[MORPHMET] thanks for support

2019-05-16 Thread andrea cardini

Dear morphometricians,
I would like to thank all those who openly and privately expressed their 
support on the issue of the BG-PCA papers, which I, regretfully, had to 
make public.


I have to stress that I am no better than anyone else and certainly 
worse than very many. I make many mistakes (including on ethics). I can 
only do my best to acknowledge my errors and apologize.



Unless I see another inaccurate report of what went (clearly) wrong, I 
am not going to pursue the issue further. Otherwise, I'll have to take 
more serious and formal steps.
To be fully clear, as I live in the country where every wrong-doing is 
justified with claims about misunderstandings, there was no 
misunderstanding whatsoever but just a lack of the most basic respect 
towards coauthors. Story over, I hope.



More apologies to Jim and Paul for my delays with our BG-PCA paper. They 
know the reasons, and I hope we may have soon a draft ready for 
submission. I anticipate that, although I may be first author, Jim will 
be the corresponding one: the long discussions and interactions with Jim 
and Paul, and especially Jim's extensive simulations (an order of 
magnitude better than mine) made us understand the problem much better 
and in fact, in the course of this, Jim found some other interesting 
issues (not strictly related to BG-PCA), that I hope he will publish in 
another paper of his.


Sincerely

Andrea


On 16/05/2019 00:37, Una Vidarsdottir wrote:
Thank you Andrea for clarifying this. You are one of the most honest and 
modest people I know, and I am glad that your side of this story is now 
in the open. You have my support, as always.

Una

On Wed, 15 May 2019, 06:33 andrea cardini, <mailto:alcard...@gmail.com>> wrote:


I have to correct Fred on this:
 > we accelerated our writing. My paper was the first to be finished,
 > probably because it is a single-authored item by an emeritus with no
 > other obligations,

No, WE did not accelerate the writing. We started a cooperation, after
my small finding, and we were supposed to work all together on this. At
some stage, we heard no more from Fred and I suggested to have two
companion papers, but NEVER got an answer from Fred.
Months later, Fred let us know he was presenting and discussing results
(without ever asking me if I was OK with this). Finally, HE decided to
go on on his own, submit and announce in this list (again letting me
know after he was done). This is an accurate reconstruction of the
events. The other one is not and Fred was not unaware that I wasn't OK:
before the preprint he just announced, he (again without ever asking)
had already done an informal presubmission to a journal and the journal
has my written complaint about it.

I let the morphometric community judge if this is the appropriate
behaviour. Certainly it is not what I teach students, but possibly
it is
what a famous retired emeritus and one of the leader of a scientific
community can do.

All the best

Andrea

PS
On a technical side, as I never thought that CVA was the source of all
evil and BG-PCA a simple solution, here too I agree that the method has
some problems but I am more than confident that it can still be WISELY
applied in many cases. That small N (especially when one works with
small differences) and large p (numbers of variables) are not desirable
in very many types of analyses is written in all introductory textbook
on multivariate stats (at least those written in simple
non-mathematical
language for non-numerically skilled people like me).
In relation to this, there's a point I raised many times for years in
this list and in some of my papers: one uses the specific landmarks
required for her/his specific aim (I am in debt to Paul O'Higgins for
teaching me this). Semilandmarks are a great tool but should be used
when really needed and bearing in mind that almost inevitably p will
become big and that might create problems. There are different views on
this, including that having many points makes beautiful pictures: I
agree but probably most of the time that is not the aim of a biologist.
However, there might be cases when even with small N semilandmarks
might
be a huge step forward and possibly the best example I know it's the
virtual reconstruction of fossils (further analysis of those data may
then be harder, because of very big p and small N).
I definitely share the frustration of many taxonomists and
palaeontologists who have often very precious material and very small
samples and want to get the most out of them. Regardless of p/N
problems, estimates of means will be then inevitably inaccurate (and
sometimes even biased, as the sample could be few and maybe related
individuals of a rare species). Sometimes those means could be OKish
(macroevo

not exactlyRe: [MORPHMET] PREPRINT: between-group principal components analysis (bgPCA)

2019-05-15 Thread andrea cardini

I have to correct Fred on this:
we accelerated our writing. My paper was the first to be finished, 
probably because it is a single-authored item by an emeritus with no 
other obligations,


No, WE did not accelerate the writing. We started a cooperation, after 
my small finding, and we were supposed to work all together on this. At 
some stage, we heard no more from Fred and I suggested to have two 
companion papers, but NEVER got an answer from Fred.
Months later, Fred let us know he was presenting and discussing results 
(without ever asking me if I was OK with this). Finally, HE decided to 
go on on his own, submit and announce in this list (again letting me 
know after he was done). This is an accurate reconstruction of the 
events. The other one is not and Fred was not unaware that I wasn't OK: 
before the preprint he just announced, he (again without ever asking) 
had already done an informal presubmission to a journal and the journal 
has my written complaint about it.


I let the morphometric community judge if this is the appropriate 
behaviour. Certainly it is not what I teach students, but possibly it is 
what a famous retired emeritus and one of the leader of a scientific 
community can do.


All the best

Andrea

PS
On a technical side, as I never thought that CVA was the source of all 
evil and BG-PCA a simple solution, here too I agree that the method has 
some problems but I am more than confident that it can still be WISELY 
applied in many cases. That small N (especially when one works with 
small differences) and large p (numbers of variables) are not desirable 
in very many types of analyses is written in all introductory textbook 
on multivariate stats (at least those written in simple non-mathematical 
language for non-numerically skilled people like me).
In relation to this, there's a point I raised many times for years in 
this list and in some of my papers: one uses the specific landmarks 
required for her/his specific aim (I am in debt to Paul O'Higgins for 
teaching me this). Semilandmarks are a great tool but should be used 
when really needed and bearing in mind that almost inevitably p will 
become big and that might create problems. There are different views on 
this, including that having many points makes beautiful pictures: I 
agree but probably most of the time that is not the aim of a biologist. 
However, there might be cases when even with small N semilandmarks might 
be a huge step forward and possibly the best example I know it's the 
virtual reconstruction of fossils (further analysis of those data may 
then be harder, because of very big p and small N).
I definitely share the frustration of many taxonomists and 
palaeontologists who have often very precious material and very small 
samples and want to get the most out of them. Regardless of p/N 
problems, estimates of means will be then inevitably inaccurate (and 
sometimes even biased, as the sample could be few and maybe related 
individuals of a rare species). Sometimes those means could be OKish 
(macroevolutionary analyses with very large differences?); most of the 
time they will be as accurate as trying to estimate the average body 
height of Italian men using a sample of 10 men from the same small 
region of Italy. Again, not my discovery: it's all in the introductory 
stats textbook, but I myself too often forget about it.




--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, Centre for Forensic Anthropology, The 
University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
https://tinyurl.com/2013-Yellow-Book


ESTIMATE YOUR GLOBAL FOOTPRINT: 
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/

SUPPORT: secondwarning.org

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[MORPHMET] new paper: elephant seal nose-metrics

2019-03-18 Thread andrea cardini

Dear All,
this out now: https://onlinelibrary.wiley.com/doi/abs/10./jzs.12276
“Nose‐metrics” of wild southern elephant seal (Mirounga leonina) males 
using image analysis and geometric morphometrics

JZSER, online first

As far as I know, it's one of the few applications of GMM on data from 
naturally behaving animals photographed in the field. By the way, if 
anyone has references of this type of work (NB not on sedated animals), 
please I'd appreciate having a pdf.


Thanks also to those who asked me reprints of the Evol. Biol. paper on 
spurious results in integration/modularity tests. Please, write me if 
you have no subscription and need the pdf, as it's not yet in my webpage.


Cheers

Andrea

--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, Centre for Forensic Anthropology, The 
University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
https://tinyurl.com/2013-Yellow-Book


ESTIMATE YOUR GLOBAL FOOTPRINT: 
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/

SUPPORT: secondwarning.org

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[MORPHMET] homology function; isotropy

2018-12-06 Thread andrea cardini

Dear all,
I took a bit of time to think about the interesting discussion on 
semilandmarks, "homology function" and isotropy (and a bit longer for 
the message to be sent for problems with email filters).


We all agree that semilandmarks can be useful. We may disagree on: when 
they're needed (I don't think that "cool pictures" is a good reason); 
whether they have cons and not only pros; and on what sliding does.


Benedikt has rightly pointed out that the issue of homology is a complex 
one. In this respect, I would not call minBEN (or minPRD) sliding 
"homology functions". It's clever maths and does exactly what Jim said 
in his message. However, I don't think we can generalize on what the 
best choice is (including not adding semilandmarks, non-sliding -as 
mentioned by others- or sliding with one or the other method).
Gunz et al., that is cited to justify why minBEN is best, use a specific 
definition of homology, i.e. geometric homology: is there a 
GENERALIZABLE demonstration (not just few examples, theoretical and ad 
hoc or real ones) that 'biological homology' (which may be defined using 
different criteria) is the same as geometric homology in all or at least 
most cases (organisms, structures etc.)?

If there isn't, one should be open to all options.

On the issues with highly multivariate Procrustes variables, it is true 
that real data have their own (true) covariance plus the covariance 
added by the superimposition (plus that of sliding, if this is done). 
With true covariance some issues will be probably less serious. This is 
also said multiple times in my recent paper on false positives in many 
tests of modularity/integration.
However, the covariance introduced by the superimposition will be always 
there and whether it is negligible will (I guess) be totally dependent 
on the structure and the set of points used to measure it. One might 
simulate some scenarios but again generalizability can't be based on few 
examples. That the superimposition introduces covariance that is not 
originally there is, in contrast, always the case, as recognized since 
the early days of GMM.


