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Rhetenor: a package of morphometrics modules for the Mesquite system |
contact: edyreson@mozart.helios.nd.edu
July 2001
This package of modules and library classes demonstrates the use of the Mesquite system to do morphometrics calculations. It is a prototype. There is much more that can be done, and opportunities for other programmers to contribute morphometrics calculations to Mesquite.
The Rhetenor package of morphometrics modules includes:
In conjuction with the standard modules in Mesquite, including Plot Tree, the charting modules, and character evolution simulations, these calculations can be used to do standard morphometric analyses, or morphometrics in a phylogenetic context.
By the way, "Evolutionary Principal Components Analysis" is a new method by W. Maddison & E. Dyreson that does PCA on reconstructed changes along branches of a tree. This results in a rotation whose first axis maximizes evolutionary change along the branches, and avoids problems of non-independence of species in a cross-species PCA. Because of the reliance on a reconstruction, it has some statistical problems as compared to related methods like Garland's ordinations on independent contrasts, but it has the advantage (for visualization purposes) that the original sample points can be plotted on the resulting axes.
The Rhetenor package is still in its infancy. There is much more that might be done. We realize that other biologists have provided programs to do some analyses in a much more sophisticated way than Rhetenor does at present. Our goal has been to introduce morphometrics into Mesquite, and to provide the groundwork that will aid other programmers to contribute their sophisticated approaches to the system. We encourage them to migrate their code to work with Mesquite.
To install Rhetenor, the "rhetenor" directory must be installed in the "mesquite" directory within "Mesquite_Folder".
There is a series of example data files in the directory "rhetenor(morphometrics)". The files are self explanatory; begin with the file whose name begins with "00".
Since this is package of modules is merely a prototype, it SHOULD NOT BE USED FOR PUBLISHED OR PRESENTED RESULTS. That is, it is not yet citable.
Rhetenor currently makes use of JAMA (http://math.nist.gov/javanumerics/jama/) for some of its matrix manipulations.
About the name Rhetenor: Rhetenor was an incidental character in Ovid's Metamorphosis, but more importantly "rhetenor" is the specific epithet for a member of the butterfly genus Morpho (morphometrics...). Coincidentally, it is also the generic name of a little-known neotropical jumping spider.
© Eric Dyreson and Wayne Maddison, 2001