Re: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread alcardini
Indeed one of my favourite examples where semilandmarks are really
useful is a paper by Hublin, Gunz et al. (with apologies for the
inaccurate ref. and mixed up order of authors) where they manage to
classify as Neanderthal a piece of cranial vault found (I believe) in
Belgium and possibly in the sea. With all the limits we mentioned,
it's probably hard to do any better.
Certainly it's not the only type of useful application but that kind
of 'forensic' analysis, where the main aim is pure classification
accuracy, is where I see (potentially) less problems. However, even
with phenetics (in the original sense of the term), putting together
all sorts of different characters and characters states, regardless of
their evolutionary significance, one could probably get a very good
and stable classification. Yet, to what extent that would be
biologically meaningful is hard to say, and we abandoned phenetics for
cladistics.
With shape data, as implied by Jim's comment to my message, we don't
yet have the same kind of understanding to be able to do the same
(some kind of 'biologically meaningful superimposition).
For now, in a way, it seems to me that it's as if we were aligning
sequences using, say, a least square method, which molecular
biologists would never use because they know much more about DNA
evolution and can model that more accurately in the alignment. We
can't. Thus, for me, semilandmarks are useful if (as in your example)
they may provide information which is relevant and there's no other
way to get. The limits will still be there but the pros may be more
than the cons. Where I disagree is the general trend to believe that
more is always better.

The field is different but I am very much sympathetic with what
Hawkins said in his review of spatial data analysis:
"This has led to a confusing
literature and a proliferation of increasingly complicated
analytical methods that are difficult to evaluate or even
understand if you are not a statistician. A tendency to ignore
assumptions of many of these complex methods does not help
matters. It has also diverted attention away from epistemo-
logical and conceptual issues of importance to our field, some
of which I have tried to highlight. Although it is self-evident
that statistics are an indispensible tool for evaluating data,
when we focus too much on methods it is natural to add new
layers of complexity as our view becomes narrower and
narrower and we try to capture every nuance of our data. But
biogeography and geographical ecology are not branches of
theoretical statistics, and there does come a point at which
analytical complexity begins to interfere with understanding."
Journal of Biogeography (J. Biogeogr.) (2012) 39, 1–9

Good night

Andrea



On 06/11/2018, Mike Collyer  wrote:
> Andrea,
>
> I am intrigued by your initial comment about adding covariance that was
> apparently absent.  I tend to think of the problem from the other
> perspective of not accounting for covariance that should be present.  As a
> thought experiment (that could probably be simulated, and maybe I am not
> correct in my thinking), I like to think of two landmark configurations that
> are the same in all regards except for one curve, where two groups have
> distinctly different curves but maybe would not be obviously distinctively
> different if an insufficient number of semi-landmarks (or none) were used to
> characterize the curve.  If one were to (maybe simulate this example and)
> use one sparse representation of landmarks and one dense representation,
> perform a cross-validation classification analysis, and calculate posterior
> classification probabilities (let’s assume equal sample sizes and,
> therefore, equal prior probabilities), I would expect that the posterior
> probabilities of the dense landmark configuration would better assign
> specimens to the appropriate process that generated them (i.e., their
> correct groups).  The posterior probabilities would be closer to 0 and 1
> because of the “added covariance”, as reflected by the squared generalized
> Mahalanobis distances, based on the pooled within-group covariance.  The
> added covariance would be essential for the posterior probabilities, if the
> sparse configurations produced similar generalized distances to group means,
> and therefore, similar posterior probabilities for classification.
>
> I’m not sure adding covariance is an issue.  To me it simply changes the
> hypothetical (null) covariance structure, which Philipp mentioned should
> probably not be assumed to be independent (isotropic).  I think your example
> might best highlight that a different multivariate normal distribution of
> residuals is to be expected with a different configuration.
>
> Cheers!
> Mike
>
>
>> On Nov 6, 2018, at 12:34 PM, alcardini  wrote:
>>
>> Yes, but doesn't that also add more covari