Last point, and here we get into the difficult maths I can't understand 
(with apologies for my dumbness): I am not convinced that the isotropic 
model is uninformative.
If data, that originally have only random noise (circular variation as 
in random digitizing error), produce a pattern that is not circular in 
an analysis, that's for me an alarm bell. Indeed, if I got it right (not 
sure ... with more apologies), the isotropic model has been extensively 
used in the past and among other things is, if I am correct, behind 
Mitteroecker et al. (Journal of Human Evolution 46 (2004) 679–698) form 
space:

"   The reader is encouraged to simulate isotropic
variations around a general mean form in two or
three dimensions, compute Centroid Size and
Procrustes shape coordinates, then produce the
principal component structure of the size–shape
spaces following this instruction. The resulting
distributions should be spherical, without any
pattern information" (p. 695).


Thanks again for comments and clarifications. Please, if someone does 
not feel like sending them to the list, feel free to reply to me 
personally: I won't share answers sent directly to me without asking.


Cheers

Andrea

--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
https://tinyurl.com/2013-Yellow-Book


ESTIMATE YOUR GLOBAL FOOTPRINT: 
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/


.


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Re: [MORPHMET] Re: semilandmarks in biology

2018-11-07 Thread andrea cardini
hese
 > issues more obvious is an argument against their use.
 >
 >
 >
 > Best,
 >
 >
 >
 > Philipp
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >
 > Am Dienstag, 6. November 2018 13:28:55 UTC+1 schrieb alcardini:
 >
 > As a biologist, for me, the question about whether or not to use
 > semilandmarks starts with whether I really need them and what
they're
 > actually measuring.
 >
 > On this, among others, Klingenberg, O'Higgins and Oxnard have
written some
 > very important easy-to-read papers that everyone doing
morphometrics should
 > consider and carefully ponder. They can be found at:
 > https://preview.tinyurl.com/semilandmarks
<https://preview.tinyurl.com/semilandmarks>
 >
 > I've included there also an older criticism by O'Higgins on EFA
and related
 > methods. As semilandmarks, EFA and similar methods for the
analysis of
 > outlines measure curves (or surfaces) where landmarks might be
few or
 > missing: if semilandmarks are OK because where the points map is
irrelevant,
 > as long as they capture homologous curves or surfaces, the same
applies for
 > EFAs and related methods; however, the opposite is also true and,
if there
 > are problems with 'homology' in EFA etc., those problems are
there also
 > using semilandmarks as a trick to discretize curves and surfaces.
 >
 > Even with those problems, one could still have valid reasons to use
 > semilandmarks but it should be honestly acknowledged that they
are the best
 > we can do (for now at least) in very difficult cases. Most of the
studies I
 > know (certainly a minority from a now huge literature) seem to
only provide
 > post-hoc justification of the putative importance of
semilandmarks: there
 > were few 'good landmarks'; I added semilandmarks and found
something;
 > therefore they work.
 >
 >
 >
 > From a mathematical point of view, I cannot say anything, as I am
not a
 > mathematician. On this, although not specific to semilandmarks, a
 > fundamental reading for me is Bookstein, 2017, Evol Biol (also
available for
 > a few days, as the other pdfs, at the link above). That paper is
one of the
 > most inspiring I've ever read and it did inspire a small section
of my
 > recent Evol Biol paper on false positives in some of the tests of
 > modularity/integration using Procrustes data. For analyses using
sliding
 > semilandmarks, the relevant figures are Figs 4-5, that suggest
how tricky
 > things can be. If someone worries that that's specific to my
example data
 > (and it could be!), the experiment is trivial to repeat on
anyone's own
 > semilandmark data.
 >
 > Taken from the data of the same paper, below you find a PCA of
rodent
 > hemimandibles (adults, within a species) using minBE slid
semilandmarks or
 > just 9 'corresponding' landmarks. The advantage of semilandmarks,
compared
 > to the 9 landmarks, is that they allow to capture a dominant
direction of
 > variation (PC1 accounting for 14% of shape variance), whose
positive extreme
 > (magnified 3 times) is shown with a really suggestive deformation
grid
 > diagram. In comparison, 9 landmarks do not suggest any dominant
direction of
 > variation (each PC explaining 9-5% of variance), the scatterplot
is circular
 > and the TPS shape diagram much harder to interpret.
 >
 > What these two PCAs have in common is that they are both analyses
of random
 > noise (multivariate random normally distributed numbers added to
a mean
 > shape).
 >
 >
 >
 > All the best
 >
 >
 >
 > Andrea
 >
 >
 >
 > 9 LANDMARKS PLUS 22 SLID SEMILANDMARKS
 >
 >
 >

<https://groups.google.com/a/morphometrics.org/group/morphmet/attach/dcce33d95d952/oclbeaidoponnmni.jpeg?part=0.1.1=1=0

<https://groups.google.com/a/morphometrics.org/group/morphmet/attach/dcce33d95d952/oclbeaidoponnmni.jpeg?part=0.1.1=1=0>>

 >
 >
 > 9 LANDMARKS
 >
 >
 >

<https://groups.google.com/a/morphometrics.org/group/morphmet/attach/dcce33d95d952/pebddfgpogepigmi.jpeg?part=0.1.2=1=0

<https://groups.google.com/a/morphometrics.org/group/morphmet/attach/dcce33d95d952/pebddfgpogepigmi.jpeg?part=0.1.2=1=0>>

 >
 >
 > --
 >
 > Dr. Andrea Cardini
 > Researc

[MORPHMET] false positives in integration/modularity after Procrustes

2018-10-22 Thread andrea cardini

Dear All,
this (links and abstract below) is out right now in Evol.Biol., with 
many thanks to Benedikt for being such a great editor (plus more thanks 
to all those who read it and helped with comments etc.!).


One of the two main Procrustes approaches that produce data for analyses 
of modularity and/or integration seems to lead to very high rates of 
false positives in some of the most common tests used in the main 
programs/packages.
The study has some simulations and explore a variety of cases (plus a 
few more in the R-script mentioned in the paper, and written by a 
reviewer). It happens all the time in those data (unless one uses such a 
small N relative to p, the number of variables, that unsurprisingly 
nothing is significant). However, it is mostly an empirical study and 
will require more work to understand how serious and general the issue 
is. This is clearly said in the paper, that also says (but I'd like to 
stress it) that:
1) the problem is not Procrustes but the way the data are used after 
Procrustes;
2) the alternative approach does not produce false positives, but may 
have low power and other issues (said multiple times but not a question 
addressed by the study), which is why there is no recommendation in 
favour of one or the other approach.


It might well be that in practice, if data have a real and strong 
covariance, the problem will have just a small effect. But it seems to 
be there all the time and there might be cases where it becomes much 
more serious.


I hope it may be useful for those interested in that type of evo-devo 
studies.

Cheers

Andrea


FINAL VERSION:
https://link.springer.com/article/10.1007%2Fs11692-018-9463-x

ALMOST (few differences!) FINAL PREPRINT:
https://www.biorxiv.org/content/early/2018/07/19/371187


Integration and Modularity in Procrustes Shape Data: Is There a Risk of 
Spurious Results?


Abstract

Studies of morphological integration and modularity are a hot topic in 
evolutionary developmental biology. Geometric morphometrics using 
Procrustes methods offers powerful tools to quantitatively investigate 
morphological variation and, within this methodological framework, a 
number of different methods has been put forward to test if different 
regions within an anatomical structure behave like modules or, vice 
versa, are highly integrated and covary strongly. Although some 
exploratory techniques do not require a priori modules, commonly modules 
are specified in advance based on prior knowledge. Once this is done, 
most of the methods can be applied either by subdividing modules and 
performing separate Procrustes alignments or by splitting shape 
coordinates of anatomical landmarks into modules after a common 
superimposition. This second approach is particularly interesting 
because, contrary to completely separate blocks analyses, it preserves 
information on relative size and position of the putative modules. 
However, it also violates one of the fundamental assumptions on which 
Procrustes methods are based, which is that one should not analyse or 
interpret subsets of landmarks from a common superimposition, because 
the choice of that superimposition is purely based on statistical 
convenience (although with sound theoretical foundations) and not on a 
biological model of variance and covariance. In this study, I offer a 
first investigation of the effects of testing integration and modularity 
within a configuration of commonly superimposed landmarks using some of 
the most widely employed statistical methods available to this aim. When 
applied to simulated shapes with random non-modular isotropic variation, 
standard methods frequently recovered significant but arbitrary patterns 
of integration and modularity. Re-superimposing landmarks within each 
module, before testing integration or modularity, generally removes this 
artifact. The study, although preliminary and exploratory in nature, 
raises an important issue and indicates an avenue for future research. 
It also suggests that great caution should be exercised in the 
application and interpretation of findings from analyses of modularity 
and integration using Procrustes shape data, and that issues might be 
even more serious using some of the most common methods for handling the 
increasing popular semilandmark data used to analyse 2D outlines and 3D 
surfaces.



--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
https://tinyurl.com/2013-Yellow-Book


ESTIMATE YOUR GLOBAL FOOTPRINT: 
http

Re: [MORPHMET] Re: Digitizing landmarks on live larvae

2018-03-14 Thread andrea cardini
I start with a "disclaimer" (and many apologies!): I read only the last 
two messages (by Jim and Carmelo), as I am stuck with teaching in this 
period.


I'd like only to suggest a reference on N vs the number of variables (in 
morphometrics but not necessarily only in this field). It's a difficult 
but very important and most interesting paper on this issue:
Bookstein, 2017, Evolutionary Biology: A Newly Noticed Formula Enforces 
Fundamental Limits on Geometric Morphometric Analyses

DOI 10.1007/s11692-017-9424-9

Cheers

Andrea

On 14/03/18 04:05, f.james.rohlf wrote:
Actually the rule is that the number of specimens should be larger than 
the number of variables 2p-4 not p landmarks in the case of 2D data.




