----- 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 -----