Re: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread alcardini
 to no biological model or hypothesis whatsoever
> (e.g., Huttegger & Mitteroecker 2011, Bookstein & Mitteroecker 2014, and
> Bookstein 2015, all three in Evol Biol). Accordingly, a deviation from
> isometry does not itself inform about integration or modularity (in any
> reasonable biological sense).
>
> The multivariate distribution of shape coordinates, including "dominant
> directions of variation," depend on many arbitrary factors, including the
> spacing, superimposition, and sliding of landmarks as well as on the number
> of landmarks relative to the number of cases. But all of this applies to
> both anatomical landmarks and sliding semilandmarks.
>
>
>
> I don't understand how the fact that semilandmarks makes some of these
> 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
>
> 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>
>
>
> 9 LANDMARKS
>
>
> <https://groups.google.com/a/morphometrics.org/group/morphmet/attach/dcce33d95d952/pebddfgpogepigmi.jpeg?part=0.1.2=1=0>
>
>
> --
>
> 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, Schoo

[MORPHMET] % of overlap of convex hulls in 2D scatterplots

2018-08-21 Thread alcardini
Dear All,
please, does anyone know if there's an R script or package to compute
the exact % of overlap of convex hulls in 2D scatterplots?
I found something but was developed for high dimensional spaces and
seems to compute that using an approximation. In 2D it should not be
too difficult to get the exact %, I guess.

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, 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

2017-11-01 Thread alcardini
you took the aligned specimens from TpsRelw and obtained the Procrustes
> (Euclidean) distance matrix from them, and did the same with the aligned
> specimens from geomorph, and then performed a matrix correlation, the
> correlation would be precisely 1.0.  This means the information is
> identical in the two superimpositions, even if they differ slightly in how
> the entire set is oriented relative to the X-Y axis.  Incidentally, in the
> above case one would also find a perfect correlation between distances from
> the GPA-aligned specimens, those shapes rotated to their principal axes, or
> differences in shape found from the thin-plate spline and uniform shape
> components taken together. For an early discussion of these issues see
> Rohlf 1999.
> However, performing the procedure above where one set of GPA-aligned
> coordinates is from MorphoJ will not produce a perfect correlation of 1.0,
> as MorphoJ uses Full Procrustes superimposition. That means the perceived
> relationships between shapes is not being represented in the same manner:
> which of course is a known difference between full and partial Procrustes
> fitting. How much of a difference one finds between a full and partial
> Procrustes alignment is dataset dependent.
> 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/~dcadams/>
> phone: 515-294-3834
> *From:*Andrey Lissovsky [mailto:andlis...@gmail.com <andlis...@gmail.com>]
> *Sent:* Tuesday, October 31, 2017 10:21 AM
> *To:* MORPHMET <morphmet@morphometrics.org>
> *Cc:* andlis...@gmail.com; volk...@yandex.ru
> *Subject:* Re: [MORPHMET] Procrustes fit
> Thank you Dean,
> Of course, numbers should differ. But in my case, there is no correlation
> between two sets. I guess that in theory the two sets should have r at
> least around 0.9?
> On Tuesday, October 31, 2017 at 5:31:51 PM UTC+3, dcadams wrote:
>Andrey,
>It is unreasonable to expect the numbers will match perfectly
>between these two software packages, as the way in which they
>perform the operations differs.  First, MorphoJ uses Full Procrustes
>fit, whereas the TPS series, geomorph, and others use Partial
>Procrustes fitting. That will make a difference.
>Second, there may be additional differences in in how the
>superimponsed specimens, and thus the consensus, is aligned relative
>to the X-Y coordinate system. Some packages allow one to rotate the
>consensus and aligned specimens to their principal axes
>post-superimposition. That too could lead to differences.
>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/~dcadams/>
>phone: 515-294-3834
>*From:*Andrey Lissovsky [mailto:andl...@gmail.com ]
>*Sent:* Tuesday, October 31, 2017 9:26 AM
>*To:* MORPHMET <morp...@morphometrics.org >
>*Cc:* andl...@gmail.com ; vol...@yandex.ru 
>*Subject:* Re: [MORPHMET] Procrustes fit
>Thank you, Andrea
>I understand that difference should be tiny, so something goes
>wrong. I enclose one of my tps files. Usually I check dots and
>commas, so the reason is probably in some different way..
>It is possible that I am mixing up menu items.. Last time I use this
>software, the labels were different.
>Now I use:
>In MorphoJ: Preliminaries -- New Procrustes fit -- Align by
>principle axes
> then: Export dataset -- Procrustes coordinates
>In TPS Relw: Actions -- Consensus
> then: File -- Save -- Aligned specimens
>Is this ok? Should these chains lead to the same results?
>On Tuesday, October 31, 2017 at 5:04:56 PM UTC+3, alcardini wrote:
>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
>-- MORPHMET may be accessed via its webpage at
> http://www.morphometrics.org
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[MORPHMET] online lectures and material of the Workshop: UWashington.EvolQuantGenetics.Jun5-9