__
F. James Rohlf, Distinguished Prof. Emeritus
Dept. Anthropology and Ecology & Evolution
Stonybrook University

 Original message 
From: Carmelo Fruciano <c.fruci...@unict.it>
Date: 3/12/18 9:51 PM (GMT-10:00)
To: MORPHMET <morphmet@morphometrics.org>
Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae

Dear Avi,

I guess it's hard to formulate any rule of thumb.

Some analyses might not be defined if the number of variables exceed the 
number of observations. Some other analyses might be defined (there is 
many distance-based analyses nowadays which circumvent that problem).


However, whether a given analysis is defined doesn't mean that the 
inference is necessarily accurate. I guess it depends on what you plan 
to test/measure and the effect size you expect.



Andrea Cardini has some papers that can give you some hint on this, such as:

Cardini & Elton 2007 - Zoomorphology

Cardini et al. 2015 - Zoomorphology

Cardini & Elton 2017 - Hystrix

They should be downloadable from his website 
https://sites.google.com/site/alcardini/home/pubs




Obviously, having an idea of variation on your own data would be better.
I hope this helps.
Carmelo




On 3/12/2018 8:27 PM, Avi Koplovich wrote:

Hi Carmelo,
Thank you for those answers.
One more question please:
I know that the number of specimens should exceed the number of the 
total landmarks (fixed-landmarks + semi-landmarks). Is there a rule of 
thumb of by how much or what ratio between specimens to semi-landmarks 
one should keep?


Thank you,

Avi


On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano wrote:



Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto:
> Hi Carmelo,
> Thank you for your answer.
> My project tests for the influence of kairomones of a predator
fish on
> the morphology of Salamander larvae during its development. To
do this,
> I take pictures every other week of larvae spawned from six
different
> females and assigned to 3 treatments: No fish, 3 caged fish, 6
caged fish.

Hi Avi,
it sounds like an interesting experiment. I will try to answer to
your
questions but keeping in mind that I'm not very knowledgeable on
salamander development.

>  1. I intend to use landmark 1 (dorsal connection of the tail
fin) as a
>     fixed factor. But I thought I may be able to use the tail tip
>     (landmark 20) and head tip (landmark 48) as fixed landmarks
as well.
>     Do you think it's ok in an ontogeny experiment?

I guess it will depend on how long into ontogeny you will track the
larvae and whether or not that point will "disappear" over ontogeny
and/or slide unreasonably (depends also on your question). You, being
knowledgeable on their biology, are the best judge on that.

> If not, do you think
>     it's ok to slide all semi-landmarks of the tail on landmark
1, and
>     all head semi-landmarks on an eye landmark? Since the eye
isn't part
>     of the head contour, is it ok if I slide one semi-landmark
to the
>     eye and all rest semi-landmarks of the head one to each
other as a
>     closed shape?

The point(s) slid relative to the eye won't be sliding along the
direction tangent to the curve you want to approximate (i.e., the
curvature of the head). A good starting point on the method could be
Gunz & Mitteroecker 2013 - Hystrix

>  2. Is it ok if landmarks 1 and 39 slid relative to each other
as well
>     as 41 and 55, since both describe a closed shape?

It's not particularly desirable (see answer above).

>  3. Another worry I have is that landmark 40 which I used to
create the
>     comb fan for both the tail and the head is too far from both
of them
>     so it doesn't bypass the bending.
>  4. I'm affraid I don't fully understand why landmark 40 can not be
>     treated as a fixed landmark. In the book of Zelditch 2004,
she says
>     that one of the basic differences between fixed-landmark and
>     semi-landmark i

[MORPHMET] FOR EARLY POST-DOCS Fwd: [dzg-evol] Berlin, Germany: College for Life Sciences Fellowships

2017-12-05 Thread andrea cardini

Dear all,
this is not strictly morphometric but it could be on a morphometric 
project and looks like a wonderful opportunity for early post-docs. I've 
asked a few more details about eligibility. Here they are:


"The program is open to all nationalities and there is no particular age 
limit however the program is dedicated to early-career scientists who 
have obtained there PhD and who have at least one first author 
publication (postdocs, junior group leaders, lecturers, assistant, 
associate and junior professors) who have no longer than five years 
their own group. The Fellowship is open to all life sciences disciplines.
Information about regular Fellowships at the Wissenschaftskolleg can be 
found here https://www.wiko-berlin.de/en/fellows/fellowships/admission/;


I would not miss the chance to try (if I wasn't too old!). Good luck.
Cheers

Andrea


 Forwarded Message 
Subject:[dzg-evol] Berlin, Germany: College for Life Sciences 
Fellowships



*GAIN TIME TO THINK! 2018/19
COLLEGE FOR LIFE SCIENCES FELLOWSHIPS
DEADLINE:  JANUARY 7, 2018*
Call for Applications
https://cfls-application.wiko-berlin.de/ 



The College for Life Sciences, a junior program of the 
Wissenschaftskolleg zu Berlin (Institute for Advanced Study), offers 
young life-sciences scholars from around the world an opportunity to 
take a break from the lab and gain time to work and develop their own 
projects and immerse themselves in an intellectually and culturally 
diverse environment.


Each year the Wissenschaftskolleg welcomes internationally recognized 
senior as well as promising junior scholars in all fields of knowledge, 
including the humanities, the social sciences and the arts and we invite 
you to become part of this "learning community". Our goal is to promote 
a kind of science that transcends disciplinary boundaries and goes 
beyond established issues and approaches.


Through the College for Life Sciences we promote scientists at the 
beginning of their career, i.e. postdocs, junior group leaders, 
lecturers, assistant, associate and junior professors.


The fellowships are intended for residencies of 3-6 months during the 
academic year 2018/19, i.e. September 2018 - June 2019.


BENEFITS OF THE FELLOWSHIP
* Three to six months' residency at the Wissenschaftskolleg in Berlin
* A full stipend based on your previous salary
* Studio accommodation on campus
* Freedom to pursue a project of your choice
* Insight into new areas of knowledge and research cultures
* Integration into a unique international community of Fellows
* Access to Berlin's excellent scholarly and scientific community
* Access to the Wissenschaftskolleg's outstanding library and IT services

We do not offer any lab space. For more details please visit:
www.wiko-berlin.de/cfls 

APPLICATION AND REQUIREMENTS
Please apply by January 7, 2018 with a project outline (about 1000 
words), a letter stating your motivation for wishing to obtain a 
fellowship (about 500 words), your complete curriculum vitae, and a list 
of your publications here: https://cfls-application.wiko-berlin.de/ 



You are completely free to choose the project that you will pursue at
the Wissenschaftskolleg; we impose no thematic presettings whatsoever.

You must have obtained your doctorate by the start of your fellowship, 
and we also require that you have at least one lead-author publication 
in a peer-reviewed journal. There are no restrictions regarding your 
discipline of origin in the life sciences, nationality, or age etc. 
Applications from scientists working at institutions in Berlin cannot be 
taken into consideration. If you have been a principal investigator for 
longer than five years, though, you are advised to apply for a regular 
fellowship at the Wissenschaftskolleg.


Dr. Ulrike Pannasch
Wissenschaftliche Koordinatorin
Academic Coordinator College for Life Sciences
ulrike.panna...@wiko-berlin.de 

WISSENSCHAFTSKOLLEG ZU BERLIN
INSTITUTE FOR ADVANCED STUDY
Wallotstrasse 19
14193 Berlin
Tel.: +49 30 89 00 1 - 255
Fax: +49 30 89 00 1 - 100
www.wiko-berlin.de/cfls 

Dr. Ulrike Pannasch
Wissenschaftliche Koordinatorin/Academic Coordinator College for Life 
Sciences

Wissenschaftskolleg zu Berlin / Institute for Advanced Study
Wallotstr. 19, 14193 Berlin
Tel. +49 - 30 - 89 001 -
255http://www.wiko-berlin.de/institution/college-for-life-sciences/ 


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[MORPHMET] error in landmarks from MRI

2017-11-08 Thread andrea cardini

Dear All,
I'd greatly appreciate references on measurement error in landmarks from 
MRI data. It does not matter if it's 2D or 3D as long as it is specific 
to MRI.


Thanks in advance.
Cheers

Andrea



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tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] pairwise matrix of vector angles in R

2017-11-03 Thread andrea cardini

Dear All,
please, does anyone know if there's an R package that, using a matrix 
with several vectors (e.g., coefficients for allometric regressions in 
different taxa), will compute the pairwise (all possible pairs of taxa) 
matrix of vector angles?


Thanks in advance for any suggestion.
Cheers

Andrea


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


ESTIMATE YOUR GLOBAL FOOTPRINT: 
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/


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Re: [MORPHMET] Procrustes fit

2017-10-31 Thread andrea cardini
Andrey, the last time I checked this (last July, I believe), differences 
between MorphoJ and TPSRelw were tiny and negligible. I compared MorphoJ 
with R in the last days, and again differences were tiny.


The first thing I'd check is whether there's an issue with commas vs 
dots as decimal separators.

If you send me the tps file, I can give a quick look.

Cheers

Andrea

On 31/10/17 11:09, Andrey Lissovsky wrote:

I guess, my question is very simple.. I didn't use geometry morphometrics for 
many years and fail to start now. Something changed.
My partial task is very easy. I have a tps file with a set of specimens with 
landmark coordinates. And O want to carry out Procrustes fit. More exactly, I 
want to have a set of Procrustes coordinates to use in another analysis.
First of all, I carried out Procrustes analysis in MorphoJ. I obtained some 
result. I didn't like it and had an idea to check Procrustes coordinates in 
TPSRelw.
In TPSRelw I used File-Save-Aligned specimens and got Procrustes coordinates, I 
hope. But... There is no correlation between PC in MorphoJ and TPSRelw. What is 
wrong in my actions? Thank you



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Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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ONLINE DATA Re: [MORPHMET] Your opinion + a tiny piece of your exotic data

2017-09-18 Thread andrea cardini

Hi Vincent,
I might help only with the data. In the last years I've started trying 
to publish data often together with papers.


