A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies.

Natalie Cooper and Gavin H. Thomas.

Chris Venditti, Andrew Meade and Rob P. Freckleton.

Code, figures, etc. for the paper in the Biological Journal of the Linnaean Society special issue on "Radiations and Extinctions in Deep Time".

Compiling the paper

To compile the paper you can use the Makefile:

make -C Manuscript

The Supporting Information file is available in PDF format here.

Analysis code

Code needed to run the Maximum Likelihood simulations and make the figures in the paper can be found in the Analyses folder.

• OUsims.R provides all R code for simulating trees and data (GHT).
• OUfigures.R provides all R code for making the simulations figures (Figure 4 and some removed in the revision and reworked as Tables 2-6) in the paper (GHT).
• OhYouFigures.R provides all R code for making the figures (1 and 3) and table for the literature review (NC).
• plotFig2.R provides all R code for making Figure 2 (RPF).
• PagelParamPlots.R provides all R code for making additional figures that were not used in the final version of the manuscript (GHT).

Simulated data and literature review data

• OU_simulations.rda contains all the data from the OU simulations.
• papers.txt contains the number of papers found in the literature review.
• literature.txt contains a summary of the papers from the literature review.
• ProfileDataRootyOU50.csv, ProfileDataTippyOU50.csv and ProfileDataYuleOU50.csv contain Likelihood profile data used to construct Figure 2.

Useful(?) functions

At one point I (NC) began to rewrite the simulations code as a series of functions using the package diversitree. These are provided in the R folder in the file OhYou_simulations.R. Feel free to play around with them!