[MORPHMET] morphospace volume

2019-09-16 Thread Damien Esquerre
Hi all,
I am interested in comparing the morphological volume or volume of 
morphospace between two groups of species. Does anyone know a good method 
to do this?
Kind regards,
Damien Esquerré, Postdoctoral Fellow, Keogh Lab
The Australian National University 

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[MORPHMET] papers with 1000+ 3D models?

2019-09-04 Thread Christy Hipsley
Hi all,

I'm looking for GM or other similar papers that include high numbers of 3D 
models, like several hundreds or over a thousand. Particularly if these 
were generated using microCT.

Thank you for any help,
Christy

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[MORPHMET] Migrating to the New Morphmet (aka morphmet2)

2019-07-02 Thread K. James Soda
Hello Everyone,

Quick update on the state of morphmet: Over the weekend, I lost some
administrative control over the 2014 version of morphmet. Fearing that this
was an indication that it would go down soon, I started sending out
invitations for a new version. At this point, most members who were
registered on morphmet as of June 20, 2019 should have received an
invitation to the newest iteration; the exceptions are those members whose
email addresses are no longer valid for Google group purposes or have opted
out of invitations to Google groups. If you did not receive an invitation,
you can join the new list by emailing morphmet2+subscr...@googlegroups.com,
then follow the instructions of the subsequent emails.

If you are reading this message, then the 2014 version of morphmet is still
distributing mail. However, I am not certain if this distribution will
continue in the future. As such, I would encourage you to start using the
new version for your morphometric needs. To re-iterate the information in
the invitations:

1) To post a message, email morphm...@googlegroups.com.

2) To access the forum, go to https://groups.google.com/d/forum/morphmet2.

If you have any difficulties with any of these tasks, please feel free to
contact me on or off of the list (k.jamess...@gmail.com).

Sincerely,

James Soda
Interim Moderator
###
Assistant Professor
Department of Mathematics
Quinnipiac University
Hamden, CT 06518
###

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Re: [MORPHMET] Morphmet in the Future

2019-07-01 Thread Hugo Benítez
I like the idea of James S. of the gmail group like geomorph and many
others e.g Evoldir.  not having Dennis with us anymore maybe James can act
as moderator of the gmail group of course if he want.

Nevertheless, Jim comments about morphometrics society also is not a bad
idea to create...  could be a great opportunity to organize more
transversal meetings to future...

Best
Hugo


El lunes, 1 de julio de 2019, F. James Rohlf 
escribió:

> That is an interesting suggestion. Whatever we do next it should not
> depend on any single individual. A problem is that we do not have a
> morphometrics society or an editor of a journal that could take ownership
> of morphmet.
>
>
>
> Jim
>
> _ _ _ _ _ _ _ _ _
>
> F. James Rohlf, Distinguished Prof. Emeritus
>
> [image: univautosig]
>
> Depts. of Anthropology and of Ecology & Evolution
>
>
>
>
>
> *From:* Murat Maga 
> *Sent:* Monday, July 1, 2019 3:03 AM
> *To:* K. James Soda ; MORPHMET <
> morphmet@morphometrics.org>
> *Subject:* RE: [MORPHMET] Morphmet in the Future
>
>
>
> Dear Morphmet community,
>
>
>
> Couple weeks prior to his sudden demise, I suggested Dennis to consider
> moving the morphmet at some point to a modern forum platform that support
> markups, code formatting and inline images.
>
>
>
> You can check out https://discourse.slicer.org to see one in action. The
> main benefit that I see is the potential for a more community build up and
> engagement. For people who prefer to receive messages as emails (myself
> included), they can configure their accounts to subscribe to messages.
>
>
>
> Discourse is open-source and free to install and to use on ones own
> servers.  There are various hosted options for a small fee too,
> https://www.discourse.org/pricing.
>
>
>
> It is sad having to talk about changes so soon after Dennis’s passing, but
> I thought it is an appropriate discussion to have.
>
>
>
> M
>
>
>
>
>
> *From:* K. James Soda 
> *Sent:* Saturday, June 29, 2019 9:10 PM
> *To:* MORPHMET 
> *Subject:* [MORPHMET] Morphmet in the Future
>
>
>
> Dear Fellow Morphometricians,
>
>
> I want to give a quick comment about the future of morphmet after Dennis's
> passing so that any necessary changes will not come as a surprise. Please
> rest assure that it is not a question of whether morphmet will continue but
> rather if any different procedures will be required to make or view posts.
> Right now, morphmet is linked to morphometrics.org, which is a domain
> that belonged to Dennis himself. As a result, it is possible that, at some
> point in the future, morphmet may temporarily go down if the
> morphmetrics.org domain becomes unavailable.
>
> What does this mean for you as a member? Right now, very little. You can
> continue to post to morphmet and new members can join morphmet without
> interruption. If in the future, this ceases to be the case, you will
> receive an invitation to a near identical Google group that will function
> in the same manner as morphmet has operated since the 2014 transition.
> Invitations will likely be distributed over the course of two to three
> days. The invitation email will include instructions on any changes to the
> submission process, which will likely only include a new email address for
> making posts and a new web address for the forum.
>
> If you have any questions or concerns, please contact me either on or off
> of the list (k.jamess...@gmail.com).
>
> Best regards,
>
> James Soda
>
> 
> Interim Moderator
> (Soon to be) Assistant Professor
> Department of Mathematics
> Quinnipiac University
> Hamden, CT 06518
> 
>
> --
> 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 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 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.
>


-- 

*Dr. Hugo A. Benítez*
Departamento de Recursos Ambientales
Facultad de Ciencias Agronómicas
Universidad de Tarapacá

Research Associate, University of Cambridge Museum of Zoology
External Researcher Faculty of Agriculture, University of Zagreb

website: http://www.morphoshape.com <http://www.hugoabenitez.com>
workphone: +56582386136

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RE: [MORPHMET] Morphmet in the Future

2019-07-01 Thread F. James Rohlf
That is an interesting suggestion. Whatever we do next it should not depend on 
any single individual. A problem is that we do not have a morphometrics society 
or an editor of a journal that could take ownership of morphmet. 

 

Jim

_ _ _ _ _ _ _ _ _

F. James Rohlf, Distinguished Prof. Emeritus



Depts. of Anthropology and of Ecology & Evolution

 

 

From: Murat Maga  
Sent: Monday, July 1, 2019 3:03 AM
To: K. James Soda ; MORPHMET 
Subject: RE: [MORPHMET] Morphmet in the Future

 

Dear Morphmet community,

 

Couple weeks prior to his sudden demise, I suggested Dennis to consider moving 
the morphmet at some point to a modern forum platform that support markups, 
code formatting and inline images. 

 

You can check out https://discourse.slicer.org to see one in action. The main 
benefit that I see is the potential for a more community build up and 
engagement. For people who prefer to receive messages as emails (myself 
included), they can configure their accounts to subscribe to messages.

 

Discourse is open-source and free to install and to use on ones own servers.  
There are various hosted options for a small fee too, 
https://www.discourse.org/pricing. 

 

It is sad having to talk about changes so soon after Dennis’s passing, but I 
thought it is an appropriate discussion to have.

 

M 

 

 

From: K. James Soda mailto:k.jamess...@gmail.com> > 
Sent: Saturday, June 29, 2019 9:10 PM
To: MORPHMET mailto:morphmet@morphometrics.org> >
Subject: [MORPHMET] Morphmet in the Future

 

Dear Fellow Morphometricians,


I want to give a quick comment about the future of morphmet after Dennis's 
passing so that any necessary changes will not come as a surprise. Please rest 
assure that it is not a question of whether morphmet will continue but rather 
if any different procedures will be required to make or view posts. Right now, 
morphmet is linked to morphometrics.org <http://morphometrics.org> , which is a 
domain that belonged to Dennis himself. As a result, it is possible that, at 
some point in the future, morphmet may temporarily go down if the 
morphmetrics.org <http://morphmetrics.org>  domain becomes unavailable.

What does this mean for you as a member? Right now, very little. You can 
continue to post to morphmet and new members can join morphmet without 
interruption. If in the future, this ceases to be the case, you will receive an 
invitation to a near identical Google group that will function in the same 
manner as morphmet has operated since the 2014 transition. Invitations will 
likely be distributed over the course of two to three days. The invitation 
email will include instructions on any changes to the submission process, which 
will likely only include a new email address for making posts and a new web 
address for the forum.

If you have any questions or concerns, please contact me either on or off of 
the list (k.jamess...@gmail.com <mailto:k.jamess...@gmail.com> ).

Best regards,

James Soda


Interim Moderator
(Soon to be) Assistant Professor
Department of Mathematics
Quinnipiac University
Hamden, CT 06518


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--- 
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to morphmet+unsubscr...@morphometrics.org 
<mailto:morphmet+unsubscr...@morphometrics.org> .

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<mailto:morphmet+unsubscr...@morphometrics.org> .

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--- 
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RE: [MORPHMET] Morphmet in the Future

2019-07-01 Thread Murat Maga
Dear Morphmet community,

Couple weeks prior to his sudden demise, I suggested Dennis to consider moving 
the morphmet at some point to a modern forum platform that support markups, 
code formatting and inline images.

You can check out https://discourse.slicer.org to see one in action. The main 
benefit that I see is the potential for a more community build up and 
engagement. For people who prefer to receive messages as emails (myself 
included), they can configure their accounts to subscribe to messages.

Discourse is open-source and free to install and to use on ones own servers.  
There are various hosted options for a small fee too, 
https://www.discourse.org/pricing.

It is sad having to talk about changes so soon after Dennis’s passing, but I 
thought it is an appropriate discussion to have.
M


From: K. James Soda 
Sent: Saturday, June 29, 2019 9:10 PM
To: MORPHMET 
Subject: [MORPHMET] Morphmet in the Future

Dear Fellow Morphometricians,

I want to give a quick comment about the future of morphmet after Dennis's 
passing so that any necessary changes will not come as a surprise. Please rest 
assure that it is not a question of whether morphmet will continue but rather 
if any different procedures will be required to make or view posts. Right now, 
morphmet is linked to morphometrics.org<http://morphometrics.org>, which is a 
domain that belonged to Dennis himself. As a result, it is possible that, at 
some point in the future, morphmet may temporarily go down if the 
morphmetrics.org<http://morphmetrics.org> domain becomes unavailable.

What does this mean for you as a member? Right now, very little. You can 
continue to post to morphmet and new members can join morphmet without 
interruption. If in the future, this ceases to be the case, you will receive an 
invitation to a near identical Google group that will function in the same 
manner as morphmet has operated since the 2014 transition. Invitations will 
likely be distributed over the course of two to three days. The invitation 
email will include instructions on any changes to the submission process, which 
will likely only include a new email address for making posts and a new web 
address for the forum.

If you have any questions or concerns, please contact me either on or off of 
the list (k.jamess...@gmail.com<mailto:k.jamess...@gmail.com>).

Best regards,

James Soda


Interim Moderator
(Soon to be) Assistant Professor
Department of Mathematics
Quinnipiac University
Hamden, CT 06518
####
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to 
morphmet+unsubscr...@morphometrics.org<mailto:morphmet+unsubscr...@morphometrics.org>.

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[MORPHMET] New article using Geometric Morphometrics as tools to assess aquatic contamination

2019-06-30 Thread Victor Hugo Garcia Merchan
Hello everyone

This is a new contribution from our research group on Evolution, Ecology
and Conservation (EECO) at de University of Quindío (Colombia):
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210348

I hope it's of interest to you.

If anything matters... everything matters.

Víctor Hugo García Merchán M.Sc, Ph.D
Associate Professor - Evolutionary genetics
Group of Evolution, Ecology and Conservation (EECO)
Universidad del Quindío (UQ)
Carrera 15 Calle 12 Norte.
630004 Armenia, Quindío (Colombia)

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[MORPHMET]

2019-06-30 Thread Tarek Ismail
Dear MORPHMET

I would like to know should centroid size correlates with measued
length or width? Or sometimes they uncorrelated.  Also, does number of
landmarks has any roles in this correlation?

Thanks in Advance

-- 
*Ass. Pro. Tarek Gad El-Kareem Ismail*

Invertebrate ZoologyZoology Dept.Faculty of ScienceSohag UniversitySohag,
P.O.Box 82524Egypt

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[MORPHMET] Morphmet in the Future

2019-06-29 Thread K. James Soda
Dear Fellow Morphometricians,

I want to give a quick comment about the future of morphmet after Dennis's
passing so that any necessary changes will not come as a surprise. Please
rest assure that it is not a question of whether morphmet will continue but
rather if any different procedures will be required to make or view posts.
Right now, morphmet is linked to morphometrics.org, which is a domain that
belonged to Dennis himself. As a result, it is possible that, at some point
in the future, morphmet may temporarily go down if the morphmetrics.org
domain becomes unavailable.

What does this mean for you as a member? Right now, very little. You can
continue to post to morphmet and new members can join morphmet without
interruption. If in the future, this ceases to be the case, you will
receive an invitation to a near identical Google group that will function
in the same manner as morphmet has operated since the 2014 transition.
Invitations will likely be distributed over the course of two to three
days. The invitation email will include instructions on any changes to the
submission process, which will likely only include a new email address for
making posts and a new web address for the forum.

If you have any questions or concerns, please contact me either on or off
of the list (k.jamess...@gmail.com).

Best regards,

James Soda


Interim Moderator
(Soon to be) Assistant Professor
Department of Mathematics
Quinnipiac University
Hamden, CT 06518


-- 
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--- 
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to morphmet+unsubscr...@morphometrics.org.


Re: [MORPHMET] Zooming when defining semilandmarks (sliders file) in tpsUtil

2019-06-25 Thread Ceci/Cali
Hi Michael, additionally, if you need to set very many semilandmarks, you
might find it faster to do it manually, by editing the sliders (.nts) file
using any text editor (if you open the file with a text editor you'll see
its structure is quite simple).
Hope this helps!
Cecilia


On Tue, Jun 25, 2019 at 2:39 PM Michael Young 
wrote:

> Hi, i'm very new to all this and I'm usually hesitant to ask remedial
> questions, this one is a doozy but I'm stuck!
>
> Using TpsUtil 1.78 through Wine Bottler (Windows emulator) on macOS.
>
>
> I got to the "make sliders file" stage & was thwarted by lack of zoom. I
> have some areas with high detail that have many landmarks close together,
> so I just can't manage to connect them correctly without being able to zoom
> in. Density is too high.
>
> Is this a limitation of the program or am I missing something simple?
>
>
>
> --
> 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.
>

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Re: [MORPHMET] Zooming when defining semilandmarks (sliders file) in tpsUtil

2019-06-25 Thread Ingrid Grueso
Hi Michael,

The only thing you need to do is to make your window larger, then the
landmarks' configuration gets bigger with it, so you can see them better.

I hope this helps! Best!

Ingrid Grueso



El martes, 25 de junio de 2019, Michael Young 
escribió:

> Hi, i'm very new to all this and I'm usually hesitant to ask remedial
> questions, this one is a doozy but I'm stuck!
>
> Using TpsUtil 1.78 through Wine Bottler (Windows emulator) on macOS.
>
>
> I got to the "make sliders file" stage & was thwarted by lack of zoom. I
> have some areas with high detail that have many landmarks close together,
> so I just can't manage to connect them correctly without being able to zoom
> in. Density is too high.
>
> Is this a limitation of the program or am I missing something simple?
>
>
>
> --
> 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.
>

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[MORPHMET] Zooming when defining semilandmarks (sliders file) in tpsUtil

2019-06-25 Thread Michael Young
Hi, i'm very new to all this and I'm usually hesitant to ask remedial 
questions, this one is a doozy but I'm stuck!

Using TpsUtil 1.78 through Wine Bottler (Windows emulator) on macOS.


I got to the "make sliders file" stage & was thwarted by lack of zoom. I have 
some areas with high detail that have many landmarks close together, so I just 
can't manage to connect them correctly without being able to zoom in. Density 
is too high. 

Is this a limitation of the program or am I missing something simple?



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Re: [MORPHMET] Dennis Slice

2019-06-22 Thread Marcia Ramírez
Dear all

What sad news!
Dr. Slice's research is fundamental in Geometric Morphometrics.
On the other hand, I am very moved by the expressions of affection and
admiration towards him that you have all expressed in your emails. Thank
you very much for sharing it with those who did not have the opportunity to
meet him in person.

My deepest sympathies to his family and friends.

Marcia Ramírez



El mié., 19 jun. 2019 a las 10:50, Ian Dworkin ()
escribió:

> Dear All,
>
>  Like everyone else, I was saddened by the loss of Dennis, far too soon.
> We only got to interact a few times in person, but even online he was (like
> the vast majority of our community) was helpful to those coming into
> morphometrics. I am wondering if those who knew him best (in terms of the
> morphometrics community) have any idea of whether we should/could set up
> some sort of fund in his honour? Maybe FSU is already considering this?
>
>
> Ian
>
> --
> 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.
>

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Re: [MORPHMET] Dennis Slice

2019-06-19 Thread Ian Dworkin
Dear All,

 Like everyone else, I was saddened by the loss of Dennis, far too soon. We
only got to interact a few times in person, but even online he was (like
the vast majority of our community) was helpful to those coming into
morphometrics. I am wondering if those who knew him best (in terms of the
morphometrics community) have any idea of whether we should/could set up
some sort of fund in his honour? Maybe FSU is already considering this?