You'll find data in (if I remember well) nts, morphologika and MorphoJ 
formats in the online first paper on the Wainer's rule (out now in 
Hystrix). That a fairly big 3D dataset (1300 something specimens). There 
are more data in different formats also in the Viscosi & Cardini, 2011, 
paper (2D leaves).
There are more data also in the two papers on mirroring one-side only 
data (from structures with object symmetry - published in 2016-17; both 
2D and 3D landmarks).


Almost all those papers and data should be easy to find using the links 
in my webpage: https://sites.google.com/site/alcardini/home/pubs


If I ever manage to find the time, I will try to start adding data also 
for some of the older stuff I published (as long as I am the owner of 
the data or the coauthors agree). That will take time, as I am not good 
at archiving data.


I am sending this to morphmet as well, as others asked me about data 
recently.


Good luck with the new package.
Cheers

Andrea


On 17/09/17 18:07, Vincent Bonhomme wrote:

Dear morphmet,

I'm writing a small R package, Modown 
<https://github.com/vbonhomme/Modown>, that defines a text-based (I'm 
aware of their limits), minimalist, readable by both humans and machines 
and provides utilities to manipulate it. It started as a personal need 
when sweating and spoiling time exporting from/to various existing 
morphometrics file format (mainly for Momocs hotline) and I'm willing to 
tackle this with this package. Not sure it would be useful elsewhere but 
it sure will be by my side.


I write to you today to ask you if you:
1- think I have forgotten a case in the current five rules 
<https://github.com/vbonhomme/Modown>
2- are keen to share some data. A very small fraction of datasets or 
even a single complete shape would be perfect. I'm particularly 
interested in exotic format. Being a newbie to everything outside 
outlines, all text-based formats including .tps, .nts, .xml and others 
are exotic to me so every single contribution will be warmly welcomed. 
Unless if you're keen to do it and explicitely write it to me, I won't, 
of course, don't share them, not even for tests or whatever.


Due to its "essentialist" nature, Modown file format could be used to 
import any kind of morphometrics data (making request #1 important) into 
R (and thus everywhere) and as a intermediate step when converting from 
one format to another (if request #2 allows decent testing).


Besides my eternal gratitude you will be duly acknowledged in the 
package (unless you dont want).


All the best from southern France,

Vincent




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tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


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WEBPAGE: https://sites.google.com/site/alcardini/home/main

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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] Re: PhD course on Bayesian stats

2017-09-12 Thread andrea cardini

Ciao Daniele,
lo manderei a DZG (dzg.e...@gmail.com) e forse a MORPHMET 
(morphmet@morphometrics.org).


Se vinco la lotteria, vengo anch'io!
A presto

Andrea

On 12/09/17 15:34, Daniele Silvestro wrote:

Hello,

I will be teaching a PhD course titled ‘Bayes in practice’ at the 
University of Gothenburg (Sweden) in October (16-20). The course aims to 
demonstrate how Bayesian algorithms actually work and how they can be 
(easily!) implemented in common programming languages such as Python and 
R. More details about the course are given here: 
http://www.forbio.uio.no/events/courses/2017/bayesinpractice.pdf.


Please feel free to share this information with anyone who might be 
interested in your labs.


I hope all is well!
Cheers,
Daniele



--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] mirror-relabeling R function

2017-07-03 Thread andrea cardini

Dear All,
please, is there an R function that I could use to mirror-relabel a 3D 
landmark configuration?

Thanks in advance.
Cheers

Andrea


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


ESTIMATE YOUR GLOBAL FOOTPRINT: 
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/


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Re: [MORPHMET] Troubles exporting data sets in MorphoJ

2017-06-29 Thread andrea cardini
Pablo, I'd first check if that depends on using commas as decimal 
separators. Those numbers in the PCA look huge. Try the English 
international options.


Even if some of the morphometric programs can deal with different 
international options, sometimes there are issues, especially when 
swapping from one software to the other. My general suggestion is to use 
the English options at least for all GMM analyses.


Cheers

Andrea

On 28/06/17 22:29, Pablo Fisichella wrote:


Dear All

I have a question regarding MorphoJ. I am investigating human skulls 
using 3D data. I obtained 3D landmarks/semilandamrks in Amira which were 
exported into R. In R I performed the sliding of semilanmarks (using 
both minimized bending energy or Procrustes distance). Subsequently, I 
imported into MorphoJ my data set . I made my analyses PCA, CVA DFA etc. 
However, when I exported the PCs scores, VC scores or regression 
residuals to perform scatterplots in a different sofware, Past for 
instance, I obtained quite extrange scatterplots (with points centered). 
Here I attach a couple of plots. Maybe some one have experienced the 
same issue? how I can solve this?. Maybe some one have experienced the 
same issue? how I can solve this?. Interestingly, when I imported the 
raw coordinates in MorphoJ derived from Amira in Morphologika format 
occurs the same thing.


any thought or advice is wellcome

thanks so much

Pablo

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Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
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WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] 1315 monkey skulls with 86 3D landmarks FREE DATASET + Wainer's Rule

2017-06-22 Thread andrea cardini

Dear All,

Sarah (in cc) and I are releasing the guenon skull database we used for 
several publications years ago together with an accompanying paper, that 
should be cited if the data are used. You can find the paper and the 
database in my publications webpage:


https://sites.google.com/site/alcardini/home/pubs

It's the very first one in the list of articles.


I apologize for the ugly preprint and the provisional reference. I've 
written to the editors to know when it is published and get a definitive 
reference but I've not received any answer in months: they're probably 
too busy. I will send a message when I finally (hopefully!) get at least 
a DOI.


Also, when the paper is published, it will be open access and there will 
be probably a link to get the data directly from the journal webpage.



Please, let me know if there's any trouble with the links and downloads.

I'd be also very happy to get some feedback on the 'Wainer's Rule', 
which in fact we don't know if it's a rule but hope it will be tested in 
more groups.



Enjoy the data and, I hope, the paper!

Cheers


Andrea



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Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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Re: size will be missing Re: [MORPHMET] Save aligned in TPSRelW

2017-06-22 Thread andrea cardini
The point is simple: the variables called centroid size and log centroid 
size in MorphoJ won't be the real size of the original structures if 
they're imported without rescaling them.
They are, in my experience, about 1 and, regardless of the reason (which 
I find less important), they're wrong. Of course, if one does not do 
anything with size, shape data will be fine. I would not risk to be 
misled, nevertheless. In fact, I might have happened to review one or 
two papers when someone was testing allometry or something else 
involving size, when size was about 1 for all specimens.


Cheers

Andrea

On 22/06/17 11:18, Paolo Piras wrote:

Hi folks/Andrea,

just to underline this:

Andrea,when you say

"an 'apparent size variable' which is a series of numbers virtually 
equal to 1 (differences will be approximation errors)."


I think that MorphoJ "reads" the actual CS values from the aligned 
coordinates saved by TPSrelw that, as you say, have lost their original 
size. However, small deviations from 1 are not due to approximation 
error as I *suspect* that the "aligned coordinates" saved by TPSrelw are 
those projected on the tangent plane (by an orthogonal [more commonly 
used] or stereographic projection) and for this reason they have 
necesarily a CS larger than 1 that is the radius of the hyperspherical 
Kendall's Shape Space. In order to reach the tangent plane from the 
sphere one necessarily must go beyond its radius (that geometrically 
*IS* the size of a configuration lying on that space) and the CS will be 
inevitably larger than 1.
An indirect proof for this would be to verify that what you call 
"approximation error" gives CS values always slightly larger than 1 and 
never smaller.
So I think there is no error in having, for those data, CS 
slightly different (=larger) from 1 as they MUST have CS larger than 1 
by construction.

However,I'm not sure at 100% if TPSrelw works as I hypothesized here..
Playing a bit with TPSrelw could unveil this.
All the best
Paolo


2017-06-22 11:00 GMT+02:00 andrea cardini <alcard...@gmail.com 
<mailto:alcard...@gmail.com>>:


Hi Pere,
there's plenty of work arounds this. I agree with Carmelo that the
nts format may be easier to edit manually, so that you can put back
the necessary labels.

HOWEVER, PLEASE BE CAREFUL because SIZE WILL BE MISSING from those
data. As most of the time you may want to analyse both size and
shape, instead of importing in MorphoJ the aligned specimens from
the TPSRelw slid configurations, I'd suggest to save the SCALED
ALIGNED SPECIMENS in TPSRelw. Jim added this option for this
purpose: this way you get the aligned specimens rescaled to the
original centroid size. Therefore, when you import them in MorphoJ
and redo the Procrustes fit, you will get both the aligned specimens
as well as their size.
In contrast, if you import the aligned data (not rescaled), size
won't be there but you may be easily tricked and think it is there,
because MorphoJ requires that you redo the Procrustes fit and then
you'll get an 'apparent size variable' which is a series of numbers
virtually equal to 1 (differences will be approximation errors).
Use the scaled aligned and you won't have this issue.

Cheers

Andrea

On 22/06/17 10:07, Pere Ibáñez wrote:

Hello All,

I am using TPSRelW to slide semilandmarks. Once I have the
consensus, I use Save aligned to export the aligned coordinates
(including slid semilandmarks) as a tps file, that I want to
import into MorphoJ.

The problem is that the file that is exported has the IDs of the
specimens empty, with no information. And MorphoJ doesn't import
it without that information, so I have to type it one by one on
the tps file. Does anyone know how to export that tps file from
TPSRelW without losing the ID?

Thanks!

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size will be missing Re: [MORPHMET] Save aligned in TPSRelW

2017-06-22 Thread andrea cardini

Hi Pere,
there's plenty of work arounds this. I agree with Carmelo that the nts 
format may be easier to edit manually, so that you can put back the 
necessary labels.


