----- Forwarded message from Joseph Kunkel -----
Date: Wed, 31 Oct 2012 19:46:05 -0400
From: Joseph Kunkel
Reply-To: Joseph Kunkel
Subject: Re: Subject: New Morphometrics Software for R
To: [email protected]
Will the CRAN binaries for GeoMorph be available in the near future?
-·. .· ·. .><((((º>·. .· ·. .><((((º>·. .· ·. .><((((º> .··.· >=-
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Joseph G. Kunkel, Emeritus Professor
Biology Department
University of Massachusetts Amherst
Amherst MA 01003
http://www.bio.umass.edu/biology/kunkel/
On Oct 31, 2012, at 7:22 PM, [email protected] wrote:
>
> ----- Forwarded message from [email protected] -----
>
> Date: Mon, 29 Oct 2012 22:27:41 -0700
> From: [email protected]
> Reply-To: [email protected]
> Subject: Subject: New Morphometrics Software for R
> To: [email protected]
>
> ----- 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: "[email protected]"
>
> 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 -----
----- End forwarded message -----
