-------- Original Message --------
Subject: Re: R-package for for shape analysis and mesh operations
[under development]
Date: Wed, 8 Feb 2012 02:36:13 -0500
From: Marie CACHERA <marie.cach...@ifremer.fr>
Organization: IFREMER
To: morphmet@morphometrics.org
dear all
I'm also using for almost a year now, and its awesome packages "shapes".
of course , I previously compare outputs with TPS, and everything sounds
goods. Doing it is a good way to make sure that you understand what
you're playing with in the "shapes" packages.
morphmet a écrit :
-------- Original Message --------
Subject: Re: R-package for for shape analysis and mesh operations
[under development]
Date: Mon, 23 Jan 2012 02:39:31 -0500
From: andrea cardini <alcard...@gmail.com>
To: morphmet@morphometrics.org
Google searching videos using something like "R-project introduction" you
will also find quite a few lectures teaching the basic stuff.
Cheers
Andrea
At 16:25 20/01/2012 -0500, you wrote:
-------- Original Message --------
Subject: Re: R-package for for shape analysis and mesh operations
[under development]
Date: Fri, 20 Jan 2012 14:25:49 -0500
From: Pedro Cordeiro Estrela <pedroestr...@yahoo.com>
Reply-To: Pedro Cordeiro Estrela <pedroestr...@yahoo.com>
To: morphmet@morphometrics.org <morphmet@morphometrics.org>
http://cran.r-project.org/doc/contrib/Paradis-rdebuts_en.pdf
________________________________________________________________
Biologia e Parasitologia de MamÃferos Silvestres Reservatórios
Pavilhão Arthur Neiva
IOC / Fundação Oswaldo Cruz
Avenida Brasil, 4365
Manguinhos
Rio de Janeiro - RJ, Brasil
21040-900
Tel: +55 (21) 2562 1253 /+55 (21) 2562 1324
Cel: + 55 (21) 8389 8788
_________________________________________________________________
|lIi___Lo¬___iIl|
------------------------------------------------------------------------
*From:* morphmet <morphmet_modera...@morphometrics.org>
*To:* morphmet <morphmet@morphometrics.org>
*Sent:* Friday, January 20, 2012 5:01 PM
*Subject:* Re: R-package for for shape analysis and mesh operations
[under development]
-------- Original Message --------
Subject: Re: R-package for for shape analysis and mesh operations [under
development]
Date: Fri, 20 Jan 2012 11:25:46 -0500
From: Anna Maria Vettraino <vettr...@unitus.it
<mailto:vettr...@unitus.it>>
To: <morphmet@morphometrics.org <mailto:morphmet@morphometrics.org>>
Dear all,
I would take advantage from the discussionâ¦I tried to use R and I felt
really stupidâ¦do you know a quick guide to learn how use it?
Thank you in advance
regards
AM
Il giorno 20/01/12 17:13, "morphmet"
<morphmet_modera...@morphometrics.org
<mailto:morphmet_modera...@morphometrics.org>> ha scritto:
>
>
>-------- Original Message --------
>Subject: Re: R-package for for shape analysis and mesh operations
[under
> development]
>Date: Fri, 20 Jan 2012 10:38:07 -0500
>From: ppi...@uniroma3.it <mailto:ppi...@uniroma3.it>
>To: morphmet@morphometrics.org <mailto:morphmet@morphometrics.org>
>CC: morphmet <morphmet@morphometrics.org
<mailto:morphmet@morphometrics.org>>
>
>
>Dear Stefan
>That seems great! There is any help documentation with
>sample files and sample scripts? It would facilitate
>the use of Morpho package...
>Thanks in advance
>Paolo
>
>-------- Original Message --------
>Subject: R-package for for shape analysis and mesh
>operations [under
>development]
>Date: Fri, 20 Jan 2012 04:33:23 -0500
>From: Stefan Schlager
><stefan.schla...@uniklinik-freiburg.de
<mailto:stefan.schla...@uniklinik-freiburg.de>>
>To: morphmet@morphometrics.org <mailto:morphmet@morphometrics.org>
>
>
>
>Dear all,
>
>as it seems that more and more people are using R and
>also are working
>with triangular meshes, I also take the opportunity to
>share some
>scripts with you:
>I am developing an R package (which are basically
>functions coded for my
>dissertation) called Morpho which allows a lot of mesh
>operations.