HOWEVER, PLEASE BE CAREFUL because SIZE WILL BE MISSING from those data. 
As most of the time you may want to analyse both size and shape, instead 
of importing in MorphoJ the aligned specimens from the TPSRelw slid 
configurations, I'd suggest to save the SCALED ALIGNED SPECIMENS in 
TPSRelw. Jim added this option for this purpose: this way you get the 
aligned specimens rescaled to the original centroid size. Therefore, 
when you import them in MorphoJ and redo the Procrustes fit, you will 
get both the aligned specimens as well as their size.
In contrast, if you import the aligned data (not rescaled), size won't 
be there but you may be easily tricked and think it is there, because 
MorphoJ requires that you redo the Procrustes fit and then you'll get an 
'apparent size variable' which is a series of numbers virtually equal to 
1 (differences will be approximation errors).

Use the scaled aligned and you won't have this issue.

Cheers

Andrea

On 22/06/17 10:07, Pere Ibáñez wrote:

Hello All,

I am using TPSRelW to slide semilandmarks. Once I have the consensus, I 
use Save aligned to export the aligned coordinates (including slid 
semilandmarks) as a tps file, that I want to import into MorphoJ.


The problem is that the file that is exported has the IDs of the 
specimens empty, with no information. And MorphoJ doesn't import it 
without that information, so I have to type it one by one on the tps 
file. Does anyone know how to export that tps file from TPSRelW without 
losing the ID?


Thanks!

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Re: [MORPHMET] number of landmarks and sample size

2017-06-01 Thread andrea cardini
ut statistical power, then I just allowed a statistical procedure 
to take me away from the biologically relevant question I sought to address.  
Andrea is correct that quality is better than quantity, but quantity can be a 
burden in either direction (too few or too many).  Additionally, statistical 
power will vary among statistical methods.  Reconsidering methods might be as 
important as reconsidering landmarks configurations.

Regards!
Mike




On May 4, 2017, at 5:19 AM, Lea Wolter <leawolter...@gmail.com> wrote:

Hello everyone,

I am new in the field of geometric morphometrics and have a question for my 
bachelor thesis.

I am not sure how many landmarks I should use at most in regard to the sample 
size. I have a sample of about 22 individuals per population or maybe a bit 
less (using sternum and epigyne of spiders) with 5 populations.
I have read a paper in which they use 18 landmarks with an even lower sample 
size (3 populations with 20 individuals, 1 with 10). But I have also heard that 
I should use twice as much individuals per population as land marks...

Maybe there is some mathematical formula for it to know if it would be 
statistically significant? Could you recommend some paper?

Because of the symmetry of the epigyne I am now thinking of using just one half 
of it for setting landmarks (so I get 5 instead of 9 landmarks). For the 
sternum I thought about 7 or 9 landmarks, so at most I would also get 18 
landmarks like in the paper.

I would also like to use two type specimens in the analysis, but I have just 
this one individual per population... would it be totally nonesens in a 
statistical point of view?

Thanks very much for your help!

Best regards
Lea

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tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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Re: [MORPHMET] Re: number of landmarks and sample size

2017-05-31 Thread andrea cardini
technique in more detail and/or run the analysis on your dataset if you 
don't mind sending me the data. The script is currently under review for 
a journal, so it's not available yet to the public.


Also, as you mention, having more shape variables (i.e., number of 
landmarks x 2 or 3 depending on 2-D or 3-D landmarks) than the number of 
specimens will generally reduce the power of statistical tests. There 
are ways to counter this issue (e.g., Q-mode approach recently proposed 
by Dean Adams).


Now, concerning the sampling of bilateral landmarks, Andrea Cardini has 
recently written a nice pair of papers on the subject:


Cardini, A. 2016. Left, right or both? Estimating and improving 
accuracy of one-side-only geometric morphometric analyses of cranial 
variation. J Zool Syst Evol Res.


Cardini, A. 2016. Lost in the other half: improving accuracy in 
geometric morphometric analyses of one side of bilaterally symmetric 
structures. Syst Biol.


These papers highlight the artifact that originates from performing 
Procrustes alignment on "one-side-only" datasets. At least for alignment 
purposes, I suggest sampling both sides of bilaterally symmetric structures.


Hope this helps.

All the best,
Aki

On Tuesday, May 9, 2017 at 12:26:04 PM UTC+1, Lea Wolter wrote:

Hello everyone,

I am new in the field of geometric morphometrics and have a question
for my bachelor thesis.

I am not sure how many landmarks I should use at most in regard to
the sample size. I have a sample of about 22 individuals per
population or maybe a bit less (using sternum and epigyne of
spiders) with 5 populations.
I have read a paper in which they use 18 landmarks with an even
lower sample size (3 populations with 20 individuals, 1 with 10).
But I have also heard that I should use twice as much individuals
per population as land marks...

Maybe there is some mathematical formula for it to know if it would
be statistically significant? Could you recommend some paper?

Because of the symmetry of the epigyne I am now thinking of using
just one half of it for setting landmarks (so I get 5 instead of 9
landmarks). For the sternum I thought about 7 or 9 landmarks, so at
most I would also get 18 landmarks like in the paper.

I would also like to use two type specimens in the analysis, but I
have just this one individual per population... would it be totally
nonesens in a statistical point of view?

Thanks very much for your help!

Best regards
Lea

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tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human 
Biology, The University of Western Australia, 35 Stirling Highway, 
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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Re: [MORPHMET] using intermediate landmarks between semilandmarks

2017-01-17 Thread andrea cardini

Dear Eli,

your question goes beyond pure methodological issues and the answer 
depends first on what you want to do.


I suggest everyone interested to read the two papers I've uploaded here:

https://drive.google.com/file/d/0BxZeFy3y3MEpcHJzQlkxUlNwMEU/view?usp=sharing

https://drive.google.com/file/d/0BxZeFy3y3MEpVWFXR09sRGZQOWs/view?usp=sharing


A brief quote from the first one:

"The choice of landmarks should be driven by the hypotheses that are 
being tested. It is possible to imagine situations  where different 
landmarks on the same structure are deemed  equivalent or not according 
to the question being asked. Thus,  in a study of bat and bird wings if 
one is interested in function, landmarks at wing tips and along the 
leading and trailing  edges may be functionally equivalent; they might 
embody the  question in being related to functionally relevant aspects 
of  form. However, these landmarks may lie on structures that  are not 
equivalent in other ways; for a study of growth or  evolution, 
alternative landmarks may be the most suited ones.  Thus, equivalence 
can mean different things according to the context; different sets of 
landmarks from the same structure  may well carry different information. 
In evolutionary studies,  all sets of landmarks may need to be combined 
because, of  course, function, growth, and other matters are all related 
to  evolution (Oxnard 2008)".


Among other many interesting considerations in the same paper and in the 
other one, the gorilla example (Fig. 7 of the first one) is particularly 
illuminating.



Good luck


Andrea



On 16/01/17 21:40, Elahep wrote:

Hello all,

Is this necessary/recommendable to use semilandmarks with intermediate 
landmarks in order to improve the accuracy and consistency of 
semilandmarks configuration?
Or is it enough to just anchor the first and the last semilandmarks 
with fixed landmarks?


Many thanks in advance,
Eli
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tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] TPS Series USERS: please, cite the correct ref.!

2017-01-03 Thread andrea cardini

Dear All,

this is just a gentle reminder for the many users of the TPS Series.

As I am reviewing a paper, I've noticed again that many, if not most, 
users have missed the new main REFERENCE FOR ALL THE PROGRAMS IN THE 
SERIES. The link to the paper and the ref. are below. Please, update 
your databases and cite it any time you publish using ANY of the TPS 
programs!



Happy 2017 to everyone, and many many many thanks again to Jim for the 
wonderful software and the very useful paper!


Cheers


Andrea


ROHLF, F. James. The tps series of software. *Hystrix, the Italian 
Journal of Mammalogy*, [S.l.], v. 26, n. 1, p. 9-12, june 2015. ISSN 
1825-5272. Available at: 
<http://www.italian-journal-of-mammalogy.it/article/view/11264>. Date 
accessed: 03 jan. 2017. doi:http://dx.doi.org/10.4404/hystrix-26.1-11264.




BibTeX:

@article{HYSTRIX11264,
author = {F. Rohlf},
title = {The tps series of software},
journal = {Hystrix, the Italian Journal of Mammalogy},
volume = {26},
number = {1},
year = {2015},
keywords = {Geometric morphometrics; landmarks; software; thin-plate 
spline; relative warps},
abstract = {The development and the present state of the “tps” series 
of software for use in geometric morphometrics on Windows-based computers are 
described. These programs have been used in hundreds of studies in mammals and 
other organisms.Download the complete issue.},
issn = {1825-5272}, pages = {9--12} doi = 
{10.4404/hystrix-26.1-11264},
url = {http://www.italian-journal-of-mammalogy.it/article/view/11264}
}



--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] comparative MA

2016-12-19 Thread andrea cardini

Dear All,

I am looking for a software for doing a major axis regression taking the 
non-independence due to phylogeny into account and test isometry in that 
framework.


In R, phytools does a SMA/RMA using comparative methods, but it's not 
MA; besides, I found a difference in df compared to SMA in smatr, and 
the difference is still there even if I use a star phylogeny in 
phytools, which should make phytools SMA identical to smatr SMA.



Any suggestion, please, for a comparative MA including a test for slope?

Many thanks in advance.

Cheers


Andrea


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Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

ESTIMATE YOUR GLOBAL FOOTPRINT: 
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/

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Re: brief comment on non-significance Re: [MORPHMET] procD.allometry with group inclusion

2016-12-12 Thread andrea cardini
Thanks both. I fully agree. I kind of did not want to mention the 
opposite case (detecting tiny effects with very large samples) not to 
raise too many issues at the same time. There's an example of that kind 
(high power in large samples) in an old paper of mine where, with a 
total N of more than 1000, we found significant slopes but R2 with 
separate lines was about 43% and with parallel was 41%, and angles of 
trajectories were on average relatively small.