Ian

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Re: [MORPHMET] Dennis Slice

2019-06-18 Thread Paolo Piras
Dear friends,
I want to join all of you in expressing my condolences for Dennis loss.
My grief goes to his family, friends and students.
I knew him in Isernia about ten years ago and I had the chance to speak
with him not only about morphometrics or science in general but also about
a great variety of arguments. I remember a very nice person, kind and
polite in any situation. As well as sharp and clever.
Our community will miss him so much...
Paolo


Il giorno mar 18 giu 2019 alle ore 00:00 Una Vidarsdottir <
una.vidarsdot...@gmail.com> ha scritto:

> Like so many I have struggled with words. I posted some on my Facebook and
> copy them here below. Oh I miss him.
>
>  I first met Dennis at the beginning of my PhD work in 1995. 24 years. We
> spent many an evening debating how best to do a certain analysis or how to
> test a certain theory. I remember a night... probably in 2006, when we
> walked the streets of Vienna through a long summernight talking the entire
> time.  Dennis was not a big ego although his mind, work and ideas might
> have merited it. In his own quiet and sometimes self-deprecating way, he
> inspired and influenced the work of the morphometrics community as a whole.
> Dennis believed his role as an academic lay in supporting this community
> to produce better and better science, from lending helpful pointers to
> fledgling researchers taking their first cautious steps in the field, to
> being a fountain of knowledge and ideas to those of us who have been
> involved much longer.
> First and foremost Dennis was my very dear friend, soul mate and entrusted
> colleague. I will miss him very much.
> (Some photos from another very warm evening in Vienna in 2008)
>
> On Mon, 17 Jun 2019, 18:27 K. James Soda,  wrote:
>
>> Sent on behalf of Dean Adams:
>>
>>
>> Colleagues,
>>
>>
>>
>> Like others I have spent the weekend grieving the passing of Dennis, and
>> trying to put my feelings of loss into words. Alas I cannot.
>>
>>
>>
>> I’ve known Dennis for 25 years, since we overlapped in Jim’s lab in the
>> 1990s. He was a constant fixture in our field, and his passing has left a
>> great hole. I will miss his positive attitude, his whit, his endless and
>> entertaining stories, and his life lessons. But mostly I will miss having
>> him in our community.
>>
>>
>>
>> I will miss you, Dennis.
>>
>>
>>
>> Dean
>>
>>
>>
>>
>>
>>
>>
>> Dr. Dean C. Adams
>>
>> Director of Graduate Education, EEB Program
>>
>> Professor
>>
>> Department of Ecology, Evolution, and Organismal Biology
>>
>> Iowa State University
>>
>> https://www.eeob.iastate.edu/faculty/adams/
>>
>> phone: 515-294-3834
>>
>> On Mon, Jun 17, 2019 at 3:53 AM K. James Soda 
>> wrote:
>>
>>> Hello Everyone,
>>>
>>> Since Friday afternoon, I have struggled to put into words the kind of
>>> adviser Dennis Slice was to his students to supplement the elegant
>>> testimonies to his abilities as a researcher, but words fail me. I do not
>>> know how I can properly portray the care and compassion that he afforded
>>> us. Despite his many accomplishments, he remained humble and never spoke
>>> down to us. He listened to our concerns with compassion and our ideas with
>>> an open mind. He treated us like family, and I know that I am not alone in
>>> saying that we felt the same way about him. Our weekly lab meetings and
>>> monthly lab dinners form some of my happiest memories of graduate school
>>> because he infused humor into our every interaction. He taught me so many
>>> things, both professionally (like people are more likely to read emails
>>> that are broken into smaller blocks) and personally (like a gentleman
>>> should always carry a handkerchief in case a lady cries). I can only hope
>>> that I as a professor will be able to foster curiosity and confidence in my
>>> students half as well as Dennis did in me.
>>>
>>> I deeply miss Dennis, and I suspect I always will.
>>>
>>> Thank you for your time,
>>>
>>> James Soda
>>>
>>> On Mon, Jun 17, 2019 at 3:19 AM Carmelo Fruciano 
>>> wrote:
>>>
>>>> This is extremely sad news. He has made enormous contributions to our
>>>> field and his figure will be greatly missed. I have had limited
>>>> interactions with him but, based on the interactions I had the
>>>> privilege
>>>> to have, I also concur with Mauro Cavalcanti that he had a ni

Re: [MORPHMET] Help with placePatch

2019-06-18 Thread Pablo Fisichella
t; for specimen 1 failed with: Error in vcgImport(tmp.name): file
> E:/Documents/hominoid/A860ho, USNM083262hy, USNM084655pan, USNM143590po,
> USNM143593po, USNM174699pan, USNM174701pan, USNM174702pan, USNM239883go,
> USNM260582goA860ho.landmarkAscii.ply does not exist
>
> Evidently the function can’t find my .ply models. As I supposed this issue
> is related to the dimnames of my array (dimnames(data)[[3]]).
>
> I followed a suggestion that Antonio Profico did to another researcher in
> the past by using the function str_sub from the package stringr to try to
> delete the extension .landmarkAscii from my array dimnames but this time
> does not work and I continue obtaining the same errors
>
> I realized that the dimnames of my array changed. For instance the
> original .ply model name is USNM260582go but the name of the same model in
> the array with NAs is USNM260582go.landmarkAscii. This is the problem
> (i.e., the extension .landmarkAscii) but since the str_sub does not work I
> used several more functions from the package stringr including:
>
> dimnames(data)[[3]]=str_remove(dimnames(data)[[3]],".landmarkAscii")
>
>
> dimnames(data)[[3]]=str_replace(dimnames(data)[[3]],".landmarkAscii",".ply")
>
> But I got the same errors
>
> I have tried additional tricks like changing the dimnames (including only
> numbers) by using this function data2=array(data, dim=c(19,3,10)) and
> changing the names of my .ply models but I got always the same error
>
> Obviously the error is related with my array dimnames but I don’t know how
> I can solve this, thus I´m looking for advice
>
> Thanks in advance for any help, advice or suggestion
>
> best wishes
>
> Pablo
>
>
>
> <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
>  Libre
> de virus. www.avast.com
> <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
>
> --
> 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.
> 
>
>
>

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Re: [MORPHMET] Help with placePatch

2019-06-17 Thread Ryan Felice
Hi Pablo, 

A small change should fix it. Remove the “prefix” argument. Whatever you set 
“prefix” to is pasted in front of each specimen name. Notice how the error says 
there is no such file "E:/Documents/hominoid/A860ho, USNM083262hy, 
USNM084655pan, USNM143590po, USNM143593po, USNM174699pan, USNM174701pan, 
USNM174702pan, USNM239883go, USNM260582goA860ho.landmarkAscii.ply”. 

This is your path ("E:/Documents/hominoid/“), then your “prefix”, then the name 
of the first specimen in “data”, which is “A860ho.landmarkAscii”, then the file 
extension, “.ply".
Try it like this:

dimnames(data)[[3]]=str_remove(dimnames(data)[[3]],".landmarkAscii”)

patched.specimens <- 
placePatch(atlas=atlas,dat.array=data,path="E:/Documents/hominoid",prefix ='', 
fileext=".ply"))

If the dimnames(data)[[3]] perfectly match the filenames of your ply files 
(without the “.ply”), it should work.

Best
Ryan


Ryan N. Felice, Ph.D
Lecturer in Human Anatomy
University College London
Department of Cell and Developmental Biology
Anatomy Building Room G23
rnfelice.com
ryanfel...@gmail.com

> On Jun 17, 2019, at 8:38 PM, Pablo Fisichella  
> wrote:
> 
> Dear All,
> 
> I’m using the function placePatch in Morpho to transfer semilandmarks from a 
> template to all specimens in my sample (n=10). Unfortunately I have failed to 
> run successfully such function. I have read some discussions here in the past 
> but some solutions that apparently functioned for other persons do not seem 
> to work in my case. Thus maybe somebody can help me with an idea or advice.
> 
> I obtained my landmarks and semilandmarks using Amira
> 
> I created an atlas (see attached pictures) which looks fine. I obtained 19 
> landmarks and 60 semilandmarks for the template.
> 
> I created a k x 3 x n array using the function read.amira.dir from the 
> Arothron package (data=read.amira.dir("E:/Documents/landmarks","auto") my 
> array is 19*3*10
> 
> Finally I used the placePatch function as follows:
> 
> placePatch(atlas=atlas,dat.array=data,path="E:/Documents/hominoid",prefix = 
> c(("A860ho, USNM083262hy, USNM084655pan, USNM143590po, USNM143593po, 
> USNM174699pan, USNM174701pan, USNM174702pan, USNM239883go, USNM260582go"), 
> fileext=".ply"))
> 
> I obtained a pxkxn array with only missing values -NAs- and I got 10 errors 
> like this for each one of my .ply models:
> 
> In place.patch(dat.array, path, atlas.mesh = atlas$mesh,  ... :matching for 
> specimen 1 failed with: Error in vcgImport(tmp.name <http://tmp.name/>): file 
> E:/Documents/hominoid/A860ho, USNM083262hy, USNM084655pan, USNM143590po, 
> USNM143593po, USNM174699pan, USNM174701pan, USNM174702pan, USNM239883go, 
> USNM260582goA860ho.landmarkAscii.ply does not exist
> 
> Evidently the function can’t find my .ply models. As I supposed this issue is 
> related to the dimnames of my array (dimnames(data)[[3]]).
> 
> I followed a suggestion that Antonio Profico did to another researcher in the 
> past by using the function str_sub from the package stringr to try to delete 
> the extension .landmarkAscii from my array dimnames but this time does not 
> work and I continue obtaining the same errors
> 
> I realized that the dimnames of my array changed. For instance the original 
> .ply model name is USNM260582go but the name of the same model in the array 
> with NAs is USNM260582go.landmarkAscii. This is the problem (i.e., the 
> extension .landmarkAscii) but since the str_sub does not work I used several 
> more functions from the package stringr including:
> 
> dimnames(data)[[3]]=str_remove(dimnames(data)[[3]],".landmarkAscii")
> 
> dimnames(data)[[3]]=str_replace(dimnames(data)[[3]],".landmarkAscii",".ply")
> 
> But I got the same errors
> 
> I have tried additional tricks like changing the dimnames (including only 
> numbers) by using this function data2=array(data, dim=c(19,3,10)) and 
> changing the names of my .ply models but I got always the same error
> 
> Obviously the error is related with my array dimnames but I don’t know how I 
> can solve this, thus I´m looking for advice
> 
> Thanks in advance for any help, advice or suggestion
> 
> best wishes
> 
> Pablo
> 
>  
> 
>  
> <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
> Libre de virus. www.avast.com 
> <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
>  
> 
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org 
> <http://www.morphometrics.org/>
> --- 
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to morphmet+unsubscr...@morphometrics.org 
> <mailto:morphmet+unsubscr...@morphometrics.org>.
> 

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Re: [MORPHMET] Dennis Slice

2019-06-17 Thread K. James Soda
Sent on behalf of Dean Adams:


Colleagues,



Like others I have spent the weekend grieving the passing of Dennis, and
trying to put my feelings of loss into words. Alas I cannot.



I’ve known Dennis for 25 years, since we overlapped in Jim’s lab in the
1990s. He was a constant fixture in our field, and his passing has left a
great hole. I will miss his positive attitude, his whit, his endless and
entertaining stories, and his life lessons. But mostly I will miss having
him in our community.



I will miss you, Dennis.



Dean







Dr. Dean C. Adams

Director of Graduate Education, EEB Program

Professor

Department of Ecology, Evolution, and Organismal Biology

Iowa State University

https://www.eeob.iastate.edu/faculty/adams/

phone: 515-294-3834

On Mon, Jun 17, 2019 at 3:53 AM K. James Soda  wrote:

> Hello Everyone,
>
> Since Friday afternoon, I have struggled to put into words the kind of
> adviser Dennis Slice was to his students to supplement the elegant
> testimonies to his abilities as a researcher, but words fail me. I do not
> know how I can properly portray the care and compassion that he afforded
> us. Despite his many accomplishments, he remained humble and never spoke
> down to us. He listened to our concerns with compassion and our ideas with
> an open mind. He treated us like family, and I know that I am not alone in
> saying that we felt the same way about him. Our weekly lab meetings and
> monthly lab dinners form some of my happiest memories of graduate school
> because he infused humor into our every interaction. He taught me so many
> things, both professionally (like people are more likely to read emails
> that are broken into smaller blocks) and personally (like a gentleman
> should always carry a handkerchief in case a lady cries). I can only hope
> that I as a professor will be able to foster curiosity and confidence in my
> students half as well as Dennis did in me.
>
> I deeply miss Dennis, and I suspect I always will.
>
> Thank you for your time,
>
> James Soda
>
> On Mon, Jun 17, 2019 at 3:19 AM Carmelo Fruciano 
> wrote:
>
>> This is extremely sad news. He has made enormous contributions to our
>> field and his figure will be greatly missed. I have had limited
>> interactions with him but, based on the interactions I had the privilege
>> to have, I also concur with Mauro Cavalcanti that he had a nice sense of
>> humor.
>> My most heartfelt condolences to his family, his friends, and all our
>> field.
>> Carmelo
>>
>>
>> --
>>
>>
>> ==
>> Carmelo Fruciano
>> Institute of Biology
>> Ecole Normale Superieure - Paris
>> CNRS
>> http://www.fruciano.it/research/
>>
>>
>> On 15/06/2019 16:55, mitte...@univie.ac.at wrote:
>> >   Dear subscribers to morphmet,
>> >
>> >   With the deepest grief we must inform you of the sudden
>> >   death on June 13 of Prof. Dennis E. Slice,
>> >   holder of the fourth Rohlf Award for Excellence in Morphometrics
>> >   and tireless founder and moderator of this newsgroup,
>> >   who suffered a heart attack in his home town of
>> >   Tallahassee, Florida. Morphometrics will not be the same
>> >   without him.
>> >
>> >  Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>> >Benedikt Hallgrimsson, June 15, 2019
>> >
>> > --
>> > 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
>> > <mailto:morphmet+unsubscr...@morphometrics.org>.
>>
>> --
>> 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.
>>
>>

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Re: [MORPHMET] Dennis Slice

2019-06-17 Thread K. James Soda
Hello Everyone,

Since Friday afternoon, I have struggled to put into words the kind of
adviser Dennis Slice was to his students to supplement the elegant
testimonies to his abilities as a researcher, but words fail me. I do not
know how I can properly portray the care and compassion that he afforded
us. Despite his many accomplishments, he remained humble and never spoke
down to us. He listened to our concerns with compassion and our ideas with
an open mind. He treated us like family, and I know that I am not alone in
saying that we felt the same way about him. Our weekly lab meetings and
monthly lab dinners form some of my happiest memories of graduate school
because he infused humor into our every interaction. He taught me so many
things, both professionally (like people are more likely to read emails
that are broken into smaller blocks) and personally (like a gentleman
should always carry a handkerchief in case a lady cries). I can only hope
that I as a professor will be able to foster curiosity and confidence in my
students half as well as Dennis did in me.

I deeply miss Dennis, and I suspect I always will.

Thank you for your time,

James Soda

On Mon, Jun 17, 2019 at 3:19 AM Carmelo Fruciano 
wrote:

> This is extremely sad news. He has made enormous contributions to our
> field and his figure will be greatly missed. I have had limited
> interactions with him but, based on the interactions I had the privilege
> to have, I also concur with Mauro Cavalcanti that he had a nice sense of
> humor.
> My most heartfelt condolences to his family, his friends, and all our
> field.
> Carmelo
>
>
> --
>
>
> ==
> Carmelo Fruciano
> Institute of Biology
> Ecole Normale Superieure - Paris
> CNRS
> http://www.fruciano.it/research/
>
>
> On 15/06/2019 16:55, mitte...@univie.ac.at wrote:
> >   Dear subscribers to morphmet,
> >
> >   With the deepest grief we must inform you of the sudden
> >   death on June 13 of Prof. Dennis E. Slice,
> >   holder of the fourth Rohlf Award for Excellence in Morphometrics
> >   and tireless founder and moderator of this newsgroup,
> >   who suffered a heart attack in his home town of
> >   Tallahassee, Florida. Morphometrics will not be the same
> >   without him.
> >
> >  Jim Rohlf, Fred Bookstein, Paul O'Higgins,
> >Benedikt Hallgrimsson, June 15, 2019
> >
> > --
> > 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
> > <mailto:morphmet+unsubscr...@morphometrics.org>.
>
> --
> 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.
>
>

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--- 
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Re: [MORPHMET] Dennis Slice

2019-06-17 Thread Carmelo Fruciano
This is extremely sad news. He has made enormous contributions to our 
field and his figure will be greatly missed. I have had limited 
interactions with him but, based on the interactions I had the privilege 
to have, I also concur with Mauro Cavalcanti that he had a nice sense of 
humor.

My most heartfelt condolences to his family, his friends, and all our field.
Carmelo


--


==
Carmelo Fruciano
Institute of Biology
Ecole Normale Superieure - Paris
CNRS
http://www.fruciano.it/research/


On 15/06/2019 16:55, mitte...@univie.ac.at wrote:

      Dear subscribers to morphmet,

      With the deepest grief we must inform you of the sudden
  death on June 13 of Prof. Dennis E. Slice,
  holder of the fourth Rohlf Award for Excellence in Morphometrics
  and tireless founder and moderator of this newsgroup,
  who suffered a heart attack in his home town of
  Tallahassee, Florida. Morphometrics will not be the same
  without him.

 Jim Rohlf, Fred Bookstein, Paul O'Higgins,
   Benedikt Hallgrimsson, June 15, 2019

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Re: [MORPHMET] Dennis Slice

2019-06-16 Thread Mantu Dubey
Shocking news. He was really very helping person. Infact, he suggested me
to join the morphometrics group. He was handling editor of one of my
publication. This is a big loss to the field of morphometrics. Rest In
Peace Prof. Slice...