>Including:
>
> * importing all kinds of mesh formats (e.g.
>obj,ply,stl,...)
> (file2mesh) and
> * exporting objects of class "mesh3d" to ascii-ply
>format (mesh2ply)
> * operations like TPS deformation, and affine
>transformations based on
> landmark informations (warp.mesh, rotmesh.onto,
>scalemesh),
> including the updating of facesâ normals.
> * the imported objects are of class "mesh3d" so
>that they can be
> rendered by the functions shade3d and wire3d from
>the rgl-package
> * a function (called slider3d) allowing sliding of
>points, surfaces
> and curves (using the bending energy criterion)
>and projecting the
> slidden points back onto the 3D-mesh.
> * There is also a function for semi-automatic
>placement of surface
> patches (place.patch - yet undocumented) onto a
>whole sample based
> on a initially defined atlas configuration.
> * Iâve included functions for im- and exporting
>landmark-data from
> landmark-IDAV (read.pts,write.pts,read.lmdta) and
>extracting the
> information, if the coordinate belongs to a curve
>or surface from
> imported pts files (c.extract), as I used this
>program to place the
> curves and the atlas surface.
> * There is also a GPA algorithm optimised for speed
>(procSym), useful
> for big sample sizes and many (semi-)landmarks,
>that also allows
> analysis of symmetry/asymmetry.
> * CVA (thanks to M. Rufino from this mailing list
>for providing nice
> examples in the documentation)
> * some permutation tests
> * graphical interface to find outliers (similar to
>MorphoJ)
>
>
>And here comes the bad part: Iâm a bit behind with
>the documentation, so
>a lot code remains unexplained :(
>
>If you're interested, you can download precompiled
>packages or the
>source code from
>https://sourceforge.net/projects/morpho-rpackage/files/
>
>It is optimised for Linux but also works on OSX and
>Windows (with some
>restrictions)!!!
>
>For the full functionality you must also download some
>command line
>tools which I coded using the header files of the
>meshlab/vcglib project
>(http://meshlab.sourceforge.net/ ,
>http://vcg.sourceforge.net/index.php/Main_Page) and
>install them (add
>them to your systemâs path). I recently managed to
>compile those not
>only for Linux but also for OSX and Windows.
>
>Read the README!!
>
>Itâs all licensed under GPL, so you also can rip it
>apart and improve or
>adapt it, if necessary.
>
>Best regards
>Stefan
>
>Stefan Schlager M.A.
>Anthropologie
>Medizinische Fakultät der der Albert Ludwigs-
>Universität Freiburg
>Hebelstr. 29
>79104 Freiburg
>
>Anthropology
>Faculty of Medicine, Albert-Ludwigs-University
>Freiburg
>Hebelstr. 29
>D- 79104 Freiburg
>
>phone +49 (0)761 203-5522
>fax +49 (0)761 203-6898
>
>
>
>
>
>
>
>--
>Paolo Piras
>Center for Evolutionary Ecology
> and
>Dipartimento di Scienze Geologiche, Università Roma Tre
>Largo San Leonardo Murialdo, 1, 00146 Roma
>Tel: +390657338000
>email: ppi...@uniroma3.it <mailto:ppi...@uniroma3.it>
>
>
Dr. Andrea Cardini
Researcher in Animal Biology
Dipartimento di Biologia, Universitá di Modena e Reggio Emilia, via Campi
213, 41100, Modena, Italy
tel: 0039 059 2055017 ; fax: 0039 059 2055548
Honorary Fellow
Functional Morphology and Evolution Unit, Hull York Medical School
University of Hull, Cottingham Road, Hull, HU6 7RX, UK
University of York, Heslington, York YO10 5DD, UK
Adjunct Associate Professor
Centre for Forensic Science , The University of Western Australia
35 Stirling Highway, Crawley WA 6009, Australia
E-mail address: alcard...@gmail.com, andrea.card...@unimore.it,
andrea.card...@hyms.ac.uk, andrea.card...@uwa.edu.au
Webpage: http://sites.google.com/site/hymsfme/drandreacardini
Datasets:
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
Editorial board for:
Zoomorphology:
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and Evolutionary Research:
http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of Mammalogy:
http://www.italian-journal-of-mammalogy.it/