Reporting also R2s, assuming that samples are large and those R2s are 
accurate, readers can judge by themselves whether an effect is really 
important (and not just statistically significant). Unfortunately, R2s 
are still missing in many papers I read or review and that concerns not 
only regressions but also simply pairwise comparisons of group means 
(pairs of taxa, sexes etc.).



Thanks everyone for your feedback!

Cheers


Andrea





On 12/12/16 15:51, Adams, Dean [EEOBS] wrote:


Andrea,

I agree that one must consider both statistical significance and 
biological meaningfulness in evaluating patterns. Considering one of 
these without the other can often get one into trouble.


Your post concerned the inability to statistically detect differences 
due to sample size limitations, and the possibility of concluding 
homogeneity from this result when it may not be the case. But as Mike 
mentioned, the opposite is also a concern. In fact, one might recall a 
discussion some months ago on Morphmet on this very issue; where large 
samples afforded the ability to discern allometric differences between 
groups, but where those statistical differences may not be 
biologically important. In both cases, critical thinking and a merger 
of statistical result and biological knowledge of the system are 
required to arrive at a well-reasoned understanding of the patterns in 
the data.


Best,

Dean

Dr. Dean C. Adams

Professor

Department of Ecology, Evolution, and Organismal Biology

   Department of Statistics

Iowa State University

www.public.iastate.edu/~dcadams/ 
<http://www.public.iastate.edu/%7Edcadams/>


phone: 515-294-3834

*From:*Mike Collyer [mailto:mlcoll...@gmail.com]
*Sent:* Monday, December 12, 2016 8:34 AM
*To:* andrea cardini <alcard...@gmail.com>
*Cc:* morphmet@morphometrics.org
*Subject:* Re: brief comment on non-significance Re: [MORPHMET] 
procD.allometry with group inclusion


Andrea,

My opinion on this is that the researcher who has collected the data 
must retain at all times a biological wisdom that supersedes a 
suggested course of action based on results from a statistical test. 
 If the purpose of a study is to assess the allometric pattern of 
shape variation within populations, then maybe the results of a 
homogeneity of slopes test can be an unnecessary burden.  If a 
researcher wants to compare the mean shapes of different groups but is 
concerned that allometric variation might differ among groups, then a 
homogeneity of slopes test could be an important first step, but I 
agree that a non-significant result should not spur the researcher to 
immediately conclude a common allometry or no allometry is 
appropriate.  Sample size, variation in size among groups, and 
appropriate distributions of specimen size within groups might all be 
things to think about.


The point you make about a potential type II error is a real concern. 
 The opposite problem is also a real concern.  One might have very 
large sample sizes and sufficient statistical power to suggest that 
allometric slopes are heterogeneous.  However, the coefficient of 
determination and/or effect size for size:group interaction might be 
quite small.  Just because there is a low probability of finding as 
large of an effect based on thousands of random permutations, is one 
ready to accept that different groups have evolved unique allometric 
trajectories?  It is easy to forget that the choice of “significance 
level” - the a priori acceptable rate of type I error - is arbitrary. 
 Making strong inferential decisions based on a binary decision for an 
arbitrary criterion is probably not wise.  I would argue that instead 
of focusing on a P-value, one could just as arbitrarily, but perhaps 
more justifiably, choose a coefficient of determination of R^2 = 0.10 
or an effect size of 2 SD as a criterion for whether to retain or omit 
the interaction coefficients that allow for heterogenous slopes.


*** Warning: pedantic discussion on model selection starts here.  Skip 
if unappealing.


One could also turn to model selection approaches.  However, I think 
multivariate generalization for indices like AIC is an area lacking 
needed theoretical research for high-dimensional shape data.  There 
are two reasons for this.  First, the oft-defined AIC is model 
log-likelihood + 2K, where K is the number of coefficients in a linear 
model (rank of the model design matrix) + 1, where the 1 is the 
dimension of the value for the variance 

[MORPHMET] PC Scores From Other PCA in MorphoJ

2016-12-12 Thread andrea cardini

Today is my morphmet-day.

A question, this time, please.


Is there anyone with experience on the "PC Scores From Other PCA" in 
MorphoJ?


I am trying to project shape coordinates on a matrix I imported and 
attached to a dataset with mean shapes, but the attached dataset does 
not show up in the menu: I can see the parent dataset (before averaging) 
with the imported covariance matrix but, as soon as I select the mean 
shapes (despite being the data to which the covar. matrix is attached), 
the imported covar. matrix vanishes. That means that I can project the 
parent dataset (non-averaged) onto the vectors from the imported matrix 
but can't do it with the mean shapes (which is my aim).



I'll do it in NTSYSpc or R, but I'd be curious to understand what I am 
getting wrong in MorphoJ.


Thanks in advance for any suggestion.


Cheers


Andrea



--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] problem fixed

2016-12-06 Thread andrea cardini
Thanks to Marko Djurakic for finding the problem with the geiger 
function, and to all others who answered with suggestions: the issue was 
that another package had a function with the same name.


Cheers


Andrea


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] geiger rescale error

2016-12-06 Thread andrea cardini

Dear All,

I've just tried the rescale function in geiger on my data and got an 
error message. As I have no experience with it, I tried the first 
example for this function in the help: same error message (see below).


Has anyone had similar issues? Probably I made some silly mistake.

Thanks in advance for your feedback.

Cheers


Andrea


geo <- get(data(geospiza))
ltrns <- rescale(geo$phy, "lambda")
plot(ltrns(0))
title("lambda: 0.0")

Error message:

Error in rescale(as.numeric(x, range = range, domain = domain, ...)) :
  (list) object cannot be coerced to type 'double'


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
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ESTIMATE YOUR GLOBAL FOOTPRINT: 
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[MORPHMET] brain-body mass allometry in mammals

2016-11-04 Thread andrea cardini

Dear All,

may I please ask you a suggestion on references?

I am looking for a reasonably recent review on the allometric 
relationship between brain and body mass in mammals.



Thanks in advance for your help, and my apologies for possible late 
answers.


Cheers


Andrea


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e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
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[MORPHMET] managed to install Morphologika in Linux

2016-10-21 Thread andrea cardini

Dear All,

this is for Linux users.


If you're interested to use Morphologika, it seems to work fine 
(although slowly) using Mint 17 (a 'version' of Ubuntu 14.04).


I had tried in the past and did not make it but probably I was just 
silly. Right now I've done it after installing PlayOnLinux but I don't 
think this matters. You probably only need Wine. However, after running 
the installation as in Windows, you may have to put manually the 
testnewmat.dll file in the Windows System32 folder and you'll probably 
have to run the program by double clicking on the exe in the program 
folder (it does not work with the link from the Wine menu).



The old Morpheus et al. also works but apparently crashes if one tries 
to estimate missing landmarks. I used to get around this by running the 
missing data commands from the DOS interface (CMD file) but that does 
not seem to work any more.



Anyway, I just wanted to share this with the (probably few) people 
interested. By the way, with Morphologika I had troubles with the 
visualization in XP but that works wonderfully well in Linux.


Have a nice weekend


Andrea



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Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
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[MORPHMET] working on just one side of skulls etc.

2016-09-12 Thread andrea cardini

Dear morphometricians,

these (below) are coming out right now. They make a simple point: if one 
is working on structures with object symmetry but he/she is using just 
one or the other side, as in many published studies, it might be often 
(but not always!) a good idea to estimate first the other half by mirror 
reflection.


Data and guidelines are provided as supplementary information.

If someone is interested and can't download the papers, please do get in 
touch with me. They're not yet in my webpage.


Cheers


Andrea


Cardini A. Lost in the other half: improving accuracy in geometric 
morphometric analyses of one side of bilaterally symmetric structures. 
Systematic Biology, in press. DOI 10.1093/sysbio/syw043 ; data: 
doi:10.5061/dryad.mr2mh

http://sysbio.oxfordjournals.org/content/early/2016/06/24/sysbio.syw043.abstract?sid=4b1c684e-da71-4c43-a2b7-4fe16346ad4c

Cardini A. - Left, right or both? Estimating and improving accuracy of 
one-side-only geometric morphometric analyses of cranial variation. 
Journal of Zoological Systematics and Evolutionary Research, in press; 
data: http://tinyurl.com/j8j3h6b DOI: 10./jzs.12144

http://onlinelibrary.wiley.com/doi/10./jzs.12144/abstract


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Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

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[MORPHMET] papers on variance difference between sexes

2016-08-24 Thread andrea cardini

Dear All,

I am looking for papers comparing variance in morphometric and other 
phenotypic traits in females and males. I am not talking about mean 
differences as in most tests of sexual dimorphism. I am interested to 
see whether people have found similar variance in a given trait in the 
two sexes or they found that one sex tends to vary more than the other.


Thanks a lot in advance for your suggestions (and pdfs, if available!).

Cheers


Andrea

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Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
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Re: [MORPHMET] comparing static, evolutionary, and ontogenetic allometry

2016-08-22 Thread andrea cardini

Hi Christy,

there's probably two main ways of doing that and they're to some extent 
related.


1) Comparing angles of vectors. Besides MorphoJ's approach to this, 
there are other resampling approaches and some of these are described in 
Zelditch et al.'s Green Book and others in papers by the Viennese group 
(Mitteroecker et al.'s papers on developmental trajectories and 
size-shape spaces) and by O'Higgins et al..


2) The MANCOVA approach, which is well described in the Green Book. With 
this, you'll find both parametric versions as well as resampling approaches.


In the Yellow Book (Hystrix 2013, link in my signature), there are at 
least a couple of papers which are relevant: one is by Sheets and 
Zelditch and the other one by Mitteroecker et al. I'd give a look also 
at the recent review on allometry by Klingenberg (2016).


