[MORPHMET] testing - ignore

[Dennis E. Slice]

I see at least one message (from Adams) has gotten through. Let's see if 
this one does from me. -ds


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[MORPHMET] Testing - ignore

[Dennis E. Slice]

Just testing to see of the server is still working. -ds

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[MORPHMET] Another test - ignore

[Dennis E. Slice]

Stop reading these! -ds

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[MORPHMET] Testing - ignore

[Dennis E. Slice]

Don't read this!

Testing server-side problems. -ds

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Re: [MORPHMET] Insect wing images needed

[Dennis E. Slice]

Replying to postdoc AND the list since a) I don't follow instructions 
very well and b) this might be of general interest.


David Houle at FSU has an automated Drosophila wing landmarking system 
(hardware and software), and has placed a lot (30k+) images on the 
Morphbank server. For more info, see...


http://www.morphbank.net/

A search for "drosophila" brings up "31924 Images"

-ds



On 3/29/17 9:35 AM, Göran Arnqvist wrote:

A postdoc of mine asked me to send along the below request to morphmet -
any help would be appreciated! Please reply straight to her. /Göran



 Forwarded Message 
Subject:[ebc-zooeco] Insect wing images needed
Date:   Wed, 29 Mar 2017 12:57:41 +
From:   Zorana Kurbalija Novicic 
Reply-To:   Zorana Kurbalija Novicic 
To: zoo...@ebc.uu.se 



Dear colleagues,


I have lost a large amount of time and energy in manually putting a
landmarks on thousands of Drosophila wings in order to perform some
geometric morphometry analysis. I am sure that I have sympathy of some
of you who are experiencing the same.


Recently I made collaboration with colleagues from IT Department
(Uppsala University) with an aim to make that boring process
automatized. Now, I am happy inform you that we are approaching the
final phase in software development and that hopefully will enable us to
perform landmarking automatically.


I am writing to you because I need your assistance. *I would very much
appreciate if you have some good quality images (tiff or jpeg) of insect
wings to share with me- so I can try to analyze the applicability of
software across different insect species *(and not only Drosophila).


Looking forward to receive the material and thanks in advance!

Kind regards

Zorana

- - -
Zorana Kurbalija Novicic, PhD
Marie Curie Fellow

Animal Ecology
Department of Ecology and Genetics
Evolutionary Biology Centre
Uppsala University, Sweden

Norbyvägen 18D
SE-752 36, Uppsala, Sweden
Mob: 0723 634 937

E-mail: zorana.novi...@ebc.uu.se
Homepage: www.zoranakurbalijanovicic.com


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[MORPHMET] Fwd: Fwd: [dzg-evol] Course: Barcelona, Spain; Phylogenetic analysis using R, 6-10 March 2017

[Dennis E. Slice]

Possibly interesting to morphmet members. Forwarded via subscriber. -ds


 Forwarded Message 
Subject: 	[dzg-evol] Course: Barcelona, Spain; Phylogenetic analysis 
using R, 6-10 March 2017

Date:   Thu, 1 Sep 2016 11:39:29 +0200
From:   dzg evol 
To: dzg evol 



Dear Colleague,

Registration is open for the fourth edition of the course *PHYLOGENETIC 
ANALYSIS USING R*, March 6th-10th, 2017.


INSTRUCTORS: Dr. Emmanuel Paradis (Institut de Recherche pour le 
Développement, France) and Dr. Klaus Schliep (University of 
Massachusetts, USA).


More information:

http://www.transmittingscience.org/courses/phylogeny/phylogenetic-analysis-using-r/ 



This course is for biologists dealing with the analysis of multiple 
molecular sequences at several levels: Populations, species, clades, 
communities. These biologists address questions relative to the 
evolutionary relationships among these sequences, as well as the 
evolutionary forces structuring biodiversity at different scales. The 
objectives are: (i) to learn the theorical bases phylogenetic analysis, 
(ii) to know how to choose a strategy of molecular data analysis at the 
inter‐ or intraspecific levels, (iii) to be able to initiate a 
phylogenetic analysis starting from the files of molecular sequences 
until the interpretation of the results and the graphics. The software 
used for this course will be centered on the R language for statistics. 
This will include the use of specialized packages particularly ape, 
phangorn, and adegenet.


