Challenge Problem 1: Phylogenetically Independent Contrasts

Part 1:

Download the following two files:

1. pic-exercise-data.csv
2. pic-exercise-tree.tre

Fit a OLS (non-phylogenetic) regression model for y~x and a phylogenetic regression model using contrasts. What do you find? Why?

Part 2 (optional):

1. Use simulated phylogenies & character data to demonstrate that OLS for data simulated on the tree results in elevated type I error. [Hint: use pbtree to simulate trees, and fastBM to simulate trait data for x & y on the tree.]
2. Show that phylogenetic independent contrasts for these same datasets results in the correct type I error.

Written by Liam J. Revell. Last updated 6 December 2016.