Especially with static allometry, you might need very large samples to 
get reliables estimates. We explored somewhat this, years ago, in 
Cardini & Elton, 2007, Zoomorphol. Also, for evolutionary allometries 
and other comparative analyses, you should take phylogeny into account 
(PGLS and the like - see papers by Rohlf, Adams etc.).


Besides P values, I would carefully check how different R2 of the models 
you're comparing are and would also carefully inspect the visualizations 
(do they suggest similar patterns across groups?).



Good luck.

Cheers


Andrea


On 19/08/16 02:34, Christy Hipsley wrote:

Dear Morphmet community,

I'm working with a big GM data set of 92 species and would like to 
statistically compare levels of static, evolutionary, and ontogenetic allometry 
to assess levels of constraint in phenotypic development.

For static and evolutionary allometry, I have regressions (shape on size for species) and 
size-corrected PCAs. I am wondering what is the best way to directly compare those in a 
statistical framework. I originally compared PC axes between the two data sets using the 
"Compare Vector Directions" option in MorphoJ, but this seems a bit 
complicated. Is a simple ANCOVA between the 2 regressions appropriate? They are at least 
by eye nearly identical.

I also have regressions for growth series of 21 of those species, but I'm not 
sure how those could be directly compared to static or evolutionary allometry. 
If I do a regression of shape on size for that data set, pooled by species, the 
R2 is slightly higher, which I expect since it is sampling over the entire 
postnatal development (from hatchling to adult). However there is a strong 
trend for some of the species to be significantly down-shifted along the 
y-axis, although the slopes remain statistically the same (tested using MANCOVA 
in GeoMorph).

Thanks for any advice on how to compare these levels or if it even makes sense 
to compare ontogenetic allometry to either of the others.

Christy
-
Christy Anna Hipsley
University of Melbourne/Melbourne Museum



--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
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Re: [MORPHMET] landmarking a translucent matching symmetry object (like flywings)

2016-07-28 Thread andrea cardini

Hi Helmi,

other may have different views, but I would work on, say, the left wing 
and the right one mirrored. Although those landmarks are likely to be 
very precise, your 'eyes' might see left and right slightly differently, 
if one is not mirrored, and you may introduce a small bias. This is of 
course testable but I would not waste the time and simply mirror the 
images using a batch command (available for instance in IRFANVIEW, which 
is free).


Good luck.

Cheers


Andrea

PS

For the GPA, the mirroring won't matter if the software (MorphoJ and 
Morphologika, for instance) can do it, but I would still worry about the 
possible bias.


On 28/07/16 09:59, Helmi Hadi wrote:

Dear morphometricians,

I have an odd question. For a translucent matching symmetry object 
like fly wings, the venation can be seen on both sides of the object. 
Should I flip one side of the wing (left or right side) and landmark 
all wings in one configuration or should I retain a sort of mirror 
image when landmarking the object. Does it matter or will it affect 
analysis later on say if I am classifying it based on side (if I add a 
left/right side classifier)?


Thank you.

Helmi Hadi,
School of Health Sciences,
Universiti Sains Malaysia,
Kelantan, Malaysia


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tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

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WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
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[MORPHMET] geomorph and other packages in Linux Ubuntu

2016-07-19 Thread andrea cardini

Dear All,
I suspect that this is obvious for the Linux geeks but it wasn't for me.
I was getting error messages while trying to install geomorph and quite 
a few other packages in R using Ubuntu.


It seems that the issue was just to install first gfortran using the 
terminal command:

sudo apt-get install gfortran
In fact, I think that something about this is mentioned for installing 
geomorph in Mac OS but I am not sure if it's said also for Linux.


I am still installing and testing software but hope that everything is 
fine now. I wanted to share this in case others had similar problems.

Cheers

Andrea


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
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Re: [MORPHMET] symmetrizing data with bilateral symmetry

2016-07-05 Thread andrea cardini

Dear Eli,
I'd say that it depends on what you want to do.

If quantifying asymmetry is one of your aims, then of course you must 
have landmarks on both sides.


If not, I'd tend to say that it's better to have the bilateral landmarks 
and then decide whether or not to 'symmetrize' the data.
However, even in this second case, as I suggested with an example in a 
paper which should be soon out in Syst. Biol., there might be cases when 
you might decide to landmark just one side to save time and money and 
maximize sampling during data collection. Then, often, by simply 
reconstructing the side with no landmarks by mirror-reflection, you 
might get a better approximation of the total configuration you would 
have had by landmarking both sides.


There might be also cases when you really want to measure just one side 
because your question is specific to that side, but I've never found one 
such case in the literature.


To symmetrize the data in MorphoJ you just need to:
1) load them as data with object symmetry;
2) do the Procrustes superimposition (and check that MorphoJ is 
'guessing' the correct pairs of bilateral landmarks);

3) save size and the symmetric component (export from the file menu);
4) restore size by multiplying the symmetric shape coordinates by the 
centroid size of the corresponding individual.
Of course, if you do all your analyses in MorphoJ, you just need to 
select each time only the symmetric component.


Cheers

Andrea


On 05/07/16 16:36, Elahep wrote:


Dear all,

I have got quite confused about object symmetry! If analyzing symmetry 
is not our purpose is this necessary to do symmetrizing procedure for 
the data that have bilateral symmetry?
I have seen some people choose only one side of the bilaterally 
symmetric object to study its shape variation (for example between 
geographic areas). In this case is this better to put landmarks in 
both sides of the midline or considering just one side is enough? If I 
want to do the symmetrizing how can I do it with tps series or Morphoj?


Any help would be appreciated!

Eli
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e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
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[MORPHMET] Morphoj with very large datasets

2016-05-27 Thread andrea cardini

Dear All,
I'm curious to know whether anyone has tried MorphoJ with large datasets 
(few thousands of specimens with, say, 100 or so shape coordinates).


I had a couple of instances of the software being unable to save the 
project. The file was quite large because there were also subsamples. 
Probably this happened on the Linux side of my machine, which in fact is 
more powerful in terms of memory etc. than the Windows side. But 
possibly the OS is not really a factor.


Thanks in advance for your feedback.
Cheers

Andrea

--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
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Re: [MORPHMET] Using Semilandmarks

2016-05-12 Thread andrea cardini
I would suggest to start with some preliminary readings on what 
semilandmarks are and imply. Among many others, these two papers are 
particularly interesting in my view (plus plenty more refs in these two 
papers themselves, as well as in G, 2013, and maybe the introduction 
to the Yellow Book Anna and I wrote).


Oxnard C., O’Higgins P., 2011. Biology Clearly Needs Morphometrics. Does 
Morphometrics Need Biology? Biological Theory. 4: 84– 97.


Klingenberg C.P., 2008. Novelty and “Homology-free” Morphometrics: 
What’s in a Name? Evol Biol. 35: 186–190.



Also this one (although not on semilandmarks) might help to understand 
the general issues of analyses of forms without clear landmarks:
O’Higgins, P. (1997). Methodological issues in the description of forms. 
Fourier descriptors and their applications in biology, 74–105.


Good luck

Andrea

On 12/05/2016 03:26, Emma Sherratt wrote:

Dear Edgar,

Semilandmarks should be slid during Procrustes superimposition; treating
them as fixed landmarks will only add error into your analyses. Therefore
the answer is simply a) use software that supports semilandmark sliding.
Your options are great. And when it comes to deciding whether to minimise
for bending energy or Procrustes distance, I suggest reading Gunz &
Mitteroecker 2013 here
<http://www.italian-journal-of-mammalogy.it/article/view/6292>. For GPA and
further analyses, I suggest using the TPS suite and MorphoJ, or geomorph if
you are confident with script-based analyses.