2017-08-26 Thread alcardini
This could be of interest for quite a few morphometricians.
Many thanks to Joe et al. for making it available online.

Cheers

Andrea



-- Forwarded message --
From: Joe Felsenstein 
Date: Fri, 25 Aug 2017 12:38:36 -0700
Subject: Re: [MORPHMET] Workshop: UWashington.EvolQuantGenetics.Jun5-9


As promised, we did make them available at the course website by the
end of the course.  The course website is

http://blogs.uw.edu/fhleqg/

and to find the lecture projections, as well as materials for the
software exercises, just click on "Schedule" -- the lecture and
exercise titles are links to the pages that each have links to display
the PDF or PPT lecture projections, as well as links to software and
datasets.


The Evolutionary Quantitative Genetics Workshop will be given again at
Friday Harbor Laboratories in 2018, with lectures from 4-8 June.  We
will announce it on Evoldir, and if possible on Morphmet as well.  An
announcement will also be posted at the Friday Harbor Labs website
under Summer 2018 courses.


Please feel free to pass this on to Morphmet.

Joe

Joe Felsenstein j...@gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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Re: [MORPHMET] Re: number of landmarks and sample size

2017-06-03 Thread alcardini
Hi Philipp,
I am not worried about the number of variables (although I am not sure
one needs thousands of highly correlated points on a relatively simple
structure and seem to remember that Gunz and you suggest to start with
many and then reduce as appropriate).

Regardless of whether point homology makes sense, I am worried that
many users believe that semilandmarks (maybe after sliding according
to purely mathematical principles) are the same as "traditional
landmarks" with a clear one-to-one correspondence. Even saying that
what's "homologous" is the curve or surface is tricky, because at the
end of the day that curve/surface is discretized using points, shape
distances are based on those points and there are many ways of placing
points with no clear "homology" (figure 7 of Oxnard & O'Higgins,
2009); indeed, in a ontogenetic study of the cranial vault, for
instance, where sutures may become invisible in adults and therefore
cannot be used as a "boundary", semilandmarks close to the sutures may
end up on different bones in different stages/individuals.

Semilandmarks are a fantastic tool, which I am happy to use when
needed, but they have their own limitations, which one should be aware
of.
Cheers