On Monday, June 17, 2019, mahendiran mylswamy  wrote:

>
> -- Forwarded message -
> From:mahendiran mylswamy 
> Date: Sun, 16 Jun 2019, 09:55
> Subject: Re: [MORPHMET] Dennis Slice
> To: R. Geeta 
> Cc: mitte...@univie.ac.at , <
> morphmet@morphometrics.org>
>
>
> Unfortunate and deeply disturbed to hear the sudden demise of Prof.
> Slice.  May his soul rest in peace.
>  I have been  one of his favourite Facebook follower and all his postings
> were very interesting and informative. Recently he had discussed with us
> about AI on Shape analysis and Colour perception in human beings were
> outstanding  ones and remains evergreen in our memories.
> My condolences to his family members and  my sincere prayers MAY HIS SOUL
> REST IN PEACE.
>
>
>
> On Sun, 16 Jun 2019, 02:04 Geeta R,  wrote:
>
>> This is shocking and unbelievable news...very saddened to hear this. My
>> deepest condolences to morphometric and other friends and family.
>> R. Geeta
>> A1/7/1 (52), 22nd Cross Street, Besant Nagar, Chennai
>> <https://www.google.com/maps/search/52),+22nd+Cross+Street,+Besant+Nagar,+Chennai?entry=gmail=g>
>> 600 090, India
>> Retired Professor, Department of Botany, University of Delhi, Delhi,
>> India; Emerita, Ecology & Evolution, SUNY
>> <http://life.bio.sunysb.edu/ee/emeritus.html>, Stony Brook, NY, USA
>> Editor, Phytomorphology <http://www.ispm.co.in/phytomorphology.html>,
>> India; Editorial Board, Journal of BioSciences
>> <https://www.ias.ac.in/Journals/Journal_of_Biosciences/Editorial_Board>,
>> India; Editorial Board, Journal of Genetics
>> <https://www.ias.ac.in/Journals/Journal_of_Genetics/Editorial_Board>,
>> India; Editorial Board, American Journal of Botany
>> <https://onlinelibrary.wiley.com/page/journal/15372197/homepage/EditorialBoard.html>,
>> USA
>>
>>
>> On Sat, 15 Jun 2019 at 20:25, mitte...@univie.ac.at <
>> mitte...@univie.ac.at> wrote:
>>
>>>  Dear subscribers to morphmet,
>>>
>>>  With the deepest grief we must inform you of the sudden
>>>  death on June 13 of Prof. Dennis E. Slice,
>>>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>>>  and tireless founder and moderator of this newsgroup,
>>>  who suffered a heart attack in his home town of
>>>  Tallahassee, Florida. Morphometrics will not be the same
>>>  without him.
>>>
>>>     Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>>>   Benedikt Hallgrimsson, June 15, 2019
>>>
>>> --
>>> 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 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 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.
>

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Fwd: [MORPHMET] Dennis Slice

2019-06-16 Thread mahendiran mylswamy
-- Forwarded message -
From:mahendiran mylswamy 
Date: Sun, 16 Jun 2019, 09:55
Subject: Re: [MORPHMET] Dennis Slice
To: R. Geeta 
Cc: mitte...@univie.ac.at , <
morphmet@morphometrics.org>


Unfortunate and deeply disturbed to hear the sudden demise of Prof. Slice.
May his soul rest in peace.
 I have been  one of his favourite Facebook follower and all his postings
were very interesting and informative. Recently he had discussed with us
about AI on Shape analysis and Colour perception in human beings were
outstanding  ones and remains evergreen in our memories.
My condolences to his family members and  my sincere prayers MAY HIS SOUL
REST IN PEACE.



On Sun, 16 Jun 2019, 02:04 Geeta R,  wrote:

> This is shocking and unbelievable news...very saddened to hear this. My
> deepest condolences to morphometric and other friends and family.
> R. Geeta
> A1/7/1 (52), 22nd Cross Street, Besant Nagar, Chennai 600 090, India
> Retired Professor, Department of Botany, University of Delhi, Delhi,
> India; Emerita, Ecology & Evolution, SUNY
> <http://life.bio.sunysb.edu/ee/emeritus.html>, Stony Brook, NY, USA
> Editor, Phytomorphology <http://www.ispm.co.in/phytomorphology.html>,
> India; Editorial Board, Journal of BioSciences
> <https://www.ias.ac.in/Journals/Journal_of_Biosciences/Editorial_Board>,
> India; Editorial Board, Journal of Genetics
> <https://www.ias.ac.in/Journals/Journal_of_Genetics/Editorial_Board>,
> India; Editorial Board, American Journal of Botany
> <https://onlinelibrary.wiley.com/page/journal/15372197/homepage/EditorialBoard.html>,
> USA
>
>
> On Sat, 15 Jun 2019 at 20:25, mitte...@univie.ac.at 
> wrote:
>
>>  Dear subscribers to morphmet,
>>
>>  With the deepest grief we must inform you of the sudden
>>  death on June 13 of Prof. Dennis E. Slice,
>>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>>  and tireless founder and moderator of this newsgroup,
>>  who suffered a heart attack in his home town of
>>  Tallahassee, Florida. Morphometrics will not be the same
>>  without him.
>>
>> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>>   Benedikt Hallgrimsson, June 15, 2019
>>
>> --
>> 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 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.
>

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[MORPHMET] Re: Dennis Slice

2019-06-16 Thread Aki Watanabe


Dear MORPHMET community,

 

I am still struggling to process this tragic news. Dennis was on my 
master’s thesis committee at Florida State University in 2010–2012. He was 
truly a great mentor who introduced me to the theory and practice of 
geometric morphometrics, which has shaped my research career in tremendous 
ways. Beyond his remarkable academic accomplishments, he was a warm, 
thoughtful, and brilliant person who always had his office door open for 
deep conversations about shape theory. I learned so much from him and 
deeply saddened by the fact that I am no longer able to discuss shape with 
him.

 

Couple things I’d like to share. When asked about what he studies, Dennis 
proudly said that he works on triangles, the most basic shape that can be 
described mathematically. He showed the beauty, elegance, and seemingly 
endless possibilities that the study of triangles can offer in his 
geometric morphometric course at FSU. As a student who had absolutely no 
background in programming, he also encouraged me to learn Python and R. One 
of my favorite quotes by him is: “If you need to do something more than 
twice, you should program it.” I tell this to many students who are 
beginning to learn coding.

 

Dennis’ passing will leave a giant hole in my heart as well as the 
morphometrics community. I feel enormously honored to have known him. For 
those who have not had the privilege of meeting Dennis, you can get a taste 
of his character watching his Rohlf Medal presentation: 
https://www.youtube.com/watch?v=DqxFfXDyFC4

 

Sincerely,

Aki

On Saturday, June 15, 2019 at 10:55:45 AM UTC-4, mitt...@univie.ac.at wrote:
>
>  Dear subscribers to morphmet,
>
>  With the deepest grief we must inform you of the sudden
>  death on June 13 of Prof. Dennis E. Slice,
>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>  and tireless founder and moderator of this newsgroup,
>  who suffered a heart attack in his home town of
>  Tallahassee, Florida. Morphometrics will not be the same
>  without him.
>
> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>   Benedikt Hallgrimsson, June 15, 2019
>

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Re: [MORPHMET] Dennis Slice

2019-06-16 Thread Sandra Milena Ospina Garcés
I'm really sorry. My condolences to all morphometricians.

El sáb., 15 de junio de 2019 9:55, mitte...@univie.ac.at <
mitte...@univie.ac.at> escribió:

>  Dear subscribers to morphmet,
>
>  With the deepest grief we must inform you of the sudden
>  death on June 13 of Prof. Dennis E. Slice,
>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>  and tireless founder and moderator of this newsgroup,
>  who suffered a heart attack in his home town of
>  Tallahassee, Florida. Morphometrics will not be the same
>  without him.
>
> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>   Benedikt Hallgrimsson, June 15, 2019
>
> --
> 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.
>

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[MORPHMET] Dennis Slice’s obituary

2019-06-16 Thread Sonja Windhager
Dear all,

Below please find the link to Dennis Slice’s obituary:
https://www.dignitymemorial.com/obituaries/tallahassee-fl/dennis-slice-8744377 
<https://www.dignitymemorial.com/obituaries/tallahassee-fl/dennis-slice-8744377>
 

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[MORPHMET] Dennis Slice

2019-06-16 Thread Sonja Windhager
We of the University of Vienna morphometrics group
are deeply saddened by the sudden death of Dennis Slice.
A guest professor here for more than fifteen years,
he was a mentor to many of our students; he was a colleague, 
a teller of uproarious tales, and altogether a very good friend.
In short, he was unique. We will miss him in all these ways.

Fred Bookstein, Cinzia Fornai, Philipp Gunz, 
Philipp Mitteroecker, Simon Neubauer, Katrin Schaefer, 
Horst Seidler, Gerhard Weber, Sonja Windhager

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[MORPHMET] Tips for MicroScribe MX

2019-06-15 Thread pbover72
Hi,
I have a MicroScribe MX, which was bought about 10 years ago. I would like 
to get more precise tips for small bones, as the tips originally provided 
with the digitizer are those ones with a plastic ball at the end. Is there 
any way to get needle-like tips? Is there any provider I could contact?
Thanks in advance for your help.
Cheers
Pere

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[MORPHMET] Beginner in 3D GMM needs help. Relaxing and sliding commands in R

2019-06-15 Thread Aurélien Lowie
Hi everybody!

I just started to play with 3D GMM but I have some questions. Not sure I am 
doing the right things. 
I landmarked (anatomical+curves) the left side of six skulls and I would like 
to get my final matrix to do my analyses. I defined my landmarks and subsampled 
the landmarks on the curves. Then I patched the landmarks on all my specimens. 
So, for now, I have my 6 specimens with the landmarks at the right place on 
them. 

And here begin the troubles… I wanted to relax and slide the landmarks to 
minimize bending energy but I think the surfaces are too different because 
unless I use a stepsize of 0 (meaning that this command is useless I think) in 
relaxing and sliding commands, the landmarks do not fit the curves anymore.
 
#relaxLM(patched[,,i], rbind(atlas[["landmarks"]],atlas[["patch"]]), slidings, 
outlines = curv, surp = surface, sur.name = NULL, mesh = 
ply2mesh(paste("./ply/",meshlist[i],sep="")), tol = 1e-50, deselect = FALSE, 
inc.check = F, iterations = 50, fixRepro = TRUE, stepsize=0)

#slider3d(relaxedtemplate4, slidings, outlines = curv, surp = surface, sur.path 
= "./ply", sur.name = NULL, meshlist = paste("./ply/",meshlist,sep=""), ignore 
= NULL, sur.type = "ply", tol = 10e-50, deselect = FALSE, inc.check = FALSE, 
recursive = TRUE, iterations = 3, initproc = TRUE, pairedLM = 0, mc.cores = 4, 
fixRepro = TRUE, stepsize =0)

I tried to play with the tolerance and/or the bending=TRUE but nothing has 
changed. 

What could I change in these commands? Are these steps mandatory to analyse the 
shape? 

Any comment, advice and suggestion is more than welcome! 

Thanks a lot for your help.

Aurélien Lowie

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[MORPHMET] Help with Discriminant analysis on MorphoJ

2019-06-15 Thread Elisa von Groll
Hello. I have never posted here, but I searched about the problem that I am 
facing and I have not find a topic. So I am posting now.


I digitalized 4 LM and 160 semiLM (4 curves) with TPSDig to analyze the 
pronotum of six beetle species (>400 specimens) and transformed the semiLM in 
LM on TPSUtil. So I had 164 LM – I also did NOT aligned them - . I opened the 
file on MorphoJ and did PCA, CVA and discriminant analysis of the pairs. 
Everything went apparently ok. (→ I know that there are many problems because 
the exaggerated number of LM).
graphic: <https://www.ibb.co/ypcbGb8>

But now I know I had too many LM. So I deleted many of them on TPSUtil (I just 
took the TPS file of the 164 LM and deleted half of them, creating a new TPS 
file). Again, I did not aligned it. I did the same analysis on MorphoJ. The PCA 
and the CVA were ok, but the discriminant analysis did not work. I tried 
everything. 

graphic: <https://www.ibb.co/j5hQq59>
 

So I gave up and did the sliders of the 164 LM, even knowing it wouldn’t be 
good for the subsequent analysis. So I used the TPSUtil  and did the sliders, 
following the manual. It took some time but I could save the aligned and scaled 
aligned data from TPSRelw. But again something went wrong 

graphic: <https://www.ibb.co/X8WdkGb>

Does someone know what might be the problem?

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Re: [MORPHMET] Dennis Slice

2019-06-15 Thread Geeta R
This is shocking and unbelievable news...very saddened to hear this. My
deepest condolences to morphometric and other friends and family.
R. Geeta
A1/7/1 (52), 22nd Cross Street, Besant Nagar, Chennai 600 090, India
Retired Professor, Department of Botany, University of Delhi, Delhi, India;
Emerita, Ecology & Evolution, SUNY
<http://life.bio.sunysb.edu/ee/emeritus.html>, Stony Brook, NY, USA
Editor, Phytomorphology <http://www.ispm.co.in/phytomorphology.html>,
India; Editorial Board, Journal of BioSciences
<https://www.ias.ac.in/Journals/Journal_of_Biosciences/Editorial_Board>,
India; Editorial Board, Journal of Genetics
<https://www.ias.ac.in/Journals/Journal_of_Genetics/Editorial_Board>,
India; Editorial Board, American Journal of Botany
<https://onlinelibrary.wiley.com/page/journal/15372197/homepage/EditorialBoard.html>,
USA


On Sat, 15 Jun 2019 at 20:25, mitte...@univie.ac.at 
wrote:

>  Dear subscribers to morphmet,
>
>  With the deepest grief we must inform you of the sudden
>  death on June 13 of Prof. Dennis E. Slice,
>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>  and tireless founder and moderator of this newsgroup,
>  who suffered a heart attack in his home town of
>  Tallahassee, Florida. Morphometrics will not be the same
>  without him.
>
> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>   Benedikt Hallgrimsson, June 15, 2019
>
> --
> 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.
>

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Re: [MORPHMET] Dennis Slice

2019-06-15 Thread Mauro Cavalcanti
What a tragic loss! I will ever miss his superb contributions to
morphometrics, as well as his nice sense of humour.

Em sáb, 15 de jun de 2019 às 11:55, mitte...@univie.ac.at <
mitte...@univie.ac.at> escreveu:

>  Dear subscribers to morphmet,
>
>  With the deepest grief we must inform you of the sudden
>  death on June 13 of Prof. Dennis E. Slice,
>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>  and tireless founder and moderator of this newsgroup,
>  who suffered a heart attack in his home town of
>  Tallahassee, Florida. Morphometrics will not be the same
>  without him.
>
> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>   Benedikt Hallgrimsson, June 15, 2019
>
> --
> 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.
>


-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio
"Life is complex. It consists of real and imaginary parts."

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Re: [MORPHMET] Dennis Slice

2019-06-15 Thread Ariadne Schulz
I never had the pleasure of meeting him. I knew him only through his work.
But his work was exceptional. This is a great loss. Condolences to those
closest to him.

On Sat, Jun 15, 2019 at 3:55 PM mitte...@univie.ac.at 
wrote:

>  Dear subscribers to morphmet,
>
>  With the deepest grief we must inform you of the sudden
>  death on June 13 of Prof. Dennis E. Slice,
>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>  and tireless founder and moderator of this newsgroup,
>  who suffered a heart attack in his home town of
>  Tallahassee, Florida. Morphometrics will not be the same
>  without him.
>
> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>   Benedikt Hallgrimsson, June 15, 2019
>
> --
> 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.
>

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Re: [MORPHMET] Dennis Slice

2019-06-15 Thread Ann Ross
I’m in utter shock and disbelief...no words except for deep sorrow...

Ann H. Ross, Ph.D., D-ABFA


> On Jun 15, 2019, at 12:20 PM, Neha Sharma  wrote:
> 
> What a loss! My condolences to the family and friends.
> 
>> On Sat, 15 Jun 2019, 20:25 mitte...@univie.ac.at,  
>> wrote:
>>  Dear subscribers to morphmet,
>> 
>>  With the deepest grief we must inform you of the sudden
>>  death on June 13 of Prof. Dennis E. Slice,
>>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>>  and tireless founder and moderator of this newsgroup,
>>  who suffered a heart attack in his home town of
>>  Tallahassee, Florida. Morphometrics will not be the same
>>  without him.
>> 
>> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>>   Benedikt Hallgrimsson, June 15, 2019
>> -- 
>> 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 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.

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Re: [MORPHMET] Dennis Slice

2019-06-15 Thread Neha Sharma
What a loss! My condolences to the family and friends.

On Sat, 15 Jun 2019, 20:25 mitte...@univie.ac.at, 
wrote:

>  Dear subscribers to morphmet,
>
>  With the deepest grief we must inform you of the sudden
>  death on June 13 of Prof. Dennis E. Slice,
>  holder of the fourth Rohlf Award for Excellence in Morphometrics
>  and tireless founder and moderator of this newsgroup,
>  who suffered a heart attack in his home town of
>  Tallahassee, Florida. Morphometrics will not be the same
>  without him.
>
> Jim Rohlf, Fred Bookstein, Paul O'Higgins,
>   Benedikt Hallgrimsson, June 15, 2019
>
> --
> 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.
>

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Re: [MORPHMET] Dennis Slice

2019-06-15 Thread Cole, Theodore M.
What terrible news.  My sympathies to all his family, friends, colleagues, and 
students.

Get Outlook for Android<https://aka.ms/ghei36>




On Sat, Jun 15, 2019 at 9:55 AM -0500, "mitte...@univie.ac.at" 
mailto:mitte...@univie.ac.at>> wrote:

     Dear subscribers to morphmet,

 With the deepest grief we must inform you of the sudden
 death on June 13 of Prof. Dennis E. Slice,
 holder of the fourth Rohlf Award for Excellence in Morphometrics
 and tireless founder and moderator of this newsgroup,
 who suffered a heart attack in his home town of
 Tallahassee, Florida. Morphometrics will not be the same
 without him.

Jim Rohlf, Fred Bookstein, Paul O'Higgins,
  Benedikt Hallgrimsson, June 15, 2019

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morphmet+unsubscr...@morphometrics.org<mailto:morphmet+unsubscr...@morphometrics.org>.

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[MORPHMET] Dennis Slice

2019-06-15 Thread mitte...@univie.ac.at
 Dear subscribers to morphmet,

 With the deepest grief we must inform you of the sudden
 death on June 13 of Prof. Dennis E. Slice,
 holder of the fourth Rohlf Award for Excellence in Morphometrics
 and tireless founder and moderator of this newsgroup,
 who suffered a heart attack in his home town of
 Tallahassee, Florida. Morphometrics will not be the same
 without him.

Jim Rohlf, Fred Bookstein, Paul O'Higgins,
  Benedikt Hallgrimsson, June 15, 2019

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[MORPHMET] Re: 2019 CALL FOR NOMINATIONS: The Rohlf Medal for Excellence in Morphometrics

2019-06-13 Thread morphmet_moderator







*
   
  Rohlf Medal Nomination Deadline  
   
*
This is a reminder that nominations for the 2019 Rohlf Medal are due by 
July 15. 

