Getting Started with Independent Contrasts

Primary Contact(s)	Created	Required Software	Example Datafile
Justen Whittall	12 March 2009	Mesquite, pdap	Aquilegia.nex	Contrasts.pdf

Mesquite is a powerful Java based platform for comparative analyses. It functions as stand-alone software for a diversity of comparative analyses. Interested users can also write their own modules for in Java that make use of Mesquite's existing architechture. For independent contrasts analysis, we will be using a Mesquite module written by Garland and Meade called pdap. This page includes instructions on downloading and installing Mesquite, followed by directions for integrating the pdap module to run within Mesquite.

A. Download and install Mesquite

1. if working on a Mac, double click on the *.dmg file and move the folder called "Mesquite Folder" to your "Applications" directory.


2. if working on a PC, install the Mesquite software within your "Program Files" directory.


3. Start Mesquite by double clicking on the green and black leaf icon to ensure the program opens without errors.

B. Download the pdap module (you want the executable, not the source file).

C. Installing the pdap module in Mesquite.

1. Close any active Mesquite windows.
   

2. Unzip the pdap.zip download.
   

3. Inside the first folder named "pdap", OPEN the “Put in Mesquite” folder
   

4. THEN copy the second “pdap” folder within it into the Mesquite folder named “mesquite” which is in “Mesquite_Folder” wherever you installed the program it in Step A above.

D. Restart Mesquite and take the Guided Tour of pdap by choosing File, Open File, then browse to find the pdap examples in the "Examples" folder that was extracted when you unzipped the pdap.zip folder. In Examples, locate Guided Tour, and open Part 1. Toggle through Parts 1-9 for a brief introduction to the pdap module and how it calculates Independent Contrasts.

Continue the Independent Contrasts Tutorial with this exercise: Correlated Floral Evolution: Evidence for Pollination Syndromes