Andrea



On 03/06/2017, mitte...@univie.ac.at <mitte...@univie.ac.at> wrote:
> I think a few topics get mixed up here.
>
> Of course, a sample can be too small to be representative (as in Andrea's
> example), and one should think carefully about the measures to take. It is
> also clear that an increase in sample size reduces standard errors of
> statistical estimates, including that of a covariance matrix and its
> eigenvalues. But, as mentioned by Dean, the standard errors of the
> eigenvalues are of secondary interest in PCA.
>
> If one has a clear expectation about the signal in the data - and if one
> does not aim at new discoveries - a few specific measurements may suffice,
> perhaps even a few distance measurements. But effective exploratory
> analyses have always been a major strength of geometric morphometrics,
> enabled by the powerful visualization methods together with the large
> number of measured variables.
>
> Andrea, I am actually curious what worries you if one "collects between
> 2700 and 10 400 homologous landmarks from each rib" (whatever the term
> "homologous" is supposed to mean here)?
>
> Compared to many other disciplines in contemporary biology and biomedicine,
>
> a few thousand variables are not particularly many. Consider, for instance,
>
> 2D and 3D image analysis, FEA, and all the "omics", with millions and
> billions of variables. In my opinion, the challenge with these "big data"
> is not statistical power in testing a signal, but finding the signal - the
> low-dimensional subspace of interest - in the fist place. But this applies
> to 50 or 100 variables as well, not only to thousands or millions. If no
> prior expectation about this signal existed (which the mere presence of so
> many variables usually implies), no hypothesis test should be performed at
> all. The ignorance of this rule is one of the main reasons why so many GWAS
>
> and voxel-based morphometry studies fail to be replicable.
>
> Best wishes,
>
> Philipp
>
> --
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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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[MORPHMET] old Morpheus et al. does truss, missing landmarks etc.

2016-11-13 Thread alcardini
t;>
>>
>> Thank you,
>>
>>
>>
>>
>>
>> Jade Racine
>>
>>
>> Master’s student
>>
>>
>> Department of Anthropology
>>
>>
>> University of Montreal, Canada
>
> Hi Jade,
>
> I am also a masters student attempting to use MorphoJ and am having a
> difficult time with the missing data. I collected 3D landmarks for a cranial
> asymmetry project and cannot get MorphoJ to run. It keeps giving me an error
> message. Did you happen to figure out what the issue was? I would truly
> appreciate any advice you might be able to share.
>
> Thank you,
>
> Rosa Perez
> Masters Student
> NCSU
> Dept of Anthropology
>
> --
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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

---
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---
Datasets:
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---
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:
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Re: [MORPHMET] How to quantify measurement error in MorphoJ?

2015-07-07 Thread alcardini
Thanks, Pedro, for suggesting our paper.

I would like to add that the data are available to replicate our study
and one can do the same for another paper (below), although those were
linear measurements. In this second paper we explain how to do the
permutation test.
Franklin D., Cardini A., Flavel A., Kuliukas A., Marks M.K., Hart R.,
Oxnard C., O’Higgins P., 2013
https://sites.google.com/site/hymsfme/drandreacardini/publications
In the more recent one on 3D to 2D data, there's something also on the
flattening of 3D structures in 2D pictures
http://www.italian-journal-of-mammalogy.it/article/view/10993/pdf_10993

I would suggest to read also Klingenberg et al., 2002 (measurement
error in the context of symmetry/asymmetry studies) and Arnqvist G.,
Martensson T., 1998 (both cited in some of my papers).

Cheers

Andrea




On 07/07/2015, Pedro Romano psrrom...@gmail.com wrote:
 Dear Louni Samira,
 You can use TPS, PAST, and MorphoJ. Check the attached files with some
 options on how you can test this. I recommend you perform not only landmark
 digitalization error test, but photographs as well.
 Bbest regards,
 Pedro

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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,
andrea.card...@uwa.edu.au

Webpage: http://sites.google.com/site/hymsfme/drandreacardini
and:
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Datasets:
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Editorial board for:
Zoomorphology:
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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] tpsDig on a Mac using LINUX-wine

2015-05-19 Thread alcardini
I've never tried them on the Mac side of my machine, but in my
experience all the TPS Series programs work well in Linux using WINE.
The 'old' Morpheus et al works too, PAST 2.x works as well.
With the TPS Series the only trick I need to do is starting the
programs directly from the installation folder: the links in the main
menu do not seem to work but this is clearly a very minor issue.