Recipients must agree to accept the award in person on October 24th, 2019 
at Stony Brook University.

The nominations of those who are not awarded the medal this year will be 
automatically rolled over for consideration in 2021. Any such application 
may be updated as appropriate.

For more information, visit https://life.bio.sunysb.edu/ee/rohlf_medal/

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[MORPHMET] Living lizard photography protocol

2019-06-10 Thread carlo . meloro

Dear all,
I wonder if you are aware of any developed protocol to collect  
morphometric data on living lizard.
I will need to work on relatively small specimens (about 50 mm Snout  
Vent Length) and would like to capture the head in dorsal and lateral  
view (with digital SLR macro 60 mm). Any method to immobilise the  
animal without creating too many issues? Or perhaps using two cameras  
in a sort of stereophotogrammetry fashion way...there are ways of  
doing this but the system I need to work on needs to be portable and  
cannot calibrate it all the time.
Any references and/or practical advise on how to collect data on live  
trapped specimens will be greatly appreciated.

Thank you
Carlo


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[MORPHMET] Replicating the scores and Mahalanobis distance

2019-06-07 Thread 'Angelo Emmanuel Ho' via MORPHMET
To those who sent me messages for helping me in my paper, thank you very 
much. Hopefully I could still ask for more help from you with my following 
concerns:

1. I have the five canonical variates (CV) score and per row are the CV 
loadings of each shape configurations. There are, let's say 15 scores 
belonging to group 1, 20 to group 2, 18 to group 3, and 24 to group 4. How 
will I replicate (through an R code) these scores such that it will 
replicate into 1000 per group, so that per CV score, there are 4000 
loadings, 1000 each? 

2. In relation to 1, how will I get the Mahalanobis distance of each group? 
I will use the Mahalanobis distance for the minimum spanning tree and 
dendogram to compare the minimum spanning tree and dendogram of the 
original sample size?

Thank you very much. 

  

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[MORPHMET] An R code for full Procrustes mean shape by GPA

2019-06-05 Thread 'Angelo Emmanuel Ho' via MORPHMET
Hello! I would like to ask for help as I use the book of Dryden and Mardia, 
"Statistical Shape Analysis with Application in R"? I cannot find where in 
the book (or maybe I just overlooked), how did he plot the mean shapes in 
Figure 8.4. Thank you very much. 

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[MORPHMET] Re: Comment and advice on bgPCA

2019-06-05 Thread Ondřej Mikula
in-sample 
> classification success is a highly biased estimate of the out-of-sample 
> classification success; hence the need for cross-validation.
>
> No single method can do all these steps well. The choice of method and 
> also the choice of landmarks really depend on the biological question and 
> the prior knowledge or hypotheses. If discrimination or classification is 
> the primary aim, cross-validation is indispensable; an ordination analysis 
> is not sufficient, perhaps not even necessary. If the signal (morphological 
> difference) is known prior to the analysis, not many landmarks are 
> necessary. Without any prior expectation, a dense landmark set may be 
> necessary to explore shape variation. But this sets fundamental limits to 
> studies of discrimination and  classification; there is a kind of 
> "uncertainty principle": for a given sample size, you cannot observe 
> arbitrarily high spatial resolution (number of variables) and the exact 
> discrimination of groups (classification success) at the same time. 
>
> Best,
>
> Philipp M.
>

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[MORPHMET] Integrated Morphometrics Package Installer

2019-06-04 Thread 'Angelo Emmanuel Ho' via MORPHMET
Hello! As I do morphometrics study, I am looking for the Integrated 
Morphometrics Package software. However, I searched the very website but it 
is not working anymore and I do not know where to find. Hopefully I may 
request for anybody for a copy of this software. Your help is very much 
appreciated. Thank you very much. 

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Re: [MORPHMET] help with "classify" in RRPP

2019-06-04 Thread Diogo Borges Provete
Hi all,
let me take advantage of this discussion and quickly add one more question. 

I have a similar scenario, in which I want to test if a set of specimens 
from one species belong to a separate species ("good species" scenario) or 
one already included in the dataset ("junior synonym" scenario). 
My problem is that, differently from Nicole, I only have two species, so 
when I build the linear model done only with the putative senior synonym it 
surely crashes because I ended up with only one level of the factor. 

How can I deal with that?

Thank you in advance,
Diogo

Em terça-feira, 7 de maio de 2019 11:10:04 UTC-4, Mike Collyer escreveu:
>
> Nicole,
>
> I assume that your intention is to summarize a species probability from 
> the several probabilities of specimens, if data sets are combined?  (I 
> think you might have used “species” twice but meant “specimen" once, below).
>
> If so, there are two ways you could do this.  One would be as you 
> suggested, summarize the distribution of posterior probabilities for a 
> species (mean, median, quartiles, etc.).  The other would be to calculate 
> something akin to species means and use these as test data, based on the 
> coefficients calculated from training data.  It might require some thought 
> as to what the training data should be, as leave one out cross-validation 
> would not make much sense.  Calculating the posterior probability for a 
> species mean after using individual specimens to estimate the mean also 
> does not make sense.  However, a resampling procedure that arbitrarily 
> divides the specimens into training and testing groups, using the first to 
> estimate coefficients and the second to obtain a mean, could be used to 
> generate a confidence interval for the posterior classification 
> probabilities of a particular species to its and other species’s groups.
>
> The second approach would involve some scripting.  The first approach can 
> be done quickly with the by() and summary() functions, e.g.,
>
> by(my.posterior.probs, species, summary)
>
> Hope that helps!
> Mike
>
> On May 7, 2019, at 9:13 AM, Nicole Ibagón  > wrote:
>
> Dear all
> I'm working with five different datasets (lateral and dorsal view of the 
> skull and jaw) of a neotropical bat genus. My research question is if one 
> species (described with a single sample), is a synonym of one of the other 
> species of the genus. I used classify function of RRPP for this purpose, 
> and it solved my question generating one posterior probability for each 
> species of each dataset. However, I would like to know there is a way to 
> generate a single posterior probability for each species.
> Should I join all the datasets before doing the classification analysis? 
> Or should I average the posterior probabilities of all the datasets? Is 
> there a better way to do it?
> Thanks
>
> -- 
> Nicole Estefanía Ibagón Escobar
> PhD Candidate in Ecology  - UFV (Brazil) 
> BSc Marine Biologist  - Utadeo (Colombia)
> ResearchGate <https://www.researchgate.net/profile/Nicole_Ibagon>
> Curriculo CVLAC 
> <http://190.216.132.131:8081/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0001219782>
> Curriculo lattes 
> <http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4371000E6>
> http://evolutionlbe.wix.com/lbeufv
>
> < <<  
>
> -- 
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>
>
>

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[MORPHMET] Comment and advice on bgPCA

2019-05-28 Thread mitte...@univie.ac.at
 regressions, p>n 
is no problem. The challenge in this step is to judge whether the observed 
differences are scientifically relevant, which may (but often does not) 
include the assessment of statistical significance. An excess of variables 
over cases can challenge statistical significance testing (multivariate 
parametric tests require full rank data and n>>p; for shape coordinates 
this ALWAYS requires dimension reduction, even for three landmarks). 

Only if group means really differ, it makes sense to relate multivariate 
group mean differences by an ordination analysis. This requires an 
interpretable metric (a "distance" function such as Procrustes distance), 
which is itself challenging and can constrain the geometric structures that 
are interpretable (e.g., Mitteroecker & Huttegger 2009, Huttegger & 
Mitteroecker 2011). Technically, this step sets no limits to the number of 
variables, but for normally distributed variables the expected value of a 
Euclidean distance increases linearly with the square root of the number of 
variables (chi distribution). This is no problem per se, but for small 
signals and many variables, the summed noise in the many landmarks can 
dominate the small signal. Also, this leads to a somewhat paradoxical 
situation: even if for each variable the estimated sample average is close 
to the population mean, the Euclidean distance between the multivariate 
sample average and the multivariate population mean increases with p. This 
relationship is also the reason why bgPC scores show too much group 
separation if p is large: the more variables, the larger the distance 
between group means, even though the within-group variances stay the same 
(for two groups, the squared Mahalanobis distance for the bgPC is approx. 
2p/n). 
Perhaps more important than the _number_ of variables is the spatial 
distribution of landmarks on the organism. E.g., structures covered by many 
landmarks more strongly affect the multivariate distance than structures 
covered by less landmarks. Semilandmarks may or may not be helpful in this 
regard for a comprehensive coverage of organisms. 

Discrimination analysis (DA) aims at assessing the success of 
classification. Classification and discrimination require the estimation of 
variance for every linear combination of the variables and thus n>>p (in 
most multivariate settings, this implies prior variable reduction). 
Reliable DA also requires a cross-validation approach and cannot be 
inferred without bias from a standard ordination analysis: PCA tends to 
underestimate classification success (group separation), whereas bgPCA, and 
even more so CVA, tends to overestimate it. DA can be considered an 
exploratory approach, but it makes only sense if group means are known to 
differ.

Discriminant function analysis (DFA), and its extension to multiple groups 
(CVA), estimate linear combinations of the measured variables that 
_maximize_ group separation and, hence, classification success. This goes 
beyond the exploratory analysis of group differences and not necessarily 
needs to be combined with an ordination analysis. Classically, it is used 
to derive a simple linear combination of the variables for efficient 
classification. It is well known  for these methods that the within-sample 
classification success is a highly biased estimate of the out-of-sample 
classification success; hence the need for cross-validation.

No single method can do all these steps well. The choice of method and also 
the choice of landmarks really depend on the biological question and the 
prior knowledge or hypotheses. If discrimination or classification is the 
primary aim, cross-validation is indispensable; an ordination analysis is 
not sufficient, perhaps not even necessary. If the signal (morphological 
difference) is known prior to the analysis, not many landmarks are 
necessary. Without any prior expectation, a dense landmark set may be 
necessary to explore shape variation. But this sets fundamental limits to 
studies of discrimination and  classification; there is a kind of 
"uncertainty principle": for a given sample size, you cannot observe 
arbitrarily high spatial resolution (number of variables) and the exact 
discrimination of groups (classification success) at the same time. 

Best,

Philipp M.

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[MORPHMET] Transmitting Science course: Geometric Morphometrics and Phylogeny, Sep 9-13, Barcelona.

2019-05-27 Thread soledad . esteban

Dear colleagues,

 

Transmitting Science course "Geometric Morphometrics and Phylogeny" has opened 
registration.

 

Dates: September 9th-13th, 2019, Barcelona.

 

Instructor: Dr. Chris Klingenberg (University of Manchester, United Kingdom)

 

Place:  Capellades, Barcelona (Spain).

 

Registration and more info: 

https://www.transmittingscience.org/courses/geometric-morphometrics/geometric-morphometrics-phylogeny/

 

PROGRAM:

 

1. Phylogeny, trees and phylogenetic reasoning.

2. Brief review of geometric morphometrics (Procrustes fit, PCA, etc.).

3. Mapping traits onto phylogenies: squared-change parsimony.

4. Practice: making/editing Nexus files, mapping morphometric data onto the 
tree (Mesquite, MorphoJ).

5. Phylogenetic signal, morphometric traits and estimating phylogeny.

6. Comparative methods: independent contrasts.

7. Application in morphometrics: evolutionary allometry and size correction.

8. Practice: comparative methods (MorphoJ).

9. Application of comparative methods: morphological integration.

10. Multi-level analyses of integration: inferring evolutionary mechanisms.

11. Application of comparative methods: partial least squares (ecomorphology, 
etc.).

12. Practice: comparative methods (cont.).

13. Morphometrics, phylogenies and qualitative characters.

14. Disparity and diversification.

15. Presentations of group work.

 

 

Please feel free to distribute this information between your colleagues if you 
consider it appropriate.

 

With best regards




Sole

 



Soledad De Esteban-Trivigno
Institut Català de Paleontologia Miquel Crusafont (ICP)

Campus de la Universitat Autònoma de Barcelona

Cerdanyola del Vallès (Barcelona). Spain

www.icp.cat
  
 

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[MORPHMET] testing - ignore

2019-05-22 Thread Dennis E. Slice
I see at least one message (from Adams) has gotten through. Let's see if 
this one does from me. -ds


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[MORPHMET] geomorph 3.1.2 available

2019-05-21 Thread Adams, Dean [EEOBS]
Colleagues,

Version 3.1.2 of geomorph is now available on CRAN as source-file, and over the 
next few days the CRAN folks will generate the binaries also.

This version is a patch, fixing some issues created when the RGL library 
recently made changes to their package - regarding how colors/materials of 3D 
meshes were handled -  which caused some cascading issues for some using 
geomorph for 3D digitizing from surface scans. Additionally, a few other minor 
issues were also cleaned up, and are documented in the NEWS file. There are 
also two more vignettes to guide users through the geomorph experience.

Dean

Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
https://www.eeob.iastate.edu/faculty/adams/
phone: 515-294-3834

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[MORPHMET] Testing - ignore

2019-05-20 Thread Dennis E. Slice

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

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[MORPHMET] morphmet - 1000 subscribers!

2019-05-19 Thread MORPHMET
I note that we recently have achieved 1000 subscribers to morphmet!

Caveat 1: Over the years, some have removed themselves from the list or 
asked me to remove them. So, there have actually been more than 1000 people 
subscribing, but we have never had 1000 subscribers on the list at the same 
time.

Caveat 2: We have about 50 addresses that are either bouncing or disabled 
indicating members who have probably moved on from their subscribed 
addresses. In the future, I will remove those with persistent bouncing 
dropping the list (temporarily, no doubt) below 1000.

-the moderator

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Re: [MORPHMET] morphmet - list problems

2019-05-19 Thread morphmet
Yeah! This msg came through. Let's see/hope if/that the list continues 
to function.

-the moderator

On 5/19/19 3:56 AM, morphmet_moderator wrote:
There seem to be some problems with the mailing list that have come to 
my attention over the past several days, e.g., it thinks every post is 
spam, but doesn't give me the chance to moderate such posts. Even I, the 
moderator, am only able to post via the website intermittently.


There is a notice that the server-side software will be changed this 
month, so I suspect this is part of the problem, but I don't know. I am 
in contact with support to try to see what is going on. For now, I have 
no idea if your individual posts to the list (including this one - 
fourth attempt) will appear.


In the meantime, please be patient.

-the moderator

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[MORPHMET] morphmet - list problems

2019-05-19 Thread morphmet_moderator
There seem to be some problems with the mailing list that have come to my 
attention over the past several days, e.g., it thinks every post is spam, 
but doesn't give me the chance to moderate such posts. Even I, the 
moderator, am only able to post via the website intermittently. 

There is a notice that the server-side software will be changed this month, 
so I suspect this is part of the problem, but I don't know. I am in contact 
with support to try to see what is going on. For now, I have no idea if 
your individual posts to the list (including this one - fourth attempt) 
will appear.

In the meantime, please be patient. 

-the moderator

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[MORPHMET] Re: PREPRINT: between-group principal components analysis (bgPCA)

2019-05-18 Thread MORPHMET
[Final, summary post.]

I thought I should post some notes about the responses to Andrea’s recent 
postings. Several people seem to have extrapolated beyond what Andrea said.

After a few months of the Cardini, O’Higgins, Rohlf, and Bookstein 
collaboration (Polly was CC:ed on the very early emails but I do not 
remember him engaging), I suggested to Andrea that there should be two 
publications not one. I could see that while writing about the same flaws 
in the same method the approaches Fred and I were taking would be difficult 
to combine in the same paper. Andrea and Paul agreed and Andrea then 
suggested to Fred that he write a paper separate from ours.  Thus, Fred did 
not unilaterally jump ahead and just write his own paper as some seem to 
have assumed. The understanding was that we expected the two papers to be 
published together as “companion papers” in some journal yet to be 
determined.

I know that Fred was concerned about the ethics of waiting a long time to 
warn people that they were using a severely flawed (I would say strongly 
biased) method.  The usage of BG-PCA seems to have increased lately and it 
did not seem fair to let people continue to write papers and dissertations 
based on this method once we knew how bad it was. His biorxiv upload and 
his announcement of it on morphmet were not a surprise to us. There were 
emails exchanged about the need to warn users. At the time, Fred told me 
that he needed to go ahead with the biorxiv upload as it was unclear how 
long it would take our ms. to be completed due to other demands on our time.

Reading Fred’s papers can take time but if one just looks at his Fig. 1 
(Google "biorxiv 627448" if you lost the link that Fred posted) you will 
see the magnitude of the problem. It is not subtle! Incidentally, the 
Cardini et al. draft also has a more extensive Figure illustrating the same 
problem as a function of n but the rest of the paper is very different. In 
fact, I found it interesting how two papers about the same defect in the 
same method and reaching the same conclusion could have so little overlap. 
Thus, Fred’s paper does not infringe on the content of the Cardini et al. 
manuscript or interfere with its publication – in fact I think it makes it 
more important as it will show the problem does not require an 
understanding of an abstract theorem. I believe the Cardini et al. paper 
will show that the defects in the method are very easy to understand and 
obvious once you think about it in the right way.


F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
Research Professor, Anthropology
Stony Brook University


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[MORPHMET] Another test - ignore

2019-05-18 Thread Dennis E. Slice

Stop reading these! -ds

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[MORPHMET] Testing - ignore

2019-05-18 Thread Dennis E. Slice

Don't read this!

Testing server-side problems. -ds

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[MORPHMET] Testing - ignore

2019-05-18 Thread morphmet_moderator
Don't read this! 

Testing server-side problems. -ds 

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[MORPHMET] Re: PREPRINT: between-group principal components analysis (bgPCA)

2019-05-16 Thread morphmet_moderator
This and related threads have now been locked.

Non-morphometric issues should be taken up elsewhere.

Non-morphometric posts/replies are subject to deletion from the web site.

Violators are subject to being put back on the "moderation" list.

