community.pl [taxon].Simulate.D.Community.pl 2) R code for creating and comparing phylogenetic diversity metrics: simulated_metric_calculation_and_comparison.R empirical_metric_calculation_and_comparison.R 3) R code and data for statistical analyses: simulated_data_analysis.R empirical_data_analysis.R simulated_interval_individual_lme_data.csv simulated_summary_interval_individual_lme_data.csv empirical_interval_individual_lme_data.csv empirical_summary_interval_lme_data.csv