Software Packages
The Polly lab produces software to assist in morphometric, phylogenetic, and ecometric analyses. Our code was developed for research that led toward our publications or for instruction in our courses. We've packaged it for use by anyone who is interested. Most of our coding is in Mathematica©, which is a general mathematical and statistical package analogous to R or Matlab. Our Mathematica add-ons require the user to already have a Mathematica license.
Geometric Morphometrics for Mathematica
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, Euclidean Distance Matrix Analysis (EDMA), and import function for TPS files.
Phylogenetics for Mathematica
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.
Snails for Mathematica
Snails for Mathematica contains functions that create digital models of snail shells using David Raup's shell coiling equations. It includes functions to export shells as meshes for 3D printing or other uses. 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.
Quantitative Paleontology for Mathematica
This Mathematica add-in package performs quantitative analyses and modeling common in the field of paleontology, including simulating diversity through time, cohort/survivorship analysis, disparity through time, principal coordinates analysis, and various GIS functions.
Modularity for Mathematica
The basic component of studying modularity and integration is identifying packages of intercorrelated traits that behave independently of other such packages. This Mathematica package performs a simple analysis of modularity on geometric morphometric landmark data and accompanies the review by Goswami and Polly (2010).