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[MORPHMET] Re: PREPRINT: between-group principal components analysis (bgPCA)

2019-05-16 Thread MORPHMET
Dear MorphMetters,

Yesterday David Polly reminded us of the existence of a 3.5-page draft 
fragment emailed by Andrea Cardini on September 5, 2018 and headed as by 
"Cardini, O'Higgins, Polly, Rohlf, Bookstein." So, yes, David Polly was 
indeed present at the creation. It begins with paragraphs of an 
introduction acknowledged to be "largely borrowed" from me and continues 
with a summary of some of Cardini's simulation results, which are 
consistent with mine but reported using mostly different simulations and 
quantifications, together with a sketch of a discussion quite different 
from mine.  This fragment, particularly its style of simulating and 
reporting, may have served later as the basis of the second of the two 
papers as I referred to it both in my Monday morphmet posting and in my 
biorxiv preprint. (I say "may have" because I have not seen any more recent 
state of that second manuscript.) So my Monday note to morphmet pointing to 
my biorxiv preprint should have mentioned the September document as part of 
the history of our project before it split into two. I apologize to David 
for not realizing the role he played in this early history, and apologize 
to Andrea for overlooking this early draft of the less algebraic half of 
our joint project.  I hope the authors of this second paper will post it to 
biorxiv as urgently as mine was posted once theirs, too, is in final draft.

FB


On Tuesday, May 14, 2019 at 1:32:24 PM UTC-4, MORPHMET wrote:
>
> Dear MorphMetters,
>
> Some of you may have been in the auditorium in the Department of Botany, 
> University of Vienna, back in March when Philipp Mitteroecker and I were 
> the two scheduled discussants for the conference "GMAustria19" on 
> applications of geometric morphometrics.  Several of the papers delivered 
> there used between-group principal components analysis (bgPCA), and after 
> each of those papers I mentioned in the course of my commentary that bgPCA 
> was fatally flawed in applications to most GMM data sets and should NEVER 
> be used here. In my keynote address, which closed the meeting, I had one 
> cryptic slide about this assertion, with an example that flashed on the 
> screen but was immediately replaced by the next slide.
>   
> The typical response to both my own talk and my criticism of the talks of 
> others, as far as bgPCA was concerned, was along the lines of "Hunh?" or 
> sometimes "What are you blathering about this time? Isn't bgPCA in the 
> standard toolkit?" I answered that the Bookstein paper they should read was 
> just then being written, as one of a pair jointly arising from 
> conversations with Andrea Cardini, Jim Rohlf, and Paul O'Higgins following 
> an original hunch of Cardini's, and that my argument would be pretty 
> convincing once it was actually written down.  The claim isn't that people 
> are using bgPCA incorrectly. They're using it according to the published 
> formulas, yes, but the method itself yields biological nonsense much too 
> often.
>  
> That was March.  In April, two different articles in Nature (one by 
> Detroit et al., one by Chen et al.) buttressed claims about sister species 
> of Homo sapiens using the bgPCA method, and so suddenly it became clear 
> that we authors had to do something quickly lest this become an epidemic of 
> bad biometrics. So 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, and it seemed like a good idea to upload the final 
> draft to https://www.biorxiv.org even before submitting the paper, so 
> that any letter to the editors of Nature could include a link to  the 
> argument as to exactly WHY bgPCA is nearly always unsound and its 
> inferences invalid for applications in contemporary GMM. 
>  
> That is the draft that has just appeared as 
>
> https://www.biorxiv.org/content/10.1101/627448v1
>
> For those of you who were at the March meeting, this is the argument 
> (complete with formulas) defending my stern condemnation there. I won't try 
> to summarize it in this morphmet note -- if you're interested, just read 
> the abstract on page 1 of the link.  For those of you who have already 
> published bgPCA analyses, you know who you are -- my paper argues strongly 
> that you need to go back and revisit the inferences of those papers in a 
> mood of much more intense multivariate skepticism.  For the rest of you, 
> please consider this draft manuscript to be a wake-up call. A technique 
> that has appeared in dozens of papers and that was, alas, specifically 
> praised by Mitteroecker and Bookstein personally (back in 2011) could 
> nevertheless, when examined closely (for the first time!), turn out to be 
>

[MORPHMET] Test post - ignore

2019-05-16 Thread morphmet_moderator
Have locked myself out of posting to the list. Trying to test. Ignore this 
message. -ds

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RE: [MORPHMET] thanks for support

2019-05-16 Thread Dominique Adriaens
Hi Andrea,

I can only applaud your courage to make such a breach on scientific ethics 
clear to the scientific community, it should be done more. In a time where 
scientific integrity is put higher and higher on the agenda (where it belongs), 
I find it striking that such practices as you unfortunately experienced still 
exist.

Looking forward to your (and your co-authors) paper!

Best
Dominique

Prof. Dr. Dominique Adriaens
Chair Educational Board Biology
tel: +32 9 264.52.19, fax: +32 9 264.53.44
E-mail: dominique.adria...@ugent.be
 
Ghent University – Department of Biology
Evolutionary Morphology of Vertebrates & Zoology Museum
K.L. Ledeganckstraat 35, B-9000 Gent
BELGIUM
Office location: click here
 
http://www.fun-morph.ugent.be/
http://www.zoologymuseum.ugent.be/



-Original Message-
From: andrea cardini  
Sent: donderdag 16 mei 2019 12:43
Cc: MORPHMET 
Subject: [MORPHMET] thanks for support

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
> 

[MORPHMET] thanks for support

2019-05-16 Thread andrea cardini
lutionary 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 <mailto:alcard...@gmail.com>,
andrea.card...@unimore.it <mailto: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 <http://secondwarning.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 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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Re: not exactlyRe: [MORPHMET] PREPRINT: between-group principal components analysis (bgPCA)

2019-05-15 Thread Una Vidarsdottir
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,  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
> (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
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@mo

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

2019-05-15 Thread Polly, P. David
.footprintnetwork.org/en/index.php/GFN/page/calculators/
SUPPORT: secondwarning.org<http://secondwarning.org>

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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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Re: [MORPHMET] PREPRINT: between-group principal components analysis (bgPCA)

2019-05-14 Thread Ian Dworkin
Fred

 I look forward to reading it. I am particularly interested since it was
probably your 2011 paper with Phillip (Mitteroecker and Bookstein, Evol
Biol 38:100-114) which advocated its use for ordination and has resulted in
its current widespread use, but which you address in an amusing way in this
current paper in figure 10 and with the term "less inappropriate" than CVA.

Ian

On Tue, 14 May 2019 at 13:32, MORPHMET  wrote:

> Dear MorphMetters,
>
> Some of you may have been in the auditorium in the Department of Botany,
> University of Vienna, back in March when Philipp Mitteroecker and I were
> the two scheduled discussants for the conference "GMAustria19" on
> applications of geometric morphometrics.  Several of the papers delivered
> there used between-group principal components analysis (bgPCA), and after
> each of those papers I mentioned in the course of my commentary that bgPCA
> was fatally flawed in applications to most GMM data sets and should NEVER
> be used here. In my keynote address, which closed the meeting, I had one
> cryptic slide about this assertion, with an example that flashed on the
> screen but was immediately replaced by the next slide.
>
> The typical response to both my own talk and my criticism of the talks of
> others, as far as bgPCA was concerned, was along the lines of "Hunh?" or
> sometimes "What are you blathering about this time? Isn't bgPCA in the
> standard toolkit?" I answered that the Bookstein paper they should read was
> just then being written, as one of a pair jointly arising from
> conversations with Andrea Cardini, Jim Rohlf, and Paul O'Higgins following
> an original hunch of Cardini's, and that my argument would be pretty
> convincing once it was actually written down.  The claim isn't that people
> are using bgPCA incorrectly. They're using it according to the published
> formulas, yes, but the method itself yields biological nonsense much too
> often.
>
> That was March.  In April, two different articles in Nature (one by
> Detroit et al., one by Chen et al.) buttressed claims about sister species
> of Homo sapiens using the bgPCA method, and so suddenly it became clear
> that we authors had to do something quickly lest this become an epidemic of
> bad biometrics. So 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, and it seemed like a good idea to upload the final
> draft to https://www.biorxiv.org even before submitting the paper, so
> that any letter to the editors of Nature could include a link to  the
> argument as to exactly WHY bgPCA is nearly always unsound and its
> inferences invalid for applications in contemporary GMM.
>
> That is the draft that has just appeared as
>
> https://www.biorxiv.org/content/10.1101/627448v1
>
> For those of you who were at the March meeting, this is the argument
> (complete with formulas) defending my stern condemnation there. I won't try
> to summarize it in this morphmet note -- if you're interested, just read
> the abstract on page 1 of the link.  For those of you who have already
> published bgPCA analyses, you know who you are -- my paper argues strongly
> that you need to go back and revisit the inferences of those papers in a
> mood of much more intense multivariate skepticism.  For the rest of you,
> please consider this draft manuscript to be a wake-up call. A technique
> that has appeared in dozens of papers and that was, alas, specifically
> praised by Mitteroecker and Bookstein personally (back in 2011) could
> nevertheless, when examined closely (for the first time!), turn out to be
> algebraic garbage when applied to data sets where there are far more shape
> coordinates than specimens. But isn't that the usual situation in GMM these
> days?
>
> As always, I welcome all responses, both positive and negative. The
> biorxiv posting is permanent, but there is plenty of time for me to make
> changes before the paper is published (at present it has not yet even been
> submitted anywhere), so feel free to try to find the flaws in my argument.
> But I hope you will want to try some of these simulations on your own
> before you argue against mine. You will also want to study the companion
> piece by Cardini, O'Higgins, and Rohlf that should likewise be available
> for download before too long.
>
> Fred Bookstein
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
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&

[MORPHMET] PREPRINT: between-group principal components analysis (bgPCA)

2019-05-14 Thread MORPHMET
Dear MorphMetters,

Some of you may have been in the auditorium in the Department of Botany, 
University of Vienna, back in March when Philipp Mitteroecker and I were 
the two scheduled discussants for the conference "GMAustria19" on 
applications of geometric morphometrics.  Several of the papers delivered 
there used between-group principal components analysis (bgPCA), and after 
each of those papers I mentioned in the course of my commentary that bgPCA 
was fatally flawed in applications to most GMM data sets and should NEVER 
be used here. In my keynote address, which closed the meeting, I had one 
cryptic slide about this assertion, with an example that flashed on the 
screen but was immediately replaced by the next slide.
  
The typical response to both my own talk and my criticism of the talks of 
others, as far as bgPCA was concerned, was along the lines of "Hunh?" or 
sometimes "What are you blathering about this time? Isn't bgPCA in the 
standard toolkit?" I answered that the Bookstein paper they should read was 
just then being written, as one of a pair jointly arising from 
conversations with Andrea Cardini, Jim Rohlf, and Paul O'Higgins following 
an original hunch of Cardini's, and that my argument would be pretty 
convincing once it was actually written down.  The claim isn't that people 
are using bgPCA incorrectly. They're using it according to the published 
formulas, yes, but the method itself yields biological nonsense much too 
often.
 
That was March.  In April, two different articles in Nature (one by Detroit 
et al., one by Chen et al.) buttressed claims about sister species of Homo 
sapiens using the bgPCA method, and so suddenly it became clear that we 
authors had to do something quickly lest this become an epidemic of bad 
biometrics. So 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, and it seemed like a good idea to upload the final 
draft to https://www.biorxiv.org even before submitting the paper, so that 
any letter to the editors of Nature could include a link to  the argument 
as to exactly WHY bgPCA is nearly always unsound and its inferences invalid 
for applications in contemporary GMM. 
 
That is the draft that has just appeared as 

https://www.biorxiv.org/content/10.1101/627448v1

For those of you who were at the March meeting, this is the argument 
(complete with formulas) defending my stern condemnation there. I won't try 
to summarize it in this morphmet note -- if you're interested, just read 
the abstract on page 1 of the link.  For those of you who have already 
published bgPCA analyses, you know who you are -- my paper argues strongly 
that you need to go back and revisit the inferences of those papers in a 
mood of much more intense multivariate skepticism.  For the rest of you, 
please consider this draft manuscript to be a wake-up call. A technique 
that has appeared in dozens of papers and that was, alas, specifically 
praised by Mitteroecker and Bookstein personally (back in 2011) could 
nevertheless, when examined closely (for the first time!), turn out to be 
algebraic garbage when applied to data sets where there are far more shape 
coordinates than specimens. But isn't that the usual situation in GMM these 
days?  
 
As always, I welcome all responses, both positive and negative. The biorxiv 
posting is permanent, but there is plenty of time for me to make changes 
before the paper is published (at present it has not yet even been 
submitted anywhere), so feel free to try to find the flaws in my argument.  
But I hope you will want to try some of these simulations on your own 
before you argue against mine. You will also want to study the companion 
piece by Cardini, O'Higgins, and Rohlf that should likewise be available 
for download before too long.    
 
Fred Bookstein

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Re: [MORPHMET] Help with surface scans

2019-05-08 Thread G Wrobe
Pablo — I use photogrammetry to create models from skulls and I’d be happy to 
share my workflow if you want to experiment with it.  It works really well in 
most cases. I’ve been curious about about the Spider scanner, so would love to 
hear about your experiences with that.  Feel free to drop me a line at 
wrob...@msu.edu <mailto:wrob...@msu.edu>.

Gabriel



> On May 7, 2019, at 5:40 PM, Pablo Fisichella  
> wrote:
> 
> Dear Ariadne
> 
> Thank you so much for your kind response and excuse my delayed reply. I´m 
> using an Artec Space Spide scanner. I´m doing some tests following several of 
> the guidelines here suggested. For lithic tools some reflecting surfaces 
> typical of some raw materials like chert produce some errors but is just a 
> matter of test. Thanks again for your advice.
> 
> All best,
> 
> Pablo
> 
>  
> <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
> Libre de virus. www.avast.com 
> <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
>  
> El sáb., 27 abr. 2019 a las 11:56, Ariadne Schulz ( <mailto:ariadne.sch...@gmail.com>>) escribió:
> I'm coming at this a bit late so I apologize if I've repeated anyone's point. 
> For your purposes photogrammetry is probably your best option particularly 
> for the lithics. Laser scanning works on bones and I used a NextEngine 
> scanner for human proximal long bones, but I think someone has already 
> mentioned that the laser doesn't capture the orbitals well and you might have 
> difficulty with tooth enamel. The photogrammetry software requires a decently 
> hefty laptop, but it's affordable and you'd be working with normal light 
> rather than lasers. I don't know that this clears up your concerns about 
> fusing scans though. If you are concerned you could do some error testing on 
> that comparing landmarks obtained on the scans to landmarks obtained 
> normally. I found the laser scans to be pretty decent, but I unfortunately 
> cannot speak to photogrammetry as I've never personally tried it.
> 
> On Mon, Apr 22, 2019 at 3:29 PM Pablo Fisichella  <mailto:fisichellapa...@gmail.com>> wrote:
> Dear All
> 
> I´m trying to obtain surface scans from human skulls and lithic artifacts 
> (projectile points). I wonder how can I get the most complete possible scans, 
> I mean usually is not possibly to obtain a complete scan at once. I know that 
> several post-scan processing software have functions to fuse and/or align the 
> different surfaces obtained and then create one surface but perhaps several 
> of you have some tips to obtain the most complete possible surface scans.
> 
> Any suggestion and advice is more than welcome
> 
> All best,
> 
> Pablo
> 
> 
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org 
> <http://www.morphometrics.org/>
> --- 
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> 
> -- 
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> <http://www.morphometrics.org/>
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Re: [MORPHMET] Help with surface scans

2019-05-08 Thread Pablo Fisichella
Dear Ariadne

Thank you so much for your kind response and excuse my delayed reply. I´m
using an Artec Space Spide scanner. I´m doing some tests following several
of the guidelines here suggested. For lithic tools some reflecting surfaces
typical of some raw materials like chert produce some errors but is just a
matter of test. Thanks again for your advice.

All best,

Pablo

<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
Libre
de virus. www.avast.com
<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

El sáb., 27 abr. 2019 a las 11:56, Ariadne Schulz ()
escribió:

> I'm coming at this a bit late so I apologize if I've repeated anyone's
> point. For your purposes photogrammetry is probably your best option
> particularly for the lithics. Laser scanning works on bones and I used a
> NextEngine scanner for human proximal long bones, but I think someone has
> already mentioned that the laser doesn't capture the orbitals well and you
> might have difficulty with tooth enamel. The photogrammetry software
> requires a decently hefty laptop, but it's affordable and you'd be working
> with normal light rather than lasers. I don't know that this clears up your
> concerns about fusing scans though. If you are concerned you could do some
> error testing on that comparing landmarks obtained on the scans to
> landmarks obtained normally. I found the laser scans to be pretty decent,
> but I unfortunately cannot speak to photogrammetry as I've never personally
> tried it.
>
> On Mon, Apr 22, 2019 at 3:29 PM Pablo Fisichella <
> fisichellapa...@gmail.com> wrote:
>
>> Dear All
>>
>> I´m trying to obtain surface scans from human skulls and lithic artifacts
>> (projectile points). I wonder how can I get the most complete possible
>> scans, I mean usually is not possibly to obtain a complete scan at once. I
>> know that several post-scan processing software have functions to fuse
>> and/or align the different surfaces obtained and then create one surface
>> but perhaps several of you have some tips to obtain the most complete
>> possible surface scans.
>>
>> Any suggestion and advice is more than welcome
>>
>> All best,
>>
>> Pablo
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "MORPHMET" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to morphmet+unsubscr...@morphometrics.org.
>>
>

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Re: [MORPHMET] help with "classify" in RRPP

2019-05-07 Thread Mike Collyer
Nicole,

I assume that your intention is to summarize a species probability from the 
several probabilities of specimens, if data sets are combined?  (I think you 
might have used “species” twice but meant “specimen" once, below).

If so, there are two ways you could do this.  One would be as you suggested, 
summarize the distribution of posterior probabilities for a species (mean, 
median, quartiles, etc.).  The other would be to calculate something akin to 
species means and use these as test data, based on the coefficients calculated 
from training data.  It might require some thought as to what the training data 
should be, as leave one out cross-validation would not make much sense.  
Calculating the posterior probability for a species mean after using individual 
specimens to estimate the mean also does not make sense.  However, a resampling 
procedure that arbitrarily divides the specimens into training and testing 
groups, using the first to estimate coefficients and the second to obtain a 
mean, could be used to generate a confidence interval for the posterior 
classification probabilities of a particular species to its and other species’s 
groups.