Requeriments: Knowledge of multivariate statistics, phylogenetics and 
molecular evolution. User level of R.


PLACE:Facilities of the Centre of Restauració i Interpretació 
Paleontologica, Els Hostalets de Pierola,Barcelona (Spain).


Organized by: Transmitting Science, the Institut Catalá de Paleontologia 
M. Crusafont and the Centre de Restauració i Interpretació 
Paleontologica de Els Hostalets de Pierola.


*Places are limited and will be covered by strict registration order.*

With best regards

Soledad De Esteban-Trivigno, PhD.

Scientific Director

Transmitting Science

www.transmittingscience.org 

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[MORPHMET] Morpheus et al.

[Dennis E. Slice]

IMPORTANT: Would please report as to the OS you are using to run the 
latest Morpheus et al.? OS X, Linux, Windows? Please include version. 
And any notes on its operation.


-ds


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Re: [MORPHMET] tpsDig on a Mac using LINUX-wine

[Dennis E. Slice]

I will chime in, too. I, too, use the tps programs on wine for all of my 
teaching and related research.


Specifically, I use a utility called Wineskin, which makes set up easy. 
You just create an Wineskin app, have it call the tps install program 
and there you have it. The only downside is you have an app for each 
program, but that can all access the harddrive.


On a side note, I started using wineskin after confusing a 
recommendation for another program - wine bottler. The person said it 
was great, too, but I haven't bothered testing it since wineskin does so 
well.


Note, the only issue I have found is the equations in the technical 
sections of the help files don't usually work out.


Yes, this is how I run the old Morpheus, too, though I hope to get all 
of the features ported to the new version eventually. Getting very 
close, though EFA is pretty far down the ToDo at the moment.


-ds

On 5/20/15 7:30 AM, alcardini wrote:

I've never tried them on the Mac side of my machine, but in my
experience all the TPS Series programs work well in Linux using WINE.
The 'old' Morpheus et al works too, PAST 2.x works as well.
With the TPS Series the only trick I need to do is starting the
programs directly from the installation folder: the links in the main
menu do not seem to work but this is clearly a very minor issue.

Thanks Jim for the continuous development of his series and for making
them cleverly simple so that they can run on other platforms with
little efforts.

Cheers

Andrea

On 19/05/2015, F. James Rohlf ro...@life.bio.sunysb.edu wrote:

Thanks!  Does that also work for 64 bit versions of the programs? tpsSmall
is a simple program, would you mind testing the 64 bit version? I am also,
of course, curious about how it works on the other emulators. I try to
program in a very standard way for maximum compatibility with Windows.



--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

P Please consider the environment before printing this email



From: Joseph Kunkel [mailto:j...@bio.umass.edu]
Sent: Tuesday, May 19, 2015 3:35 PM
To: ro...@life.bio.sunysb.edu; morphmet@morphometrics.org
Cc: Joe Kunkel
Subject: tpsDig on a Mac using wine



Dear Jim and Morphmet,



I just want to comment on using tpsDig on a Mac.  tps Dig is my go-to
software for 2-D landmark digitizing of images.  To digitize I would
previously have to use one of my PCs in my lab which was often a pain.  I
was reluctant to use several of the PC-on-your-Mac options because they
meant partitioning your disc or in some sense running two separate worlds on
your Mac which always made me nervous for several security software reasons.


Using the emulation program, wine (https://www.winehq.org/), has changed
everything.  It works as a unix program run from your Mac Terminal console.
I have tested several of the tps suite of software from Rohlf and they work
like a charm.  One trick however to get around the need for a ‘right-click’
in tpsDig is to redefine the right-click as something else such as a
track-pad tap which works like a charm.

Thank you wine for allowing me to ‘go home’ and do tpsDig on my Macs!

