Re: [MORPHMET] Morphmet in the Future

[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
> ---
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>
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>


-- 

*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 
workphone: +56582386136

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[MORPHMET] Workshop Geometric Morphometrics using R, Concepcion, Chile 2019

[Hugo Benítez]

Dear Morphometricians

Just to remember you that the deadline for applications are the end of
December 2018

The application are open for the course: *"An Introduction to geometric
morphometrics, a workshop using R"* to be given by the team who created the
"geomorph" package, *Dr. Dean Adams, Dr. Mike Collyer and Dr. Antigoni
Kaliontzopoulou.*

This course will be in English language and it will be held at the
Universidad de Concepción, Chile, on *April 8-12, 2019.*

The selection will be competitive according to CV and intention letter that
must be sent to morfot...@gmail.com, or hugobenit...@gmail.com and previous
knowledge on GM and using the R software will be a priority.

The application period will be until *December 30, 2018.*  More details you
can visit my  website: http://www.morphoshape.com
Best wishes

-- 

*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 
workphone: +56582386136

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[MORPHMET] An Introduction to geometric morphometrics, a workshop using R, Concepcion, Chile 2019

[Hugo Benítez]

Dear Morphomet Community

It's a pleasure for me to inform that after hard organization work and
thanks to *CONICYT REDES DE INVESTIGACIÓN: RED170182 (Universidad de
Tarapacá and Universidad de Concepción)*, I have been able to coordinate a
completely free course with three specialists on geometric morphometrics in
R.

I am happy to announce that "application" is open for the course: *"An
Introduction to geometric morphometrics, a workshop using R"* to be given
by the team who created the "geomorph" package, *Dr. Dean Adams, Dr. Mike
Collyer and Dr. Antigoni Kaliontzopoulou.*

This course will be in English language and it will be held at the
Universidad de Concepción, Chile, on *April 8-12, 2019.*

The selection will be competitive according to CV and intention letter that
must be sent to morfot...@gmail.com, or hugobenit...@gmail.com and previous
knowledge on GM and using the R software will be a priority.


The application period will be until *December 30, 2018.*  More details
will be soon in my website: http://www.morphoshape.com
Best wishes

-- 

*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 
workphone: +56582386136

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Re: [MORPHMET] Generating CVA plots using morphoJ

[Hugo Benítez]

Dear Nelly

Please select the original dataset at the Project Tree first and then
perform the CVA...

You have to select the Dataset that have the information you want to study
and then the correct data type... Looking in your picture that option seems
to be correct.

So maybe, the problem come from the availability of classifier, did you set
your classifier before?

So steps

1- Select the classifiers you need and the ones you will use at the CVA
(e.g. population, species, etc)
how to do it:  go to Preliminares (Extract new classifier fom ID or edit
Classifier)

2- Select the original Dataset you want to perform the CVA

3- After check that the dataset and data type are correct in the CVA,
select the classifier and should work.

I hope that helps

Best wishes

Hugo A. Benitez



2017-07-12 2:18 GMT-04:00 Nelly :

>
>
>
> I am learning use of morphoJ for geometric morphometrics. I have generated
> PCA plots for my data. However, when i try to generate CVA plots, i get
> this warning; kindly assist.
>
>
>
>
>
> --
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> ---
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>



-- 

*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 
workphone: +56582386136

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Re: [MORPHMET] MorphoJ Text File Formatting

[Hugo Benítez]

Dear Alicja

This problem is normal when you are trying to open a file that was
digitized in TPS Dig in MorphoJ and when you are creating the project, you
DID NOT select the option TPS  in filetype...

By default MorphoJ when you create a new dataset the filetype is text,
change it for TPS and the problem should be solve!

Let me know if you have any problem later.

Best wishes

Hugo

2017-04-25 4:43 GMT-03:00 Alicja Witwicka :

> Hello everyone,
> I am a complete beginner in geometric morphometrics and I have met one
> problem. Namely, when I try to upload the .tps file created in tpsUTIL to
> MorphoJ software I receive the following communicate:
>
> "Problem with the text file: Line 1 contains less than two entries:
> LM=7
> Note: A frequent reason for this problem is that the file contains
> delimiters other than commas or tab stops.
> Errors occurred in the reading process.
> The new dataset could not be created."
>
> I have tried to change the data manually but it does not work. Anyway, I
> have too many specimens to manage that in such a way. Do you possibly know
> where I can find the source of that problem?
>
> Best regards,
> Alicja
>
> --
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-- 

*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 
workphone: +56582386136

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Re: [MORPHMET] MorphoJ and hidpi screen on windows 10

[Hugo Benítez]

Dear Murat

If you save the graphic in vector scale .ps, svg or another of those, you
can open the images using adobe illustrator or other similar and can be
easily changed from there sadly the font of the axis can not be change
automatically by the software as far I know.

Try using one of the graphic software I gues there are  not hard for this
kind of changes or optimization.