The second approach would involve some scripting.  The first approach can be 
done quickly with the by() and summary() functions, e.g.,

by(my.posterior.probs, species, summary)

Hope that helps!
Mike

> On May 7, 2019, at 9:13 AM, Nicole Ibagón  wrote:
> 
> Dear all
> I'm working with five different datasets (lateral and dorsal view of the 
> skull and jaw) of a neotropical bat genus. My research question is if one 
> species (described with a single sample), is a synonym of one of the other 
> species of the genus. I used classify function of RRPP for this purpose, and 
> it solved my question generating one posterior probability for each species 
> of each dataset. However, I would like to know there is a way to generate a 
> single posterior probability for each species.
> Should I join all the datasets before doing the classification analysis? Or 
> should I average the posterior probabilities of all the datasets? Is there a 
> better way to do it?
> Thanks
> 
> -- 
> Nicole Estefanía Ibagón Escobar
> PhD Candidate in Ecology  - UFV (Brazil) 
> BSc Marine Biologist  - Utadeo (Colombia)
> ResearchGate <https://www.researchgate.net/profile/Nicole_Ibagon>
> Curriculo CVLAC 
> <http://190.216.132.131:8081/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0001219782>
> Curriculo lattes 
> <http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4371000E6>
> http://evolutionlbe.wix.com/lbeufv <http://evolutionlbe.wix.com/lbeufv>
> 
> < <<  
> 
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org 
> <http://www.morphometrics.org/>
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Re: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe

2019-05-07 Thread morphmet
 474.6507
85.1190 135.9783473.3503
79.3694 122.8234477.4590
78.4327 115.8613477.4715
84.2949 108.1328485.4598
97.2760 93.4345 481.8105
89.2901 111.8870483.4924
90.0784 117.8522490.4405
91.4313 106.3994494.9362
79.4173 144.0817472.9395
88.3825 141.0176474.3985
90.9274 140.2106477.6371
85.2512 140.7932478.2403

I would apreciate if somebody could help me.
Please don't hesitate to ask me for more details.

King regards
Azadeh




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[MORPHMET] help with "classify" in RRPP

2019-05-07 Thread Nicole Ibagón
Dear all
I'm working with five different datasets (lateral and dorsal view of the
skull and jaw) of a neotropical bat genus. My research question is if one
species (described with a single sample), is a synonym of one of the other
species of the genus. I used classify function of RRPP for this purpose,
and it solved my question generating one posterior probability for each
species of each dataset. However, I would like to know there is a way to
generate a single posterior probability for each species.
Should I join all the datasets before doing the classification analysis? Or
should I average the posterior probabilities of all the datasets? Is there
a better way to do it?
Thanks

-- 
Nicole Estefanía Ibagón Escobar
PhD Candidate in Ecology  - UFV (Brazil)
BSc Marine Biologist  - Utadeo (Colombia)
ResearchGate <https://www.researchgate.net/profile/Nicole_Ibagon>
Curriculo CVLAC
<http://190.216.132.131:8081/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0001219782>
Curriculo lattes
<http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4371000E6>
http://evolutionlbe.wix.com/lbeufv

< <<

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RE: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe

2019-05-07 Thread Adams, Dean [EEOBS]
To add briefly to Dennis' comment. If landmark estimation is the route taken, 
both TPS-based and regression-based imputation are implemented in geomorph.

Dean

Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
https://www.eeob.iastate.edu/faculty/adams/
phone: 515-294-3834

-Original Message-
From: morphmet  
Sent: Tuesday, May 7, 2019 8:18 AM
To: morphmet@morphometrics.org
Subject: Re: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe

It depends on what is wrong with the data (I haven't checked it). 
Morpheus et al. can be used to correct data after visual inspection or mark bad 
data points as missing or delete whole sets of coordinates for particular 
points.

The easiest way to do this is to get the data into a form importable by 
Morpheus - NTSYSpc is the easiest, and import the data. You can then set up 
links between points (there is a menu option). Then, you can just page through 
the objects looking for one whose links are obviously wrong. You can then swap 
points (another menu option) until they are in the correct order. For this, it 
is useful to use the plot Opts button to set the point plotting symbol as 
"number", which locates the points with their number, e.g., "1", "2", etc.

You can also mark any offending points (with genuinely bad data) as "missing" 
or delete points/landmarks. If there are too few or too many, you can insert 
missing points (which will be marked as missing data) or delete specific points 
from specific objects.

Another suggestion to find objects with bad points is to do a PCA plot (I use 
R) to check for any outliers.

If there are a few scattered points with missing data at the end of all of 
this, the data can be filled in using missing data imputation - mean 
substitution is the only method currently implemented. Mean substitution 
generally does not affect parameter estimates, but does result in error 
estimates that are undervalued - there is more variance than apparent in the 
data since mean values were substituted for missing data.

-ds

PS: NTSYSpc format for import. On the first line, 1 is NTSYS for rectangular 
data matrix, n is for the number of objects in the file (you have to provide a 
number, not 'n'); a number representing the number of landmarks, p, times the 
number of dimensions, 3 in your case; and a '0' 
indicating there are no missing data in the data set. If there are missing 
data, then the '0' is replace by something like "1 -999", where the '1' 
indicates the presence of missing data and the next item, e.g., -999, is the 
code used to indicate missing data...

1 n nDimxp 0
x1 y1 z1
x2 y2 z2
...
xp yp zp

...repeated (except for the first line) for more objects

On 5/7/19 8:09 AM, Azadeh Mohaseb wrote:
> Dear all
> I am a post-doc researcher on GMM and I work on equids bones. Recently, I 
> digitized some modern equid bones by a microscribe and then I realized that 
> the 3d coordinates of some of these individuals are not correcte.
> As I don't have access to these bones to digitize them again, I wondered if 
> you could help me to fix this problem.
> I send you the correct coordinates of one individual and the incorrect 
> coordinates of another one. These two individuals have been digitized at the 
> same time, with same microscribe and the same settings on machine and 
> software.
> 
> Individual 1: correct
> 
> 228.6438  203.1991156.5325
> 220.2511  204.6701143.3459
> 223.9106  202.3835121.6829
> 242.5923  225.1355121.4050
> 240.4551  225.8690136.0673
> 238.9128  226.4731141.2689
> 240.9662  226.0292146.4538
> 243.8571  223.4773158.7283
> 248.3989  203.3913162.7939
> 247.9284  204.2474147.2226
> 249.7594  202.0327140.3145
> 247.2640  205.0845134.1143
> 246.3540  204.5467115.9491
> 88.1469   334.5199162.2996
> 79.0490   330.4259152.7271
> 74.0790   325.4809142.4243
> 79.8139   324.6076119.4693
> 86.4637   331.0746115.0139
> 88.8453   333.9695120.4097
> 87.0741   333.9286128.0646
> 85.8100   336.1603144.5840
> 83.5972   335.3779150.5125
> 90.8324   337.0566156.8697
> 92.3339   337.9303154.
> 87.5753   339.9321145.9987
> 93.6211   346.3407145.2005
> 98.7993   344.1494152.6361
> 89.2627   341.3373127.1407
> 91.0691   339.7504123.6672
> 94.9706   

[MORPHMET] How to fix erroneous 3D coordinates took by microscribe

2019-05-07 Thread Azadeh Mohaseb
Dear all
I am a post-doc researcher on GMM and I work on equids bones. Recently, I 
digitized some modern equid bones by a microscribe and then I realized that the 
3d coordinates of some of these individuals are not correcte. 
As I don't have access to these bones to digitize them again, I wondered if you 
could help me to fix this problem. 
I send you the correct coordinates of one individual and the incorrect 
coordinates of another one. These two individuals have been digitized at the 
same time, with same microscribe and the same settings on machine and software. 

Individual 1: correct

228.6438203.1991156.5325
220.2511204.6701143.3459
223.9106202.3835121.6829
242.5923225.1355121.4050
240.4551225.8690136.0673
238.9128226.4731141.2689
240.9662226.0292146.4538
243.8571223.4773158.7283
248.3989203.3913162.7939
247.9284204.2474147.2226
249.7594202.0327140.3145
247.2640205.0845134.1143
246.3540204.5467115.9491
88.1469 334.5199162.2996
79.0490 330.4259152.7271
74.0790 325.4809142.4243
79.8139 324.6076119.4693
86.4637 331.0746115.0139
88.8453 333.9695120.4097
87.0741 333.9286128.0646
85.8100 336.1603144.5840
83.5972 335.3779150.5125
90.8324 337.0566156.8697
92.3339 337.9303154.
87.5753 339.9321145.9987
93.6211 346.3407145.2005
98.7993 344.1494152.6361
89.2627 341.3373127.1407
91.0691 339.7504123.6672
94.9706 342.5350123.9575
93.9787 344.1297127.5435

Individual 2: incorrect

117.190772.8549 331.5414
63.8556 106.7571324.6544
64.2134 108.2755327.6326
125.581822.1134 446.8474
117.373526.4359 458.0952
110.488427.9800 458.7083
111.163221.4185 461.2170
106.153618.8334 468.0809
71.8894 25.9454 248.6469
49.2014 61.3649 250.9960
50.9447 62.2230 251.7744
31.1992 99.5425 270.7333
38.6410 96.3750 268.3234
104.840276.1165 472.1013
104.034379.0076 464.1394
81.7345 108.8425464.0654
85.9537 128.9866461.4308
88.6260 142.0624468.9539
96.1857 130.2672474.6507
85.1190 135.9783473.3503
79.3694 122.8234477.4590
78.4327 115.8613477.4715
84.2949 108.1328485.4598
97.2760 93.4345 481.8105
89.2901 111.8870483.4924
90.0784 117.8522490.4405
91.4313 106.3994494.9362
79.4173 144.0817472.9395
88.3825 141.0176474.3985
90.9274 140.2106477.6371
85.2512 140.7932478.2403

I would apreciate if somebody could help me. 
Please don't hesitate to ask me for more details. 

King regards
Azadeh


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[MORPHMET] centroid size is smaller than 1.0e-10

2019-05-02 Thread Rahma Amen
.67212045018443E+001 
-1.63276127137189E+002 
5.03221266530894E+001 -1.66320997236516E+002 8.38826572756146E+001 
-1.68289309852983E+002 1.17431512160154E+002 -1.71312095670915E+002 
1.51044522344847E+002 -1.71297623367666E+002 1.84001355430608E+002 
-1.70313365611671E+002 
2.17204798558342E+002 -1.65307005519892E+002 2.53419615918270E+002 
-1.56439347013685E+002 2.82360880813375E+002 -1.47311662817820E+002 
3.00601611367004E+002 -1.48713677649688E+002 3.48530072360158E+002 
-1.54249181656786E+002 
3.83950566438537E+002 -1.58504595517060E+002 4.15695827440232E+002 
-1.62215160614080E+002 4.49012956499523E+002 -1.66244844422965E+002 
4.81866439858338E+002 -1.72199058967884E+002 5.14811229360960E+002 
-1.78164671779469E+002 
5.48037195946946E+002 -1.83179672728190E+002 5.80874888739359E+002 
-1.89120090051336E+002 6.14209286058765E+002 -1.96154698465101E+002 
6.49505476441106E+002 -2.03539039334882E+002 6.83913090655664E+002 
-2.08607594535180E+002 
7.13462051423125E+002 -2.12128000803427E+002 

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[MORPHMET] Re: New Article: Reflections on a Biometrics of Organismal Form

2019-04-30 Thread morphmet_moderator
Third time's a charm?
The previous, shorter link directs you through FSU libraries with a 
requisite login.
Trying again. I think this will take you directly to the article...

https://link.springer.com/article/10.1007/s13752-019-00320-y

-ds [the MORPHMET moderator]
On Tuesday, April 30, 2019 at 11:01:15 AM UTC-4, MORPHMET wrote:
>
> [Posted on behalf of Dr. Bookstein] 
>
> Dear MorphMetters, 
>
> I'm happy to announce that my paper "Reflections on a Biometrics of 
> Organismal Form" has just been posted for open access by the Springer 
> journal Biological Theory. You can get a free copy by pointing your browser 
> at 
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__link.springer.com_journal_13752=DwIBAg=HPMtquzZjKY31rtkyGRFnQ=T8Sxf-U51iRHIXQayyjGAA=xOGtb5kpXyYsx7O1ZPeSGHSsh8sLGcIwYOsLoNWTC3I=wQclw8xhArX7488PAUkyik6iPqlhj-vA5-el7VYzF-E=
>  
>
> and clicking on what is, for now, the top entry in the Latest Articles 
> table on the home page. 
>
> This article is a sequel to my 2015 article in Benedikt Hallgrimsson's 
> journal Evolutionary Biology that introduced the BE-PwV plot as the best 
> tool for studying integration in GMM data sets. I trace the basic idea here 
> back nearly a hundred years, not to D'Arcy Thompson but to a 
> hitherto-untranslated critique of his ideas by the Vivarium group under 
> Hans Przibram in Vienna arguing that the only valid way that a biologist 
> should study organismal form is by direct experimental observation of 
> transformation grids: "Thompson's holistic deformations can be made 
> comprehensible if we can visualize a space lattice upon the living form, so 
> as to assess how each little piece changes its shape under conditions that 
> vary by species. Here lies open a rich, nearly undeveloped field that 
> invites a mathematization, one whose erection we hope will begin very 
> soon." But the timing seems to have slipped a bit, namely, by 97 years. The 
> new paper argues that BE-PwV is exactly the "mathematization" they were 
> envisioning, which could not be made empirical until the development of 
> geometric morphometrics, and further that it is the only morphometric 
> method consistent with the most fundamental fact in all of biology, "the 
> repetitive production of organized heterogeneity" (Hotchkiss 1958) or, as 
> Walter Elsasser put it in 1987, "the transfer of information over finite 
> intervals of time without an intermediate message." For instance, the new 
> article demonstrates how to recognize a growth-gradient explicitly even in 
> the presence of unstructured residual variability. I close with a plea that 
> others help me build the bridge that we need so urgently between the 
> arithmetic of today's burgeoning image-based data resources and the 
> rhetoric of biological explanations of organismal form both over evolution 
> and over development. 
>
> As always I welcome all comments on these ideas, enthusiastic or 
> otherwise. 
>
>    Fred Bookstein 
>

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[MORPHMET] Re: New Article: Reflections on a Biometrics of Organismal Form

2019-04-30 Thread MORPHMET
For some reason, the link to the article I rec'd was excessively long. 
After some research, I figured out how to edit the original post, but 
elected not to since many receive messages as email. I am not sure they 
would get/see the edit. Hence, I provide a shorter link here:

https://link-springer-com.proxy.lib.fsu.edu/journal/13752

-ds [the MORPHMET moderator]

On Tuesday, April 30, 2019 at 11:01:15 AM UTC-4, MORPHMET wrote:
>
> [Posted on behalf of Dr. Bookstein] 
>
> Dear MorphMetters, 
>
> I'm happy to announce that my paper "Reflections on a Biometrics of 
> Organismal Form" has just been posted for open access by the Springer 
> journal Biological Theory. You can get a free copy by pointing your browser 
> at 
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__link.springer.com_journal_13752=DwIBAg=HPMtquzZjKY31rtkyGRFnQ=T8Sxf-U51iRHIXQayyjGAA=xOGtb5kpXyYsx7O1ZPeSGHSsh8sLGcIwYOsLoNWTC3I=wQclw8xhArX7488PAUkyik6iPqlhj-vA5-el7VYzF-E=
>  
>
> and clicking on what is, for now, the top entry in the Latest Articles 
> table on the home page. 
>
> This article is a sequel to my 2015 article in Benedikt Hallgrimsson's 
> journal Evolutionary Biology that introduced the BE-PwV plot as the best 
> tool for studying integration in GMM data sets. I trace the basic idea here 
> back nearly a hundred years, not to D'Arcy Thompson but to a 
> hitherto-untranslated critique of his ideas by the Vivarium group under 
> Hans Przibram in Vienna arguing that the only valid way that a biologist 
> should study organismal form is by direct experimental observation of 
> transformation grids: "Thompson's holistic deformations can be made 
> comprehensible if we can visualize a space lattice upon the living form, so 
> as to assess how each little piece changes its shape under conditions that 
> vary by species. Here lies open a rich, nearly undeveloped field that 
> invites a mathematization, one whose erection we hope will begin very 
> soon." But the timing seems to have slipped a bit, namely, by 97 years. The 
> new paper argues that BE-PwV is exactly the "mathematization" they were 
> envisioning, which could not be made empirical until the development of 
> geometric morphometrics, and further that it is the only morphometric 
> method consistent with the most fundamental fact in all of biology, "the 
> repetitive production of organized heterogeneity" (Hotchkiss 1958) or, as 
> Walter Elsasser put it in 1987, "the transfer of information over finite 
> intervals of time without an intermediate message." For instance, the new 
> article demonstrates how to recognize a growth-gradient explicitly even in 
> the presence of unstructured residual variability. I close with a plea that 
> others help me build the bridge that we need so urgently between the 
> arithmetic of today's burgeoning image-based data resources and the 
> rhetoric of biological explanations of organismal form both over evolution 
> and over development. 
>
> As always I welcome all comments on these ideas, enthusiastic or 
> otherwise. 
>
>    Fred Bookstein 
>

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[MORPHMET] PhD Opportunity in human shape measurement

2019-04-30 Thread Simon Choppin
Hello all,

I work in the area of 3D imaging of humans and human measurement. I'm 
particularly interested in the application of this technology to measure 
shape. We have developed some techniques based on geometric morphometrics 
and we now want to move to the next stage of trying to link shape to 
health/performance.
 I'm looking for potential PhD students but struggling to find potential 
applicants with the right interests and skill set. I thought this might be 
the right place!

There is a potential for a scholarship open to UK/EU students
 I have some details about my project idea here 
<https://engineeringsport.co.uk/2019/03/31/the-role-of-3d-body-shape-in-assessing-health-risk/>
There is some information about the application process here 
<https://www.shu.ac.uk/campaigns/research-degrees-in-sport-and-physical-activity>

Feel free to contact me directly for questions or queries or pass on to 
potentially interested parties.

