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

```
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
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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/)

```

### Re: Understanding Morphologika

```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.

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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Dept. of Scientific Computing
Florida State University
Dirac Science Library
Tallahassee, FL 32306-4120
-
Guest Professor
Department of Anthropology
University of Vienna
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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/)

```

### morphometric functions for R users

```).
# 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: MORPHMET - progress, but not there, yet.

```By reply, I mean respond - there will be an Accept This Invitation
button within the email. -ds

On 7/31/14, 3:23 AM, morphmet wrote:

I have been making progress preparing the migration to the new system,
but not quite there, yet. I hope to have this done by or over the weekend.

I am writing this to let you know that when MORPHMET does come back up,
you will receive an invitation to join the new list (actually just the
old list in a new environment). You need to reply to this message when
you receive it to continue to be a subscriber to the new (=old) MORPHMET.

-dslice

```

### Re: [MORPHMET] combining 3D datasets

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

```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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### [MORPHMET] Morpheus et al.

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

```
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).

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,

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

Scientific Director

Transmitting Science

www.transmittingscience.org

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### Re: [MORPHMET] Insect wing images needed

```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

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 -

Forwarded Message
Subject:[ebc-zooeco] Insect wing images needed
Date:   Wed, 29 Mar 2017 12:57:41 +
From:   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).

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] testing - ignore

```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

```

Testing server-side problems. -ds

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### [MORPHMET] Another test - ignore

```

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### [MORPHMET] Testing - ignore

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

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