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

Cheers

Andrea

On 19/05/2015, F. James Rohlf ro...@life.bio.sunysb.edu wrote:
 Thanks!  Does that also work for 64 bit versions of the programs? tpsSmall
 is a simple program, would you mind testing the 64 bit version? I am also,
 of course, curious about how it works on the other emulators. I try to
 program in a very standard way for maximum compatibility with Windows.



 --

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

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

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

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

 P Please consider the environment before printing this email



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



 Dear Jim and Morphmet,



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


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

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

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

 Joseph G. Kunkel, Emeritus Professor

 Biology Department

 UMass Amherst

 Amherst MA 01003

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







 --
 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.



-- 
NO DOCX, XLSX AND PPTX, PLEASE!!!

COAUTHORS AND CONTRIBUTORS, PLEASE, FOR SHARING FILES, CONVERT THEM IN DOC,
XLS (UNLESS LONGER THAN 256 COLUMNS) AND PPT


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,
andrea.card...@uwa.edu.au

Webpage: http://sites.google.com/site/hymsfme/drandreacardini
and:
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

Datasets:
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
Editorial board for:
Zoomorphology:
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and Evolutionary Research:
http://www.wiley.com/bw/journal.asp?ref=0947-5745site=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.


Re: [MORPHMET] high-throughput 2D scanning using photo-scanner

2015-02-05 Thread alcardini
Hi Henry,
do you mean using a flat-bed scanner to take pics of 3D structures?
I've done that on marmot hemimandibles (papers with Nagorsen in my
webpage). You'll find the test of its accuracy here:
http://www.italian-journal-of-mammalogy.it/article/view/10993
It's one of the datasets in the study. Compared to 3D data, results
were pretty good and similar (only slightly worse) to those obtained
by taking pictures. However, this will be specific to the data and the
study hypothesis.

The 3D and 2D landmarks on photos of hemimandibles are provided as
suppl. info. Those of the scanned images are not but, as I said,
they're very similar to the photos. Anyway, I am happy to share those
too. Just need a spare moment to look for the data.


I was about to do this again myself on carabids but gave up as the
curator who gave me the specimens was not too happy about it.
For a macroevolutionary comparison, where differences are large, I
suspect the error may be relatively small. With very small specimens
there may be problems with resolution and with big ones there could be
issues with depth and, at least in carabids, with big ones their
curvature (e.g., pronotum and head relative to the abdomen) does not
make them ideal.
Curiously, my experience is that, at least with cheap scanners, the
old ones are better. They have more depth of field.

I am pretty sure that other people have done similar 'experiments'.
Good luck with your project.
Cheers

Andrea


On 03/02/2015, henry wallace henry.ee.wall...@gmail.com wrote:
 I am contemplating a project involving small insects.  Data would be pixel
 areas or distances of head, thorax, abdomen.  2D measurements.  Large
 numbers of specimens required.

 With appendages removed, the insects would be mounted on a flat surface,
 such as poster board or paper, which is then scanned using a desktop
 scanner (photo-scanner).  Dozens could be scanned at single time and the
 resulting images can be cropped for data gathering.

 Was just wanting initial reactions and/or recommendations on the approach.

 H.

 --
 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.



-- 
NO DOCX, XLSX AND PPTX, PLEASE!!!

COAUTHORS AND CONTRIBUTORS, PLEASE, FOR SHARING FILES, CONVERT THEM IN DOC,
XLS (UNLESS LONGER THAN 256 COLUMNS) AND PPT


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,
andrea.card...@uwa.edu.au

Webpage: http://sites.google.com/site/hymsfme/drandreacardini
and:
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

Datasets:
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
Editorial board for:
Zoomorphology:
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and Evolutionary Research:
http://www.wiley.com/bw/journal.asp?ref=0947-5745site=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.