Supplemental Code

for 

Hiscott, G., Fox, C. Parry, M. and Bryant, D. Efficient recycled 
       algorithms for quantitative trait models on phylogenies. 
       http://arxiv.org/abs/1512.00890


EFNdata			Directory containing phylogeny and trait data for EFN paper (formatted)
ExperimentOutput  	Directory which simulations output data in (error if not present)
R input.txt		R code used to create diagram with coloured phylogeny
experiment1.m		Matlab code running Simulation 1.
experiment2.m		Matlab code running Simulation 2.
experiment3.m		Matlab code running Simulation 3.
plotFigures.m		Plot graphs with output from Simulations
readEFNdata.m		Read data relating to EFN trait analysis
thresholdGauss.m	Compute likelihoods using Gaussian kernel quadrature
thresholdLikelihood.m	Version of thresholdGauss which was uploaded to Matlab Central
thresholdPosterior.m	Compute likelihoods and posterior densities using Gaussian kernel quadrature
thresholdSimpsons.m	Compute likelihoods using Simpsons quadrature


For more information, contact David Bryant: david.bryant@otago.ac.nz