Emma

~~~

Emma Sherratt, PhD.


Postdoctoral Researcher in the Keogh Lab
<http://biology-assets.anu.edu.au/hosted_sites/Scott/>
Division of Evolution, Ecology & Genetics
Research School of Biology
116 Daley Road
The Australian National University
Acton, ACT  2601
AUSTRALIA

email: emma.sherr...@gmail.com
tel: +61 2612 53029
mob: +61 4234 19966
Twitter: @DrEmSherratt <https://twitter.com/DrEmSherratt>

Caecilians are legless amphibians...

*  __
 (\   .-.   .-.   /_")
  \\_//^\\_//^\\_//
   `"`   `"`   `"`*

learn more about them here: www.emmasherratt.com/caecilians




On 12 May 2016 at 09:26, Edgar Esteban Herrera Collazos <
edgaresteba...@gmail.com> wrote:


Dear Morphometricians,

I'm conducting a study on fish taxonomy using integrative taxonomy, my
first approach is using Geometric Morphometrics.

For GM I decided to use Landmarks and Semilandmarks. My question is: Is
there any difference or advantage between using a) a software that supports
semilandmark sliding or b) by entering each semilandmark as a landmark?

Best regards

--
Edgar Esteban Herrera Collazos B.Sc.

Postgraduate Student at Pontificia Universidad Javeriana
Ichthyology Laboratory 108B Ed 53 - 3208320 Ext 4127
---
Estudiante de Posgrado en la Pontificia Universidad Javeriana
Laboratorio de Ictiología 108B Ed 53 - 3208320 Ext 4127


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--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
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THANKS Re: [MORPHMET] using regression residuals for other analyses

2016-03-29 Thread andrea cardini
 9, p. 110, 2009.

I hope this leads to useful discussion!

Cheers

Ian

dwor...@mcmaster.ca <mailto:dwor...@mcmaster.ca>



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Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, Centre for Forensic Science , The 
University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia


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WEBPAGE: https://sites.google.com/site/alcardini/home/main


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[MORPHMET] using regression residuals for other analyses

2016-03-24 Thread andrea cardini

Dear All,
this is something that, I believe, has already come up in the past. 
However, I'd like to check it again.


What are the issues with, say, regressing shape on size, saving 
residuals and using those in further analyses (e.g., other regressions 
or testing group differences etc.)?


I suspect that all the factors (size, other predictors, groups etc.) 
should be incorporated in a single model and may have a partial 
intuition about some of the problems with rerunning, instead, analyses 
on residuals but I'd be very grateful to know how those with a better 
understanding of the methods see it.


Thanks in advance.
Cheers

Andrea


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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[MORPHMET] condylobasal length

2016-03-21 Thread andrea cardini

Hi All,
a very simple question on a definition, please.
Is there a univocal undisputed definition of condylobasal length? Or, 
are some researchers measuring slightly different things sometimes?


Comments, pdfs or images are most welcome.
Thanks in advance.

Cheers

Andrea


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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[MORPHMET] cranial size and body mass in felids

2016-03-03 Thread andrea cardini

Dear All,
I'd be greatly very grateful for any suggestion 
on papers or web-pages with information on 
cranial size (length or other) and body mass in felids.

References and/or pdf are most appreciated.
Thanks a lot in advance.
Cheers

Andrea




Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e 
Geologiche, Università di Modena e Reggio Emilia, 
Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


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Re: [MORPHMET] Sliding Semilandmarks

2016-02-18 Thread andrea cardini
Mike, does this mean that, in general, the 
position of the semilandmarks is strongly sample 
dependent, which would mean that also the shape 
distances might change remarkably despite the 
fact one has the same number of points on exactly the same surface?
Say that I have two samples, A and B. I first (1) 
superimpose (and slide) within A. Then I do the 
same with both A and B together (2). Could I get 
appreciable differences between A1 and A2 just because of the sliding?


All Procrustes shape distances depend on the 
sample composition. However, in my experience, 
differences between A1 and A2 tend to be 
negligible with 'standard' landmarks. Is this 
different with semilandmarks? Are there 
sensitivity analyses that explore the issue (if it's an issue)?


Thanks in advance.
Cheers

Andrea

At 17:06 18/02/2016, Collyer, Michael wrote:
Contrary to your logic, subsetting your sample 
could have an effect.  Your mean configuration 
would change in each of the subsamples, from the 
mean of your original sample, thus changing the 
reference configuration used in the separate 
GPAs performed.  The reference configuration has 
a prominent role in the sliding of landmarks.



Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e 
Geologiche, Università di Modena e Reggio Emilia, 
Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


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Re: [MORPHMET] 3D Shape Change Visualization

2015-12-15 Thread andrea cardini
ng to do though, I 
think you might want to try geomorph in R. It's 
really quite versatile if a little daunting. I 
hope this wasn't too basic ... let me know how you get on.


Best,
Ari

On Mon, Dec 14, 2015 at 5:18 AM, Jay Devine 
<<mailto:jaypatrickdev...@gmail.com>jaypatrickdev...@gmail.com> wrote:

Hello again, Morphmet!

I received an immense amount of help with my 
last question, so I figured I would try again! 
My silly question this time concerns 3D visualization of shape change.


I've been able to successfully create wireframe 
graphs for my data, but for some reason I can 
not create transformation grids. I'm aware that 
you need to right-click on the "PC shape 
changes" background to change the type of graph. 
Unfortunately, transformation grids doesn't 
appear as an option for me to choose. Is there 
perhaps a preliminary step I need to do?


Does anyone know why this could be happening?

Thanks in advance for your time and consideration.

Respectfully,

Jay

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Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e 
Geologiche, Università di Modena e Reggio Emilia, 
Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


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Re: [MORPHMET] 3D Shape Change Visualization

2015-12-14 Thread andrea cardini
Jay, as far as I know, you can't do that with 
MorphoJ but you can do it with Morphologika and 
the old Morpheus (not sure about the new one, but 
Dennis will tell you if it's possible).


Cheers

Andrea


At 06:18 14/12/2015, Jay Devine wrote:

Hello again, Morphmet!

I received an immense amount of help with my 
last question, so I figured I would try again! 
My silly question this time concerns 3D visualization of shape change.


I've been able to successfully create wireframe 
graphs for my data, but for some reason I can 
not create transformation grids. I'm aware that 
you need to right-click on the "PC shape 
changes" background to change the type of graph. 
Unfortunately, transformation grids doesn't 
appear as an option for me to choose. Is there 
perhaps a preliminary step I need to do?


Does anyone know why this could be happening?

Thanks in advance for your time and consideration.

Respectfully,

Jay

--
MORPHMET may be accessed via its webpage at 
<http://www.morphometrics.org>http://www.morphometrics.org

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Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e 
Geologiche, Università di Modena e Reggio Emilia, 
Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


--
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Re: [MORPHMET] phylogenetic signal

2015-10-29 Thread andrea cardini

Dear Bryan,
this is something I used to be more interested in 
some time ago and I've never done any systematic review of the literature.


In my experience, although it is often assumed 
that allometry confounds the phylogenetic signal 
(as it was apparently the case in the radiation 
of vervet monkeys 
doi:10.1016/j.jhevol.2007.09.022), I would not be 
so sure that one can easily generalize. We have a 
recent example in the temporal bone of apes ( 
http://dx.doi.org/10.1016/j.jhevol.2015.06.012 ) 
where we found exactly what you mentioned (the 
signal in shape was dominated by allometry); 
however, interestingly it was size and allometry 
that had the stronger signal and controlling for 
allometry almost removed any congruence of shape with phylogeny.


It would be really nice to see an updated review 
on this issue sooner or later in the literature.

Cheers

Andrea


At 14:15 28/10/2015, you wrote:


Morphometricians,


Id like to gather some opinions on measuring 
phylogenetic signal from GM data.Â



For many GM analyses, size-free shape data 
(e.g., residuals from a regression) are used in 
analyses of variation/covariation. However, I 
less often see size and shape analyzed 
independently when measuring phylogenetic 
signal. If most of the shape variation is 
allometric, it would seem that the phylogenetic 
signal for uncorrected shape variables may 
approach the strength of the phylogenetic signal 
for size alone. However, I have not found this 
to be the case with several datasets.



Has anyone examined this in detail?Â


Thanks-

-Bryan

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Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e 
Geologiche, Università di Modena e Reggio Emilia, 
Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

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
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


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[MORPHMET] geometric morphometrics in Budapest

2015-06-09 Thread andrea cardini

Dear All,
I was wondering whether there's anyone doing (or 
interested in) geometric morphometrics in Budapest.


Thanks in advance for any answer.
Cheers

Andrea



Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy

tel. 0039 059 2058472

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
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=0947-5745site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


--
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Re: [MORPHMET] CVA and Discriminant Analysis in Morpho J

2015-02-11 Thread andrea cardini
 
receiving emails from it, send an email to 
mailto:morphmet+unsubscr...@morphometrics.orgmorphmet+unsubscr...@morphometrics.org.



Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy


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
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=0947-5745site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


--
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[MORPHMET] estimates of (some) errors in geometric morphometrics

2015-01-16 Thread andrea cardini

Dear morphometricians,
I'd like to thank all those who helped me with 
refs, suggestions etc. when I asked questions on 
sampling error in geometric morphometric studies, 
as well as on errors made by using 2D images of 3D objects.
Two small studies I made (one with a couple of 
colleagues) are coming out. They're, as usual, 
exploratory and simplistic. I take the blame for 
all possible mistakes but hope they may stimulate 
others to investigate more and do better.


Cardini A., Seetah K., Barker G., 2015. How many 
specimens do I need? Sampling error in geometric 
morphometrics: testing the sensitivity of means 
and variances in simple randomized selection 
experiments. Zoomorphology, in press. DOI: 10.1007/s00435-015-0253-z

http://link.springer.com/article/10.1007/s00435-015-0253-z
(reprints available on request; probably soon also in my webpage)

Cardini A., 2014. Missing the third dimension in 
geometric morphometrics: how to assess if 2D 
images really are a good proxy for 3D structures? 
Hystrix, in press. DOI:10.4404/hystrix-25.2-10993

http://www.italian-journal-of-mammalogy.it/article/view/10993/pdf_10993
(free and open access)

Cheers

Andrea







Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy


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
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=0947-5745site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

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[MORPHMET] trick for editing svg images from MorphoJ + reference about 2D/3D

2014-11-14 Thread andrea cardini

Dear All,
this is something I've just found out. Maybe it's 
well known or even somewhere in the help file of MorphoJ.


I was looking for a way of editing svg images 
from MorphoJ in Inkscape so that, for instance, 
if I want to erase the light blue mean shape in 
the background (including landmarks and their 
numbers), I don't have to select each feature one 
by one after ungrouping the objects in the file.
Contrary to CorelDraw one cannot apparently get a 
list of objects and simultaneously select them in 
Inkscape. However, I tried this 
http://www.inkscapeforum.com/viewtopic.php?f=5p=8910 
and it worked wonderfully well.


If someone has the same issue, I hope this helps.


I take the chance to ask if anyone knows papers 
where people compared analyses in 2D with 
analyses on the same samples and landmarks in 3D.
I've not found much but I am sure there's more. 
Thanks in advance for any suggestion and/or pdf.


Cheers

Andrea





Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy


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
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=0947-5745site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


[MORPHMET] sampling error references

2014-09-02 Thread andrea cardini

Dear All,
I am drafting a short follow up (kind of) of 
Cardini  Elton's (2007, Zoomorphol.) paper on 
sampling error in geometric morphometrics.

I am just focusing on means and variances.

I've not found that many references on this type 
of issue. If anyone has suggestions (or pdfs), they're much appreciated.

Thanks in advance.

Cheers

Andrea


Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy


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
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=0947-5745site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


[MORPHMET] sampling error references

2014-09-01 Thread andrea cardini

Dear All,
I am drafting a short follow up (kind of) of 
Cardini  Elton's (2007, Zoomorphol.) paper on 
sampling error in geometric morphometrics.

I am just focusing on means and variances.

I've not found that many references on this type 
of issue. If anyone has suggestions (or pdfs), they're much appreciated.

Thanks in advance.

Cheers

Andrea





Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy


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
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


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=0947-5745site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.