-·.  .· ·.  .º·.  .· ·.  .º·.  .· ·.  .º .··.· =-
  =º}

Joseph G. Kunkel, Emeritus Professor

Biology Department

UMass Amherst

Amherst MA 01003

j...@bio.umass.edu mailto:j...@bio.umass.edu







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Re: [MORPHMET] combining 3D datasets

[Dennis E. Slice]

Sorry, folks. I meant to send the previous message from this and not the 
moderator account. Too much power for one person to wield.


-ds

On 2/6/15 7:00 PM, Bryan McLean wrote:

Hi all,

I have 3D landmark data from two different views (lateral and ventral)
of some rodent skulls. I would like to append these data, based on the 4
landmarks they have in common.

Could someone give me leads on the best software for doing this kind of
manipulation?

Thank you-
-Bryan

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morphometric functions for R users

[Dennis E. Slice]

).
   # Thus, we get 200 variables * Number of
individuals
harm[ii,]=c(Ne$an, Ne$bn, Ne$cn, Ne$dn)
# OR
#Ne=NEF(newd1[newd1$ind==ii,c(X,Y)], n=20)
#harm[ii,]=c(Ne$A, Ne$B, Ne$C, Ne$D)
}
rm(Ne)

#1st approach
  co=harm2
  tharn=apply(co, 2, sum)
  Power=apply(matrix(tharn, 20, 4),1,sum)
  po1=round(cumsum(Power[-1])/sum(Power[-1]),3)[2:19]

  # Add a curve with Cumulative variance explained by the
coeffcients
  vharn=apply(harm, 2, var)
  variation=apply(matrix(vharn,20,4),1,sum)
  var1=round(cumsum(variation[-1])/sum(variation[-1]),3)[2:19]

  # and plot it
  par(las=1, mar=c(1,4,1,1), mfrow=c(1,1))
  plot(po1*100, typ=o, col=2, cex=.7, pch=16, ylab=c(%
explained), axes=F,
ylim=c(min(var1*100),101), main=How many harmonics?)
  box()
  axis(2)
  abline(h=100, col=lightblue, lwd=2)
  abline(v=c(1:19), col=8,  lty=3)
  abline(h=seq(0,100,5), col=lightblue,  lty=3)
  text(1:19, rep(101,19), c(2:19), cex=.7)
  points(2:19, var1*100, typ=o, col=4, cex=.7, pch=17, lty=2)
  legend(bottomright, c(Total power,Variance explained),
text.col=c(2,4), cex=.7, box.col=0)

  kk=list(Total comulative power=po1*100, Variance
explained=var1*100)
  kk
  }

--
Dennis E. Slice
Associate Professor
Dept. of Scientific Computing
Florida State University
Dirac Science Library
Tallahassee, FL 32306-4120
-
Guest Professor
Department of Anthropology
University of Vienna
-
Software worth having/learning/using...
 Linux (Operating System: Ubuntu, CentOS, openSUSE, etc.)
 OpenOffice (Office Suite: http://www.openoffice.org/)
 R package (Stats/Graphics environment: http://www.r-project.org/)
 Eclipse (Java/C++/etc IDE: http://www.eclipse.org/)
 Netbeans (Java/C++/etc IDE: http://netbeans.org/)
 Zotero (FireFox bibliographic extension: http://www.zotero.org/)

Re: Understanding Morphologika

[Dennis E. Slice]

w.r.t. problem 2. The curvature of shape space, itself, introduces some 
purely geometric variation that is picked up by PCA. For 2D, you expect 
to lose 4 dimensions of variation. In fact, you get three exactly zero 
eigenvalues and one very, very small one. The latter (usually, but I can 
construct counter examples) reflecting the curvature of GPA space.


-ds

morphmet wrote:



 Original Message 
Subject: Understanding Morphologika
Date: Wed, 3 Mar 2010 09:41:33 +
From: a.vanhete...@roehampton.ac.uk
To: morphmet_modera...@morphometrics.org




Dear Colleagues



I have two unrelated issues, for which I don’t understand what 
Morphologika is calculating exactly.




