T_method
A program for Roff's T-method of matrix comparison.
by Liam J. Revell
Plan 9 port by Peter A. Cejchan


Introduction

T_method is a program for the computation and hypothesis testing of T
and T 2 following Roff et al. (1999).
The T-method of Roff (1999) involves the calculation of the summed
absolute values of the elements of two symmetrical matrices, in other
words:

A ij is the covariance between traits i and j in matrix A, while B ij
is the corresponding covariance in matrix B.
T 2 can also be used, calculated similarly:

Hypothesis testing is conducted by permuting individuals (as
multivariate deviations from population means) between data arrays and
calculating pseudovalues of T or T 2 from the randomization procedure
(T r and T 2 r). Significance is evaluated as the fraction of times T>
T r (or T 2> T 2 r).

Installation - Plan 9

To install in Plan 9, type mk install. You might want to edit the mkfile first, especially if you don't store your binaries in $home/$objtype/bin


Input file format

Input files should be created as plain text.The input file format is as follows:

The header contains the information about the
populations - POP1='name', and N1='sample size for population 1,' etc.
CHARS='number of phenotypic traits in the data array.' The first
column of the raw data is the population ID in integer form
(corresponding to POP# in the header). The subsequent columns are
phenotypic data from each individual.

NOTE ON FILE FORMAT - This program will probably be finicky about file
format, so be careful to follow the format presented herein and the
format of the example data file available with T_method.

Running T_method

Running T_method is easy. The program will give you several prompts.

When prompted for input file, enter the name of the data file to be
analyzed. Data from the randomization distribution can be output to a
file. This output file contains the observed values of T and T 2
followed by m -1 pseudovalues from the randomization procedure, where
m is the number of randomizations selected (the original data order is
consider one'randomization'). Finally, when prompted for the number of
randomizations, enter the number desired. The program is quite fast,
so selecting a very large number (10 5 or 10 6) is not unreasonable
(however it will make the output file with the randomization
distribution large).

The T_method output

Values for T and T 2 are provided, as are significances estimated from
the randomization procedure. A significant T indicates that matrices
are significantly different from one another.

The output file with the pseudovalues of T from the randomization
procedure is optional. In this file, obs. indicates the observed values, and the integers
below it indicate the rank of the randomization.

References

1. Roff, D. A., T. A. Mousseau, and D. J. Howard. 1999. Variation in
genetic architecture of calling song among populations of Allonemobius
socius, A. fasciatus, and a hybrid population: drift or selection?
Evolution 53:216-224.

Also....

2. Bégin, M., and D. A. Roff. 1999. An analysis of G matrix variation
in two closely related cricket species, Gryllus firmus and G.
pennsylvanicus. J. Evol. Biol. 14:1-13.

2. Bégin, M., and D. A. Roff. 2003. The constancy of the G matrix
through species divergence and the effects of quantitative genetic
constraints on phenotypic evolution: a case study in crickets.
Evolution 57:1107-1120.


Contact information

Please contact me by email with any questions, or if you find the
program useful. My email is ljrevell@artsci.wustl.edu, and my other
contact information is listed below.

Although I have thoroughly tested the program, I encourage users to do
the same and I would be happy to hear about any bugs you might find.

Liam J. Revell
Department of Biology
Washington University
St. Louis, MO 63130
(314) 935-7256

Content copyright. Last updated 13 Aug. 2006.

Plan 9 port by:

Peter A. Cejchan
Lab of Paleobiolohy and Paleoecology
Institute of Geology,
Academy of Sciences
Rozvojova 135
16502 Prague 6
Czechia, EU
<cej@gli.cas.cz>
Last update Wed Mar 14 09:24:40 MET 2007.