Thanks for your help,

Simon Choppin

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[MORPHMET] New Article: Reflections on a Biometrics of Organismal Form

2019-04-30 Thread MORPHMET
[Posted on behalf of Dr. Bookstein] 

Dear MorphMetters, 

I'm happy to announce that my paper "Reflections on a Biometrics of 
Organismal Form" has just been posted for open access by the Springer 
journal Biological Theory. You can get a free copy by pointing your browser 
at 

https://urldefense.proofpoint.com/v2/url?u=https-3A__link.springer.com_journal_13752=DwIBAg=HPMtquzZjKY31rtkyGRFnQ=T8Sxf-U51iRHIXQayyjGAA=xOGtb5kpXyYsx7O1ZPeSGHSsh8sLGcIwYOsLoNWTC3I=wQclw8xhArX7488PAUkyik6iPqlhj-vA5-el7VYzF-E=
 

and clicking on what is, for now, the top entry in the Latest Articles 
table on the home page. 

This article is a sequel to my 2015 article in Benedikt Hallgrimsson's 
journal Evolutionary Biology that introduced the BE-PwV plot as the best 
tool for studying integration in GMM data sets. I trace the basic idea here 
back nearly a hundred years, not to D'Arcy Thompson but to a 
hitherto-untranslated critique of his ideas by the Vivarium group under 
Hans Przibram in Vienna arguing that the only valid way that a biologist 
should study organismal form is by direct experimental observation of 
transformation grids: "Thompson's holistic deformations can be made 
comprehensible if we can visualize a space lattice upon the living form, so 
as to assess how each little piece changes its shape under conditions that 
vary by species. Here lies open a rich, nearly undeveloped field that 
invites a mathematization, one whose erection we hope will begin very 
soon." But the timing seems to have slipped a bit, namely, by 97 years. The 
new paper argues that BE-PwV is exactly the "mathematization" they were 
envisioning, which could not be made empirical until the development of 
geometric morphometrics, and further that it is the only morphometric 
method consistent with the most fundamental fact in all of biology, "the 
repetitive production of organized heterogeneity" (Hotchkiss 1958) or, as 
Walter Elsasser put it in 1987, "the transfer of information over finite 
intervals of time without an intermediate message." For instance, the new 
article demonstrates how to recognize a growth-gradient explicitly even in 
the presence of unstructured residual variability. I close with a plea that 
others help me build the bridge that we need so urgently between the 
arithmetic of today's burgeoning image-based data resources and the 
rhetoric of biological explanations of organismal form both over evolution 
and over development. 

As always I welcome all comments on these ideas, enthusiastic or otherwise. 

   Fred Bookstein 

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[MORPHMET] new article out on digital morphology data openness based on Morphmet survey

2019-04-29 Thread Christy Hipsley
Dear Morphmet community,

Almost 2 years ago Emma Sherratt and I posted a survey here asking your 
feedback on generation and use of digital morphology data, and we are happy 
to announce that those results have now been published in a Comment article 
in Scientific Data titled '*Psychology, not technology, is our biggest 
challenge to open digital morphology data*', available here ->
https://www.nature.com/articles/s41597-019-0047-0.

We thank everyone again who participated, and many others who have engaged 
in similar conversations over the years. 

Best,
Christy + Emma


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Re: [MORPHMET] Help with surface scans

2019-04-27 Thread Ariadne Schulz
I'm coming at this a bit late so I apologize if I've repeated anyone's
point. For your purposes photogrammetry is probably your best option
particularly for the lithics. Laser scanning works on bones and I used a
NextEngine scanner for human proximal long bones, but I think someone has
already mentioned that the laser doesn't capture the orbitals well and you
might have difficulty with tooth enamel. The photogrammetry software
requires a decently hefty laptop, but it's affordable and you'd be working
with normal light rather than lasers. I don't know that this clears up your
concerns about fusing scans though. If you are concerned you could do some
error testing on that comparing landmarks obtained on the scans to
landmarks obtained normally. I found the laser scans to be pretty decent,
but I unfortunately cannot speak to photogrammetry as I've never personally
tried it.

On Mon, Apr 22, 2019 at 3:29 PM Pablo Fisichella 
wrote:

> Dear All
>
> I´m trying to obtain surface scans from human skulls and lithic artifacts
> (projectile points). I wonder how can I get the most complete possible
> scans, I mean usually is not possibly to obtain a complete scan at once. I
> know that several post-scan processing software have functions to fuse
> and/or align the different surfaces obtained and then create one surface
> but perhaps several of you have some tips to obtain the most complete
> possible surface scans.
>
> Any suggestion and advice is more than welcome
>
> All best,
>
> Pablo
>
> --
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[MORPHMET] Re: Help with surface scans

2019-04-27 Thread Robert Selden
 

Hi Pablo,

 

I work pretty extensively with surface scans of ceramics, lithics, human 
crania, mandibles, and femurs (some examples here - 
https://sketchfab.com/zac_selden), and would be happy to discuss the 
methods that I use off-list if you are interested. 

 

I would also encourage you to review the MORPHMET archive as questions 
regarding 3D scanning and data collection pop up pretty regularly.

 

Respectfully,

Zac Selden

 

 

 

“*The absence of evidence is not evidence of absence*.” – Carl Sagan, *The 
Demon-Haunted World: Science as a Candle in the Dark*

*Robert Z. Selden Jr., Ph.D., R.P.A.* *|* *Research Associate*

Heritage Research Center
Stephen F. Austin State University
*P* 936.468.3953 | *F* 936.468.2190 | *E* zsel...@sfasu.edu

 

The views and opinions expressed in this message are my own and do not 
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On Monday, April 22, 2019 at 9:29:07 AM UTC-5, Pablo Fisichella wrote:
>
> Dear All
>
> I´m trying to obtain surface scans from human skulls and lithic artifacts 
> (projectile points). I wonder how can I get the most complete possible 
> scans, I mean usually is not possibly to obtain a complete scan at once. I 
> know that several post-scan processing software have functions to fuse 
> and/or align the different surfaces obtained and then create one surface 
> but perhaps several of you have some tips to obtain the most complete 
> possible surface scans.
>
> Any suggestion and advice is more than welcome 
>
> All best,
>
> Pablo
>

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Re: [MORPHMET] Help with surface scans

2019-04-25 Thread Pablo Fisichella
Dear All,

Thank you very much for all of your suggestions. I really appreciate your
advice. I´ll chek in detail all of your suggestions and I'll communicate
again if needed.

with kind regards,

Pablo

<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
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El mié., 24 abr. 2019 a las 0:41, Murat Maga () escribió:

> Dear Pablo,
>
>
>
> It has been a while I worked with surface scanners. When I was using a
> Konica/Minolta system (15 years ago), we will do a rotational scan (using a
> turntable), at specified interval (say every 20-30 degrees of rotation).
> Then the software will stitch them together and then we would evaluate the
> missed regions in 3D rendering, then reposition the specimen accordingly
> and capture missing portions as individual snapshots and patch the 3D
> reconstruction. So essentially it was a trial and error process.
>
>
>
> I think the quality of and the speed of the reconstruction software have
> improved tremendously (almost to the point of real-time in some cases), but
> I believe process is essentially the same. Perhaps someone with more recent
> knowledge of this technology can chime in.
>
>
>
> M
>
>
>
> *From:* Pablo Fisichella 
> *Sent:* Monday, April 22, 2019 7:29 AM
> *To:* morphmet@morphometrics.org; morphmet_modera...@morphometrics.org
> *Subject:* [MORPHMET] Help with surface scans
>
>
>
> Dear All
>
> I´m trying to obtain surface scans from human skulls and lithic artifacts
> (projectile points). I wonder how can I get the most complete possible
> scans, I mean usually is not possibly to obtain a complete scan at once. I
> know that several post-scan processing software have functions to fuse
> and/or align the different surfaces obtained and then create one surface
> but perhaps several of you have some tips to obtain the most complete
> possible surface scans.
>
> Any suggestion and advice is more than welcome
>
> All best,
>
> Pablo
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>

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[MORPHMET] Postdoc positions - MCZ

2019-04-24 Thread Pedro Romano
Hi guys,

There are two new NSF funded postdoc positions available in the MCZ for
Vertebrate Paleontology: 1 in biomechanics and 1 with histology. It may be
of interest to some of you. For more information:

https://academicpositions.harvard.edu/postings/8941

https://academicpositions.harvard.edu/postings/8939

best regards,
Pedro

---
*Pedro S. R. Romano*
Professor Associado I
Departamento de Biologia Animal <http://www.dba.ufv.br/>
Universidade Federal de Viçosa <https://www.ufv.br/>
+55 31 38993775

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Re: [MORPHMET] Help with surface scans

2019-04-24 Thread Abel Bosman
Dear Pablo,

While I am unsure about lithic artifacts (as I don't have much experience
in scanning these), I have personally succesfully used a NextEngine laser
scanner to scan human crania. As you say, while it is not possible to get a
complete scan in one go, it is usually possible to do it in two sittings.
In the first instance, you place the cranium so that it is resting on its
basicranium (more or less Frankfurt Horizontal) and complete a full 360
scan. Then, you fix the cranium in place so that its occipital bone is on
the plateau and frontal bone upwards. Then you perform the second scan.
Later down the line, you can stitch these two together quite easily using
the software that comes with the scanner (ScanStudio), or use something
like Meshlab. For this stitching, you just need to make sure that you have
homologous landmarks that you can use to tell the software which structures
should align.

Ofcourse, if you have a Breuckmann structured light scanner or similar with
a wider field of view, it will be a bit easier to scan the crania, although
you still need to do two sittings, since you are not capturing the area on
which your specimen is resting-
If it is available for you, I would advise looking into a handheld scanner,
like the Artec Spider. The newer models are super fast, easy to use, and
you scan in real time, meaning that you can quite easily turn your specimen
around, continue scanning and stitch everything together with the
accompanying software.

Note that with all of these, it will still be quite difficult to get some
of the more complex areas scanned. For example, the NextEngine sometimes
has trouble in scanning the oribital roofs, as the lasers cannot reach this
area easily. Something like the Artec has less issue with this, as you can
move the scanner around more freely (as opposed to conventional scanners,
where you move the specimen around and not the scanner). Lithic artifacts
might be easier, but their reflective surfaces (think obisidian) might give
you other issues since they can scatter the lasers projected by some of
this hardware.

Hope this helps and if you have any specific questions, please let me know.

With kind regards,
Abel

Op wo 24 apr. 2019 om 05:44 schreef Murat Maga :

> Dear Pablo,
>
>
>
> It has been a while I worked with surface scanners. When I was using a
> Konica/Minolta system (15 years ago), we will do a rotational scan (using a
> turntable), at specified interval (say every 20-30 degrees of rotation).
> Then the software will stitch them together and then we would evaluate the
> missed regions in 3D rendering, then reposition the specimen accordingly
> and capture missing portions as individual snapshots and patch the 3D
> reconstruction. So essentially it was a trial and error process.
>
>
>
> I think the quality of and the speed of the reconstruction software have
> improved tremendously (almost to the point of real-time in some cases), but
> I believe process is essentially the same. Perhaps someone with more recent
> knowledge of this technology can chime in.
>
>
>
> M
>
>
>
> *From:* Pablo Fisichella 
> *Sent:* Monday, April 22, 2019 7:29 AM
> *To:* morphmet@morphometrics.org; morphmet_modera...@morphometrics.org
> *Subject:* [MORPHMET] Help with surface scans
>
>
>
> Dear All
>
> I´m trying to obtain surface scans from human skulls and lithic artifacts
> (projectile points). I wonder how can I get the most complete possible
> scans, I mean usually is not possibly to obtain a complete scan at once. I
> know that several post-scan processing software have functions to fuse
> and/or align the different surfaces obtained and then create one surface
> but perhaps several of you have some tips to obtain the most complete
> possible surface scans.
>
> Any suggestion and advice is more than welcome
>
> All best,
>
> Pablo
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
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> To unsubscribe from this group and stop receiving emails from it, send an
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>
> --
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> ---
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RE: [MORPHMET] Help with surface scans

2019-04-23 Thread Murat Maga
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[MORPHMET] Help with surface scans

2019-04-22 Thread Pablo Fisichella
Dear All

I´m trying to obtain surface scans from human skulls and lithic artifacts
(projectile points). I wonder how can I get the most complete possible
scans, I mean usually is not possibly to obtain a complete scan at once. I
know that several post-scan processing software have functions to fuse
and/or align the different surfaces obtained and then create one surface
but perhaps several of you have some tips to obtain the most complete
possible surface scans.

Any suggestion and advice is more than welcome

All best,

Pablo

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Re: [MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-15 Thread Miguel Eduardo Delgado Burbano
Dear Antonio,

Thank you very much for your functions. All of them work very well. I
realized that a simple modification of the function read.landmarks from the
nat package allows load into the R console Avizo Landmarks in ascii format
but not semilandmark curves. Again thanks for your kind help.

All best,

Miguel


El lun., 15 de abr. de 2019 5:46 p. m., Antonio Profico <
antonio.prof...@uniroma1.it> escribió:

> Hi Miguel,
>
> thanks for sending me the example files. You can use the existing
> functions embedded in Arothron:
>
> library(Arothron)
> land.set<-"landmarksfromAvizo"
> set<-read.amira.set(land.set,"auto") #this is an array
> bspline<-"bsplinefromAvizo"
> set_2<-read.amira.set(bspline,"auto") #this is an array
> LineSet<-"linesetfromAvizo"
> curve_temp<-read.path.amira(LineSet) #this is a data.frame
> curve<-as.matrix(curve_temp)
>
> library(Morpho)
> #sample evenly spaced points (10 in this case) along "curve"
> ev.sp.points<-equidistantCurve(curve,10)
>
> Best,
>
> Antonio
>
> Il giorno lun 15 apr 2019 alle ore 01:35 Antonio Profico <
> antonio.prof...@uniroma1.it> ha scritto:
>
>> Hi Miguel,
>>
>> please send me the two files from Avizo (.ladmarkAscii) and B-splines
>> (.am).
>> Are you sure that read.amira.set() doesn't work with the .landmarkAscii
>> files from Avizo?
>>
>> I'll add these two functions in Arothron and before to submit the new
>> release to the CRAN I'll send them to you.
>>
>> Best,
>>
>> Antonio
>>
>> Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano <
>> mdelgadoburb...@gmail.com> ha scritto:
>>
>>> Dear All,
>>>
>>> I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from
>>> Avizo (Standard Edition 7.1.0). I have used previously the Arothron and Nat
>>> packages to load landmarks derived from Amira into the R console. Now
>>> using the Avizo files such packages do not seem to work. Somebody has a
>>> script to read Avizo files in R or know a way to succesfully load such
>>> files into the R console? Thanks for any suggestion
>>>
>>> All best,
>>>
>>> Miguel
>>>
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>>
>>
>> --
>> __
>>
>> Antonio Profico
>> PhD
>> Department of Environmental Biology – Dipartimento di Biologia Ambientale
>> SAPIENZA Università di Roma
>>
>> MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
>> Subscription: https://groups.google.com/forum/#!forum/microwear/join
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>> Subscription: https://groups.google.com/forum/#!forum/arothron/join
>>
>> Lab.  06 4991 2690
>> Mob. 3293440766
>>
>
>
> --
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>
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> PhD
> Department of Environmental Biology – Dipartimento di Biologia Ambientale
> SAPIENZA Università di Roma
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Re: [MORPHMET] A question about geometric morphometrics

2019-04-15 Thread Joseph Kunkel
With reference to the Yang Chang skull group query:

I am a devotee of Analysis of Dispersion combined with Factorial Design of CR 
Rao (1965).

The model is  Y = XB

Y is a n by 3k+c matrix of n rows of k xyz coordinates plus c covariates such 
as size and weight covariates.

X is a n by p design matrix of assignment multipliers to chose the B matrix 
factor values. 

-the elements of X are usually 1s, 0s and -1s.

B is a matrix of p by 3k+c factors which are tested for their significance as 
factors.

As usual the solution is B = (X’X)^-1(X’Y).

3k columns of Y are the matrix of landmarks rotated and resized by the usual 
landmark alignment process. And one of the c columns of the Y matrix is the 
resizing size value produced in the alignment.

I use the Analysis of Dispersion (Rao 1965) to test the significance and obtain 
the crossproducts matrices that reduces the total sums of squares and 
crossproducts matrix Y’Y for the mean and independent factors, in your case the 
groups of skulls.

The residual covariance matrix is used to test for the significance of the 
factors which at this point are not corrected for the covariance with size (for 
instance).

Next, within Rao's Analysis of Dispersion one tests the factor crossproducts 
matrices of the Y columns for whether there is any additional information in 
one or more of the covariates (such as the size column).  If there is no 
additional info in the size covariate one can ignore it.  If one or more 
covariates is significant one can change the Equation to be:

Y’ = ZB = [Yc | Yd | X]B

Y' is the Y matrix with the covariate columns removed.

Yc and Yd are the significant covariate columns appended to the design matrix X 
to create Z extended design.

That system of matrix equations is solved the same way as previously but since 
c and d covariates are likely not independent of the factor design columns 
their sums of squares and crossproducts reduction are calculated by subtraction 
rather than being independently calculable.

This is all quite simple if one is familiar with factorial design, just 
generalized to a n by 3k Y matrix of observations.

It is explained in matrix algebra by Rao (1965).

I have implemented it in R if you have the patience of following the rules of 
design matrices and choosing factors to be tested independently or by 
subtraction.

I am not sure Jim would approve of this specific approach but I am convinced 
that it is correct and gives you a test of significance as well as a way of 
calculating the expected Y', Yhat.

Yhat = ZB

Which provides with the factors which allows computation of average differences 
between factor groups and with chosen c and d covariate effects.

CR Rao (1965) Linear Statistical Inference and Its Applications.John Wiley & 
Sons, New York, 522pp.
I have recently upgraded my R scripts to be consistent with recent versions of 
R. The two relevant R-scripts are Andy.R and ad info.R

http://www.bio.umass.edu/biology/kunkel/pub/r_scripts/andy/ 
<http://www.bio.umass.edu/biology/kunkel/pub/r_scripts/andy/>

The sample inputs found there are csv matrices that a simple YX matrices of 
appended Y and design matrix X.

If you need help with their use I am available by Email.