Firstly, I am having difficulties with the Procrustes Superimposition 
performed in Morphologika. I was under the impression that scaling, 
rotation, reflection and translation could be switched on and off and 
that the subsequent principal component analysis would be performed on 
the Procrustes coordinates as you instructed Morphologika to calculate 
them.


Now my problem is the following:

If I perform Procrustes superimposition without scaling and perform PCA 
afterwards or Procrustes superimposition with scaling and PCA 
afterwards, the Procrustes coordinates are different, as would be 
expected. However, the PC scores are almost identical (a few small 
differences 5 decimals behind the comma). This is not what I would 
expect. Since some of my specimens are twice the size of some others, I 
would expect the first PC to show size (both isometric and allometric), 
however, it is showing the same signal as the PCA on the full Procrustes 
superimposition coordinates.


I am confused about what Morphologika calculates exactly to come to 
these results.


And I have not been able to reproduce either of the PCA plots of 
Morphologika with SPSS, even though I am forcing SPSS to use the 
covariance matrix instead of the correlation matrix.


Any help or suggestions of what might be going on would be greatly 
appreciated.




My second issue relates to the number of principal components calculated 
by Morphologika.


In the help file it is stated: Principal components analysis of 
specimens with k landmarks in m dimensions results in km-m-m(m-1)-1 
eigenvectors; the principal components of variation of shape.


In my dataset I have 15 landmarks and 3 dimensions, so I think that 
should result in 15*3-3-3*(3-1)-1=35 principal components. However, 
Morphologika is giving me 38 principal components in the output. I don’t 
understand the discrepancy and would appreciate it if anybody could 
explain where the extra three principal components come from.




Thanking you all in advance.



Best wishes,



Anneke van Heteren


Anneke H. van Heteren
School of Human and Life Sciences
Roehampton University
Whitelands College
Holybourne Avenue
London SW15 4JD
Tel: +44 (0) 20 8392 3728
E-Mail: a.vanhete...@roehampton.ac.uk



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--
Dennis E. Slice
Associate Professor
Dept. of Scientific Computing
Florida State University
Dirac Science Library
Tallahassee, FL 32306-4120
-
Guest Professor
Department of Anthropology
University of Vienna
-
Software worth having/learning/using...
 Linux (Operating System: Ubuntu, CentOS, openSUSE, etc.)
 OpenOffice (Office Suite: http://www.openoffice.org/)
 R package (Stats/Graphics environment: http://www.r-project.org/)
 Eclipse (Java/C++/etc IDE: http://www.eclipse.org/)

[Fwd: Testing...nothing to see here. Move alone...]

[Dennis E. Slice]

Repeating test. -ds

 Original Message 
Subject: Testing...nothing to see here. Move alone...
Date: Wed, 23 Dec 2009 11:15:23 -0500
From: Dennis E. Slice dsl...@morphometrics.org
To: morphmet morphmet@morphometrics.org

Testing to see if the list has really and mysteriously switched some
options.

-ds
--
Dennis E. Slice
Associate Professor
Dept. of Scientific Computing
Florida State University
Dirac Science Library
Tallahassee, FL 32306-4120
-
Guest Professor
Department of Anthropology
University of Vienna
-
Software worth having/learning/using...
 Linux (Operating System: Ubuntu, CentOS, openSUSE, etc.)
 OpenOffice (Office Suite: http://www.openoffice.org/)
 R package (Stats/Graphics environment: http://www.r-project.org/)
 Eclipse (Java/C++/etc IDE: http://www.eclipse.org/)



--
Dennis E. Slice
Associate Professor
Dept. of Scientific Computing
Florida State University
Dirac Science Library
Tallahassee, FL 32306-4120
-
Guest Professor
Department of Anthropology
University of Vienna
-
Software worth having/learning/using...
 Linux (Operating System: Ubuntu, CentOS, openSUSE, etc.)
 OpenOffice (Office Suite: http://www.openoffice.org/)
 R package (Stats/Graphics environment: http://www.r-project.org/)
 Eclipse (Java/C++/etc IDE: http://www.eclipse.org/)