Software
http://hdl.handle.net/2022/14228
2015-07-28T08:45:32ZPhylogenetics for Mathematica (Ver. 2.1)
http://hdl.handle.net/2022/14614
Phylogenetics for Mathematica (Ver. 2.1)
Polly, P. David
This add-in package for Mathematica performs basic phylogenetic functions, including reading and drawing Newick format trees, calculating phylogenetically independent contrasts, reconstructing ancestral values for continuous traits, performing random walks, and simulating continuous traits on phylogenetic trees. The file is a ".m" file, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line "<<PollyPhylogenetics", using either this suggested name or another.
2012-07-24T00:00:00ZGeometric Morphometrics for Mathematica (Ver. 9.0)
http://hdl.handle.net/2022/14613
Geometric Morphometrics for Mathematica (Ver. 9.0)
Polly, P. David
This Mathematica add-on package performs common geometric morphometric functions. Includes Procrustes superimposition, thin-plate spline graphics, Centroid Size calculation, Procrustes distance calculation, Mantel tests, Ancestral Node reconstruction, Eclidean Distance Matrix Analysis (EDMA), and import function for TPS files.
Installation: The file is a ".m" file, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line "<<PollyMorphometrics", using either this suggested name or another. If some functions do not work, load the MultivariateStatistics and Combinatorica packages.
2012-07-24T00:00:00ZModularity for Mathematica
http://hdl.handle.net/2022/14541
Modularity for Mathematica
Polly, P. David; Goswami, Anjali
Morphological integration is correlation of parts, the integration of morphological traits or features that must function, grow, or be passed to offspring on as working units. Individual integrated units are modules, a group of traits that are highly correlated among themselves but only loosely correlated with traits in other modules. The study of integration and modularity was first developed by Olson and Miller (1958) and expanded on by Cheverud (1982), Zelditch (1988), Wagner (1995), Raff (1996), Klingenberg (2000), Mitteroecker (2007) and many others.
The basic component of studying modularity and integration is identifying packages of intercorrelated traits that behave independently of other such packages, whether through ontogeny, across individuals within a population, or during the course of evolution. This package performs a simple analysis of modularity on geometric morphometric landmark data.
This package accompanies the review by Goswami and Polly (2010). Users are referred to that paper for a discussion of the methods embedded in this package, including their strengths and weaknesses, and for elaboration of other methods that address broader problems.
2010-10-30T00:00:00Z