----- Forwarded message from Joseph Kunkel -----
Date: Thu, 1 Nov 2012 16:41:44 -0400
From: Joseph Kunkel
Reply-To: Joseph Kunkel
Subject: Re: Subject: New Morphometrics Software for R
To: morphmet@morphometrics.org
Thanks. The binary was posted shortly after I requested. I am looking forward
to an input as good as the one devised by Jim Rohlf where an initial landmark
set provides a template for locating landmarks for subsequent specimens. The
current productivity is in its early stages of development.
-·. .· ·. .><((((º>·. .· ·. .><((((º>·. .· ·. .><((((º> .··.· >=-
=º}}}}}><
Joseph G. Kunkel, Emeritus Professor
Biology Department
University of Massachusetts Amherst
Amherst MA 01003
http://www.bio.umass.edu/biology/kunkel/
On Nov 1, 2012, at 12:18 PM, morphmet_modera...@morphometrics.org wrote:
>
> ----- 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: morphmet@morphometrics.org
>
> Will the CRAN binaries for GeoMorph be available in the near future?
>
> -·. .· ·. .><((((º>·. .· ·. .><((((º>·. .· ·. .><((((º> .··.· >=-
> =º}}}}}><
> 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, morphmet_modera...@morphometrics.org wrote:
>
>>
>> ----- 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 -----
>
> ----- End forwarded message -----
>
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