----- Forwarded message from "Otarola-Castillo, Erik"
<eotarolacasti...@fas.harvard.edu> -----
Date: Mon, 7 Oct
2013 08:54:14 -0400
From: "Otarola-Castillo, Erik"
<eotarolacasti...@fas.harvard.edu>
Reply-To: "Otarola-Castillo,
Erik" <eotarolacasti...@fas.harvard.edu>
Subject: RE: 3D
semilandmark software pipeline
To: "morphmet@morphometrics.org"
<morphmet@morphometrics.org>
Will,
The R package “geomorph” will allow you to incorporate sliding semilandmarks in 3D to your Procrustes fitting. You can use its internal programs to select the 3D sliding semilandmarks. Alternatively, if you already have assigned 3D semilandmarks to your specimen (e.g., in Landmark) you can “tell” geomorph to conduct the sliding algorithm on them. You could then export the Procrustes aligned coordinates into other software such as MorphoJ, however, geomorph also allows you to conduct a wide array of analyses within the R environment. For further details, you might want to take a look at Adams and Otarola-Castillo 2013 and at the geomorph .pdf manual.
Here is the citation for the above paper:
Adams, D.C., and E. Otárola-Castillo. 2013. geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution. 4:393-399
Cheers,
Erik
_____________________________________________
Erik Otárola-Castillo
Department of Human Evolutionary Biology
Department of Statistics
Harvard University
11 Divinity Ave, Cambridge, MA 02138
Phone: 631-796-7331
R package ‘geomorph’ blog: http://www.geomorph.net/
Website: www.people.fas.harvard.edu/~eotarolacastillo
______________________________________________
From: morphmet_modera...@morphometrics.org
[mailto:morphmet_modera...@morphometrics.org]
Sent: Wednesday, October 02, 2013 9:41 PM
To:
morphmet@morphometrics.org
Subject: 3D semilandmark software
pipeline
----- Forwarded message from William Ary <williamjames...@gmail.com> -----
Date: Mon, 30 Sep 2013 01:28:40 -0400
From: William Ary <williamjames...@gmail.com>
Reply-To: William Ary <williamjames...@gmail.com>
Subject: 3D semilandmark software pipeline
To: morphmet@morphometrics.org
Hello all-
I am using a 3D morphometrics software pipeline that begins with UC Davis Landmark and ends with MorphoJ and I want to adapt it for use with semilandmarks. Are there any other softwares I need to slide my semilandmarks as assigned with Landmark software before importing them for a procrustes fit and PCA? If so, are they compatible with MorphoJ or must it be done in another package? I am considering using Shapes or Geomorph in R, but I don't know if it is necessary to switch over.
Thanks!
Will Ary
MS Candidate,
Berta Lab
Department of Biology
San Diego State University
williamjames...@gmail.com
----- End forwarded message -----
----- End forwarded message
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