Joe
-·.  .· ·.  .><º>·.  .· ·.  .><º>·.  .· ·.  .><º> .··.· >=-   
=º}><
Joseph G. Kunkel, Research Professor
122C/125 Pickus Center for Biomedical Research
Marine Science
University of New England
Biddeford ME 04005
http://www.bio.umass.edu/biology/kunkel/ 
<http://www.bio.umass.edu/biology/kunkel/>


> On Apr 11, 2019, at 5:31 AM, yang Chang  wrote:
> 
> I want to compare skull morphology using geometric morphometrics from several 
> species with different diets in a same genus. But I don't know much about how 
> to analyze these shape data. What statistical analysis can I do? I know that 
> principal component analysis can be done to visualize shape variations. So 
> can I use the original coordinate data? Do I need to remove the effects of 
> size and phylogenetic relationships to do principal component analysis? If 
> so, do I use PGLS to do the regression of shape and size, and then use the 
> obtained residual as the principal component analysis? In addition to this 
> analysis, what other aspects can I do? Looking forward to reply.Thanks very 
> much!
> 
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[MORPHMET] A question about geometric morphometrics

2019-04-15 Thread yang Chang
I want to compare skull morphology using geometric morphometrics from several 
species with different diets in a same genus. But I don't know much about how 
to analyze these shape data. What statistical analysis can I do? I know that 
principal component analysis can be done to visualize shape variations. So can 
I use the original coordinate data? Do I need to remove the effects of size and 
phylogenetic relationships to do principal component analysis? If so, do I use 
PGLS to do the regression of shape and size, and then use the obtained residual 
as the principal component analysis? In addition to this analysis, what other 
aspects can I do? Looking forward to reply.Thanks very much!

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Re: [MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-15 Thread Antonio Profico
Hi Miguel,

thanks for sending me the example files. You can use the existing functions
embedded in Arothron:

library(Arothron)
land.set<-"landmarksfromAvizo"
set<-read.amira.set(land.set,"auto") #this is an array
bspline<-"bsplinefromAvizo"
set_2<-read.amira.set(bspline,"auto") #this is an array
LineSet<-"linesetfromAvizo"
curve_temp<-read.path.amira(LineSet) #this is a data.frame
curve<-as.matrix(curve_temp)

library(Morpho)
#sample evenly spaced points (10 in this case) along "curve"
ev.sp.points<-equidistantCurve(curve,10)

Best,

Antonio

Il giorno lun 15 apr 2019 alle ore 01:35 Antonio Profico <
antonio.prof...@uniroma1.it> ha scritto:

> Hi Miguel,
>
> please send me the two files from Avizo (.ladmarkAscii) and B-splines
> (.am).
> Are you sure that read.amira.set() doesn't work with the .landmarkAscii
> files from Avizo?
>
> I'll add these two functions in Arothron and before to submit the new
> release to the CRAN I'll send them to you.
>
> Best,
>
> Antonio
>
> Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano <
> mdelgadoburb...@gmail.com> ha scritto:
>
>> Dear All,
>>
>> I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from
>> Avizo (Standard Edition 7.1.0). I have used previously the Arothron and Nat
>> packages to load landmarks derived from Amira into the R console. Now
>> using the Avizo files such packages do not seem to work. Somebody has a
>> script to read Avizo files in R or know a way to succesfully load such
>> files into the R console? Thanks for any suggestion
>>
>> All best,
>>
>> Miguel
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "MORPHMET" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to morphmet+unsubscr...@morphometrics.org.
>>
>
>
> --
> __
>
> Antonio Profico
> PhD
> Department of Environmental Biology – Dipartimento di Biologia Ambientale
> SAPIENZA Università di Roma
>
> MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
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> Lab.  06 4991 2690
> Mob. 3293440766
>


-- 
__

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Department of Environmental Biology – Dipartimento di Biologia Ambientale
SAPIENZA Università di Roma

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Re: [MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-14 Thread Miguel Eduardo Delgado Burbano
Dear Murat and Antonio,

Thanks for your fast response. Of course Murat here I attach the
corresponding files (they derived from Avizo not from Amira)

Antonio yes I tried to use the Arothron function read.amira.set () but the
following error appeared: argument "nland" is missing, with no default.

Here I attach three files one is Landmarks_LLM1_landmarksAscii (landmarks
from a human lower molar) and one B-spline in Avizo binary (*.am) format
and the same file in Avizo ascii (*.am) format
(zan0084_manleft_mirrored_01_curve_LM1.am and
zan0084_manleft_mirrored_01_curveascii_LM1.am)

Thanks for your help

All best,


El lun., 15 de abr. de 2019 8:15 a. m., Murat Maga  escribió:

> Dear Antonio and Miguel,
>
>
>
> Would it be possible to share those files with me as well? I would like to
> implement a way to import Amira landmark files into our SlicerMorph
> package, but we don’t have any to play with.
>
>
>
> Best,
>
> M
>
>
>
>
>
> *From:* Antonio Profico 
> *Sent:* Sunday, April 14, 2019 4:35 PM
> *To:* Miguel Eduardo Delgado Burbano 
> *Cc:* MORPHMET ;
> morphmet-requ...@morphometrics.org
> *Subject:* Re: [MORPHMET] Script to read Avizo landmarks and B-splines
>
>
>
> Hi Miguel,
>
>
>
> please send me the two files from Avizo (.ladmarkAscii) and B-splines
> (.am).
>
> Are you sure that read.amira.set() doesn't work with the .landmarkAscii
> files from Avizo?
>
>
>
> I'll add these two functions in Arothron and before to submit the new
> release to the CRAN I'll send them to you.
>
>
>
> Best,
>
>
> Antonio
>
>
>
> Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano <
> mdelgadoburb...@gmail.com> ha scritto:
>
> Dear All,
>
>
>
> I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from Avizo
> (Standard Edition 7.1.0). I have used previously the Arothron and Nat
> packages to load landmarks derived from Amira into the R console. Now
> using the Avizo files such packages do not seem to work. Somebody has a
> script to read Avizo files in R or know a way to succesfully load such
> files into the R console? Thanks for any suggestion
>
>
>
> All best,
>
>
>
> Miguel
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
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> To unsubscribe from this group and stop receiving emails from it, send an
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>
>
>
>
> --
>
> __
>
> Antonio Profico
> PhD
> Department of Environmental Biology – Dipartimento di Biologia Ambientale
> SAPIENZA Università di Roma
>
> MicroWeaR mailing list: https://groups.google.com/forum/#!forum/microwear
>
> Subscription: https://groups.google.com/forum/#!forum/microwear/join
>
>
>
> Arothron mailing list: https://groups.google.com/forum/#!forum/arothron
> <https://groups.google.com/forum/#!forum/microwear>
>
> Subscription: https://groups.google.com/forum/#!forum/arothron/join
>
>
> Lab.  06 4991 2690
> Mob. 3293440766
>
> --
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> ---
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# Avizo 3D ASCII 2.0


define Markers 11

Parameters {
Color "1.0.9",
NumSets 1,
ContentType "LandmarkSet"
}

Markers { float[3] Coordinates } @1

# Data section follows
@1
1.069824981689453e+002 3.230857086181641e+001 7.741726684570313e+001 
1.067253570556641e+002 3.117101860046387e+001 7.906603240966797e+001 
1.071337509155273e+002 3.062068939208984e+001 8.174322509765625e+001 
1.044278793334961e+002 3.029200363159180e+001 8.385526275634766e+001 
1.035018234252930e+002 3.330528259277344e+001 8.359550476074219e+001 
1.009194259643555e+002 3.421195983886719e+001 8.097939300537109e+001 
1.022753219604492e+002 3.590150451660156e+001 7.821498870849609e+001 
1.029237899780273e+002 3.457044982910156e+001 7.538016510009766e+001 
1.053571166992188e+002 3.398883819580078e+001 7.497612762451172e+001 
1.059745407104492e+002 3.266828918457031e+001 7.570597839355469e+001 
1.031460418701172e+002 3.211197662353516e+001 7.892

Re: [MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-14 Thread Antonio Profico
Hi Miguel,

please send me the two files from Avizo (.ladmarkAscii) and B-splines (.am).
Are you sure that read.amira.set() doesn't work with the .landmarkAscii
files from Avizo?

I'll add these two functions in Arothron and before to submit the new
release to the CRAN I'll send them to you.

Best,

Antonio

Il giorno lun 15 apr 2019 alle ore 01:26 Miguel Eduardo Delgado Burbano <
mdelgadoburb...@gmail.com> ha scritto:

> Dear All,
>
> I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from Avizo
> (Standard Edition 7.1.0). I have used previously the Arothron and Nat
> packages to load landmarks derived from Amira into the R console. Now
> using the Avizo files such packages do not seem to work. Somebody has a
> script to read Avizo files in R or know a way to succesfully load such
> files into the R console? Thanks for any suggestion
>
> All best,
>
> Miguel
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>


-- 
__

Antonio Profico
PhD
Department of Environmental Biology – Dipartimento di Biologia Ambientale
SAPIENZA Università di Roma

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Subscription: https://groups.google.com/forum/#!forum/microwear/join

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Subscription: https://groups.google.com/forum/#!forum/arothron/join

Lab.  06 4991 2690
Mob. 3293440766

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[MORPHMET] Script to read Avizo landmarks and B-splines

2019-04-14 Thread Miguel Eduardo Delgado Burbano
Dear All,

I'm using landmarks (.ladmarkAscii) and B-splines (.am) derived from Avizo
(Standard Edition 7.1.0). I have used previously the Arothron and Nat
packages to load landmarks derived from Amira into the R console. Now using
the Avizo files such packages do not seem to work. Somebody has a script to
read Avizo files in R or know a way to succesfully load such files into the
R console? Thanks for any suggestion

All best,

Miguel

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[MORPHMET] tpsUtil update

2019-04-10 Thread f.james.rohlf


I have uploaded ver. 1.78 of tpsUtil to the http://life.bio.sunysb.edu/morph
website.

 

It just fixes an internal exception error when one completes the "unbending"
option (after the output file was saved). Thanks to Gabriel Gazzana Barros
for reporting the problem.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] geomorph 3.1.1 released on CRAN

2019-04-03 Thread Adams, Dean [EEOBS]
Colleagues,

I'm pleased to announce that geomorph 3.1.1 is now available on CRAN. As 
always, all changes are noted in the NEWS file and in the appropriate help 
pages. To install geomorph 3.1.1 from within R, simply type:

install.packages('geomorph')

We wish to emphasize that this was a rather substantial update; thus, users are 
highly encouraged to consult all help files for additional information. Though 
some functions have been deprecated, all analyses previously available in 
geomorph are still available (though some more advanced options are now 
accessed in slightly modified form).  Also, to ease users through this 
transition, we have developed a vignette that describes the differences in the 
current version, and how to implement various analyses using the newer 
notation. The vignette is distributed with the installation of geomorph, and 
may be accessed by typing:

browseVignettes(package="geomorph")

In particular, users will notice a change in usage of the 'procD' family of 
functions for assessing linear models. Beginning with geomorph 3.1.1, only 
'procD.lm' and 'procD.pgls' remain, and these have greatly enhanced 
functionality. For instance, one may now utilize type I, type II, or type III 
sums of squares, may specify the error term against which various factors are 
evaluated (to incorporate random effects in simple mixed model designs), and 
may incorporate object-covariance matrices describing non-independence.  
Additionally, pairwise comparisons of means, of slopes, and of within-group 
variation may be accomplished using the 'pairwise' function based off of fitted 
models from 'procD.lm' or 'procD.pgls'. The functions: procD.allometry, 
advanced.procD.lm, and nested.update, have all been deprecated, as their 
analyses are now accomplished (and enhanced) via these other functions. These 
enhancements were made possible by use of the RRPP package (Collyer and Adams, 
2018: Methods Ecol. Evol) which is now more tightly interconnected with 
geomorph.

Finally, for graphical visualization of shapes, we encourage users to explore 
the new picknplot.shapes function, which allows one to select locations from 
just about any kind of plot obtained in geomorph, and generate estimates of 
shapes that correspond to those locations (much like in the TPS series). Also, 
the new plotAllometry function provides several graphical plots commonly used 
in allometric studies. We hope these new graphical options provide additional 
flexibility and usability of geomorph.

Best to all,

Dean, Mike, and Antigoni (the geomorph team)


Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
https://www.eeob.iastate.edu/faculty/adams/
phone: 515-294-3834

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Re: [MORPHMET] Question about MorphoJ/Landmarking

2019-03-27 Thread Amanda Hale
Hi Sara,

In the Preliminaries menu in MorphoJ there is the option to Select Landmarks 
where you can include/exclude any landmarks in your total set. This will create 
a new dataset with only the landmarks you want.

As for informative landmarks, that depends on the structure under study as well 
as sample size. I recommend picking up many of Dr. Klingenberg’s references, 
the Zelditch text (green book) and many, many more to asses the validity of 
landmark dimensionality to sample size and shape characterization.

Best,
Amanda

Amanda R. Hale, M.A., C-FASE II

> On Mar 25, 2019, at 8:41 AM, Sara Schoen  wrote:
> 
> Hello!
> 
> I'm working on the beginnings of a masters thesis and part of it is taking 
> over a project from a previous student. I am learning MorphoJ to help finish 
> that project, but the original student used 14 landmarks (LMs) and we've 
> realized some of those are not helpful in our anaylsis. They act as noise and 
> I've been asked to exclude those points. 
> 
> Is there a way for me to exclude those LMs (as in only consider 1-9 and 
> ignore 10-14) in MorphoJ or would it be better to just start over? 
> 
> If I start over, is there a certain number of LMs I *need* to have? Is there 
> a minimum? How will this change the results if I don't have a lot? The "New" 
> method would include 9 LMs. 
> 
> Thank you to any help/advice you can give me!
> 
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RE: [MORPHMET] Question about MorphoJ/Landmarking

2019-03-27 Thread Murat Maga
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A good place for you to start is the MorphoJ manual. Specifically the Preli=
minaries section
http://www.flywings.org.uk/MorphoJ_guide/frameset.htm?index.htm

As for how the selection of landmarks will affect the results, short answer=
 is it depends. We use landmarks to model a complex shape in a simple and r=
eproducible way. If your end goal is somehow dependen

RE: [MORPHMET] Visualizing shape differences in PCA

2019-03-27 Thread Adams, Dean [EEOBS]
Charles, 

There are several ways to do what you wish within geomorph.  First, the 
plotTangentSpace function does allow one to specify which axes are plotted. 
This can be useful for obtaining shape deformations along the extremes of axes 
other than PC1 and PC2. 

A more flexible option is to use the function shape.predictor. Here, one 
provides scores, say for a given PC or a regression, and can obtain predicted 
shapes based on them. The help file provides example usage for this, and many 
other  applications (e.g., obtain shape deformations for mean shapes, predicted 
shapes, etc.).

Finally, I will also mention that we are about to release a new version of 
geomorph which will include capabilities to select locations in statistical 
plots, which will allow shape visualization of those locations in real time.  I 
will post more on this in the near future.

Hope this helps,

Dean

Dr. Dean C. Adams
Director of Graduate Education, EEB Program
Professor
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
https://www.eeob.iastate.edu/faculty/adams/
phone: 515-294-3834


-Original Message-
From: Charles Zhang  
Sent: Monday, March 25, 2019 4:38 PM
To: MORPHMET 
Subject: [MORPHMET] Visualizing shape differences in PCA

Dear all,

I'm using the Geomorph package in R to do the PCA. It shows the negative-most 
and positive-most shapes of a PC, which is really great. I just want to ask if 
there is any way to visualize shape change along a certain PC? 

I know that Morphologika does this by allowing one to move the cursor along a 
PC to visualize shape change. However, when I import my data to process in the 
Morphologika, it always reports error. Perhaps it is because I use too many 
semilandmarks but too few specimens.

Could you please tell me if there is an alternative way to visualize shape 
differences along a PC, rather than just at the two-end points?

Thank you very much for taking your time to look at my question!

Best regards,
Charles

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[MORPHMET] Question about MorphoJ/Landmarking

2019-03-27 Thread Sara Schoen
Hello!

I'm working on the beginnings of a masters thesis and part of it is taking over 
a project from a previous student. I am learning MorphoJ to help finish that 
project, but the original student used 14 landmarks (LMs) and we've realized 
some of those are not helpful in our anaylsis. They act as noise and I've been 
asked to exclude those points. 

Is there a way for me to exclude those LMs (as in only consider 1-9 and ignore 
10-14) in MorphoJ or would it be better to just start over? 

If I start over, is there a certain number of LMs I *need* to have? Is there a 
minimum? How will this change the results if I don't have a lot? The "New" 
method would include 9 LMs. 

Thank you to any help/advice you can give me!

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[MORPHMET] Visualizing shape differences in PCA

2019-03-27 Thread Charles Zhang
Dear all,

I'm using the Geomorph package in R to do the PCA. It shows the negative-most 
and positive-most shapes of a PC, which is really great. I just want to ask if 
there is any way to visualize shape change along a certain PC? 

I know that Morphologika does this by allowing one to move the cursor along a 
PC to visualize shape change. However, when I import my data to process in the 
Morphologika, it always reports error. Perhaps it is because I use too many 
semilandmarks but too few specimens.

Could you please tell me if there is an alternative way to visualize shape 
differences along a PC, rather than just at the two-end points?

Thank you very much for taking your time to look at my question!

Best regards,
Charles

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[MORPHMET] New Publication

2019-03-25 Thread Javier Santos
Dear Group,

I would like to bring to your attention a publication in course that I have 
just uploaded on the BioRxiv server. It is a direct extract of a chapter in my 
recently defended PhD dissertation:

"Morphological variation in Blommersia pelvic shape coincides with muscular 
architecture and parallels genus phylogenetic evolution"
https://www.biorxiv.org/content/10.1101/586248v1

I believe the manuscript may be the first time the Generalized Procrustes 
Surface Analysis (GPSA; Pomidor et al., 2016) has been successfully applied to 
a biological hypothesis. In any case, I would like to have feedback on the 
interpretation of the results from the experts of the Morphmet community. The 
article will be sent to peer review once the formal description of a couple of 
the species used have been published.

Any and all feedback are welcome as comments on the BioRxiv server or directly 
to me by email. Thank you in advance, and I hope you find the study interesting 



Best wishes,
Javier H. Santos-Santos

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