Analysis code for Angiosperm diversification rate paper
R
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
R_packages
R_scripts
data_files
.gitignore
LICENSE
README.md

README.md

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