-------- Original Message --------
Subject: Re: R-package for for shape analysis and mesh operations
[under development]
Date: Thu, 9 Feb 2012 12:51:53 -0500
From: Ruth Flatscher <[email protected]>
To: [email protected]
hi Karl,
to your first warning message: I have already worked with other packages
in R and got similar warnings that they were built under a newer version
than I am using on my computer... but I usually just ignored it and
everything worked fine, same as under the new R, so this must not
necessarily mean that there will be problems. I also tried to use Morpho
under R 2.10, and apparently it works.
To the second problem: when you call the package from the library, do
you really put its name under envirted commas, like you did in your
e-mail?: library("Morpho")?
Then leave them out - it won't work that way with any package. The
second thing you could check is whether after extracting the
installation folder you just took the subfolder "Morpho" inside and
copied it to your library... because only that way you can call the
package from R.
Hope this might help.
Best wishes,
Ruth
ps - btw, what leaves are you working on? I'd find that interesting,
because I'm also a "plant person"...
----------------------------------------------
Mag. Ruth Flatscher
Department of Systematic and Evolutionary Botany
Rennweg 14
1030 Vienna
Austria
On 9 February 2012 17:50, morphmet <[email protected]
<mailto:[email protected]>> wrote:
-------- Original Message --------
Subject: RE: R-package for for shape analysis and mesh operations
[under development]
Date: Tue, 7 Feb 2012 15:46:42 -0500
From: Murat Maga <[email protected] <mailto:[email protected]>>
Organization: University of Washington
To: <[email protected] <mailto:[email protected]>>
Are you using 64 bit or 32 bit version of R? Not 100% sure, but you
may want to try it with 32 bit version of the R.
M
-----Original Message-----
From: morphmet [mailto:morphmet_moderator@__morphometrics.org
<mailto:[email protected]>]
Sent: Tuesday, February 07, 2012 12:25 PM
To: morphmet
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: Sat, 21 Jan 2012 23:30:33 -0500
From: Karl Fetter <[email protected]
<mailto:[email protected]>>
To: [email protected] <mailto:[email protected]>
I'm trying to use this new Morpho package to do a CVA of leaf data that
I've superimposed (GPA) using tpsRelw.
I've downloaded the package and manually placed it in my library, so I
can see the package in Rstudio, but when I try to install it, I get
this
message:
Installing package(s) into
‘/Library/Frameworks/R.__framework/Versions/2.14/__Resources/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘Morpho’ is not available (for R version 2.14.1)
And when I use library("Morpho") , it obviously doesn't load the
package
and I get this message:
Error: package ‘Morpho’ is not installed for 'arch=x86_64'
Can someone give me some advice to get the package installed correctly?
Thanks in advance,
Karl Fetter
UNC-CH
On Jan 20, 2012, at 4:26 PM, morphmet wrote:
-------- Original Message --------
Subject: Re: R-package for for shape analysis and mesh
operations [under development]
Date: Fri, 20 Jan 2012 15:24:55 -0500
From: Dean Adams <[email protected] <mailto:[email protected]>>
To: [email protected]
<mailto:[email protected]> <[email protected]
<mailto:[email protected]>>
Anna,
There are many options to easing into R. One I recommend is:
"An Introduction to R" by the R Development Core Team. You can
find a
PDF of this book on the CRAN web site:
http://cran.r-project.org/doc/__manuals/R-intro.pdf
<http://cran.r-project.org/doc/manuals/R-intro.pdf>. Of course,
there are
MANY other books for learning R, but this is a good place to start.
Also, Julien Claude's book "Morphometrics with R" has a chapter
that
introduces some elementary R-concepts, as well as routines for
implementing many basic morphometric approaches.
Dean
--
Dr. Dean C. Adams
Associate Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
Ames, Iowa
50011
www.public.iastate.edu/~__dcadams/
<http://www.public.iastate.edu/%7Edcadams/>
phone: 515-294-3834 <tel:515-294-3834>
On 1/20/2012 1:01 PM, morphmet wrote:
-------- 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<[email protected]
<mailto:[email protected]>>
To:<[email protected]
<mailto:[email protected]>__>
Dear all,
I would take advantage from the discussion…I tried to use R
and I felt
really stupid…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_moderator@__morphometrics.org
<mailto:[email protected]>> 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: [email protected] <mailto:[email protected]>
To: [email protected]
<mailto:[email protected]>
CC: morphmet<morphmet@__morphometrics.org
<mailto:[email protected]>>
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.schlager@uniklinik-__freiburg.de
<mailto:[email protected]>>
To: [email protected]
<mailto:[email protected]>
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 faces’ 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.
* I’ve 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: I’m 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/
<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://meshlab.sourceforge.net/> ,
http://vcg.sourceforge.net/__index.php/Main_Page
<http://vcg.sourceforge.net/index.php/Main_Page>) and
install them (add
them to your system’s path). I recently managed to
compile those not
only for Linux but also for OSX and Windows.
Read the README!!
It’s 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
<tel:%2B49%20%280%29761%20203-5522>
fax +49 (0)761 203-6898 <tel:%2B49%20%280%29761%20203-6898>
--
Paolo Piras
Center for Evolutionary Ecology
and
Dipartimento di Scienze Geologiche, Università Roma Tre
Largo San Leonardo Murialdo, 1, 00146 Roma
Tel: +390657338000 <tel:%2B390657338000>
email: [email protected] <mailto:[email protected]>
