----- Forwarded message from morphmet_modera...@morphometrics.org ----- Date: Mon, 29 Oct 2012 22:27:41 -0700 From: morphmet_modera...@morphometrics.org Reply-To: morphmet_modera...@morphometrics.org Subject: Subject: New Morphometrics Software for R To: morphmet@morphometrics.org
----- Forwarded message from Dean Adams ----- Date: Mon, 29 Oct 2012 14:29:17 -0400 From: Dean Adams Reply-To: Dean Adams Subject: Subject: New Morphometrics Software for R To: "morphmet@morphometrics.org" Hello all, We are happy to announce the release of GeoMorph: a morphometrics package in R for the collection and analysis of landmark-based geometric morphometric data. It is available on the CRAN package website. Geomorph provides routines for all stages of a geometric morphometric analysis in two and three-dimensions. It allows one to read, manipulate, and digitize 2D and 3D landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform statistical analyses of shape variation and covariation, and provide graphical depictions of shapes and patterns of shape variation. Geomorph follows the data structures previously utilized in R in the 'shapes' package as well as in J. Claude's book 'Morphometrics with R'. There are two important components of geomorph that we emphasize. First, geomorph allows GPA of both landmarks and semilandmarks for 2D and 3D data. As such, data from points, curves, and surfaces may be combined and used in a geometric morphometric shape analysis. Second, geomorph allows digitization from 3D surface scans directly in R (one can also read in existing data). Thus, one may use the R environment for all stages of a geometric morphometric analysis. Here is a list of some general features of the present version of geomorph: 1: Data Collection - read tps files - read nts files - read Morphologika files - read ply files - read vrml files - estimate missing landmarks using the Bending Energy approach - digitize points, curves, and surface landmarks from 3D surface scans - digitize 2D points from images - various data manipulation routines (for data read into R via other means, and for exporting geomorph results) 2: Shape Variable Generation - GPA of landmarks (points) and semilandmarks (curve and surface points) using bending energy of Procrustes distance minimization 3: Statistical Analyses - Procrustes Anova/Regression - Analysis of vectors and trajectories of phenotypic change - Modularity analyses (both PLS and RV approaches) - Assessment of phylogenetic signal *NOTE: R already has MANOVA, regression, PLS capabilities, so shape data obtained from geomorph can simply be included in this analysis pipeline 3: Visualization - GPA scatterplots - Shape differences between specimens (deformation grids, landmark displacements) - Scatterplot of shapes in tangent space - Allometry plots using several current approaches (CAC, regression scores, predicted regression lines) - Plotting phenotypic trajectories - Plotting phylogenies in tangent space Over time we will incorporate additional routines in geomorph to enhance its flexibility. Dean Adams and Erik Otarola-Castillo -- Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University Ames, Iowa 50011 www.public.iastate.edu/~dcadams/ phone: 515-294-3834 ----- End forwarded message ----- ----- End forwarded message -----