sgordon007 / angio-pulse

Analysis code for Angiosperm diversification rate paper

angio-pulse

Analysis code for Angiosperm diversification rate paper.

Directory structure

• R_packages Archived versions of R packages needed for analyses
• R_scripts Scripts to run analyses
• data_files Data files

Instructions

Install archived versions of R packages

Install both of these from source (in R_packages/).

R_packages/phylo_0.12.0105.tar.gz R_packages/turboMEDUSA_0.92-3.tar.gz

Run MEDUSA analysis

To do this, use the analysis file:

MEDUSA_analysis.R

This script carries out the MEDUSA analysis of the ML tree and the 100 PL replicates.

Run clade-age diversity analysis

To do this, use the analysis file:

age_richness_analysis.R

You can also repeat the simulations used to generate a null distribution of age-richness correlations under a model of progressive radiations. Run:

age_richness_simulation.R

Run the polyploidy analyses.

Use the script:

polyploidy_analyses.R