Best wishes
Hugo



El miércoles, 8 de febrero de 2017, Murat Maga  escribió:

> Is there a way to correctly scale font size in MorphoJ on high resolution
> display?
>
> It doesn’t seem to honor the windows’ inherent font scaling, and the
> default fonts are too small. I have to use the magnifying glass and it gets
> tedious very quickly.
>
>
>
> M
>
> --
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> 
> .
>


-- 

*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 
workphone: +56582386136

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[MORPHMET] Curso Teórico Practico: "Introducción a la Morfometría Geométrica” (Tacna, Peru)

[Hugo Benítez]

Dear Morphometricians

I´m pleased to announce a course of Introduction to Geometric 
Morphometrics,  *the language of the course will be Spanish* and will be 
held at Universidad Nacional Jorge Basadre Grohmann,  Tacna,  PERU (April 
10-14, 2017)

-

Estimados Colegas


Mediante el presente correo anuncio el Curso Teórico Practico: 
"Introducción a la Morfometría Geométrica” el cual se dictara el próximo 
10-14 de Abril en la Ciudad de Tacna Perú (Universidad Nacional Jorge 
Basadre Grohmann)  el valor de la inscripción será de 300 soles 
aproximadamente 88 dólares.   

Para mayor informacion de inscripciones escribir a:  
cursomorfometriageometr...@gmail.com

La informacion aparecera pronto tambien en www.morphoshape.com

Programa Potencial:  

 

*Lunes*

 

-  Introducción: ¿Qué es la Morfometría?  Conceptos en Morfometría 
tradicional y Morfometría Geométrica.

-  Software disponibles y sus diferencias. 

-  Adquisición de datos, digitalización (Landmarks y Semilandmarks). 

-  Tamaño y Forma, Análisis de Procrustes Generalizado, Espacios 
Morfométricos.

-  Practica digitalización. 

 

*Martes*

 

-  Matrices de Covarianza y Visualización de resultados en 
Morfometría Geométrica:  Thin Plate-Spline, Tipos Warps (Principal, 
Partial, Relative).

-  Análisis exploratorios, Análisis de Componentes principales (PCA) 

-  Practica visualización de resultados.

 

*Miércoles*

 

-  Error de Medición en Morfometría geométrica.

-  Distinciones entre grupo de individuos: Análisis discriminante y 
Canónicos (CVA).

-  Alometría (Corrección del tamaño en la forma) Regresión 
multivariada.

-  Practica Error de Medición, distinción de grupos y regresión 

 

*Jueves*

-  Simetría, Tipos de Simetría y aplicaciones con énfasis en 
estudio de estabilidad del desarrollo (Asimetría Fluctuante).

-  Integración Morfológica.

-  Modularidad.

-  Practica.

 

*Viernes*

-  Morfometría y Filogenia

-  Practica y Cierre curso (Posible exposiciones estudiantes) 

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Re: [MORPHMET] Loss of indentifiers in MorphoJ

[Hugo Benítez]

Dear Chrissy

That generally occur when the ID keyword is not set automatically in TPS
after every image, but there is a trick very quick and easy and MorphoJ
will read the name of your IMAGES that have the correct ID names.

So OPEN YOUR TPS file in notepad and have a look this (I copied an example
with 5 landmarks) if  *ID said a number*  is the thing MorphoJ is already
recognizing in your File...

LM=5
252.0 1000.0
341.0 943.0
651.0 917.0
834.0 851.0
735.0 679.0
IMAGE=AMac2F01_l.jpg
*ID=0*


This can be FIX easily with a text editor by changing every occurrence of
"ID=" into something else, for instance (use in notepad rename all ID to
"@ID=") and save the file with other name.

Now open the file with MorphoJ again and check your identifiers (always
remember select TPS file in MorphoJ). If this is done, MorphoJ will use the
IMAGE= keyword instead.  and everything will work perfectly.

Let me know if you need further help.

Best wishes

Hugo

2016-04-04 12:25 GMT+01:00 Christina Berry :

> Hey guys,
>
> very simple problem that I can't seem to fix, I have converted my image
> files using tpsUtil to then place landmarks on the newly created TPS file
> in tpsDig2.  Now when I import this into MorphoJ and go to extract new
> classifiers from ID string I am finding that all my file ID's have gone and
> are replaced by numbers 0-19 (there are 20 samples in the file).  I have
> gone back to my file in tpsDig2 and checked that each image still has it's
> ID and it does but it seems to disapeerr once in MorphoJ.
>
> Please help!
>
> Chrissy
>
> --
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-- 
Hugo A. Benítez
   Biologist
  MSc in Zoology
PhD (c) Evolutionary Biology
University of Manchester
http://www.morphoshape.com 

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Re: [MORPHMET] image names tps series

[Hugo Benítez]

Dear Patrick



If you have already named your images and you want to use the names to set
the classifiers in MorphoJ you have 2 options.


 MorphoJ read the ID files of the TPS files by defect but you will only
have the ID name if you rename every figure at the landmarking
process.  Therefore
Option 1: Go to your TPS Dig and for every picture already digitized set
the ID name. (go to option / Specimen info / and name the ID of your
specimens and press OK)  after rename all the ID names save the new TPS
file and import again to MorphoJ,  and you will have the name now instead
0,1,2,3.

Option 2: Is modifying the TPS file.  In my opinion this option is easier
if you already have the pictures with landmarks.   Open the TPS file with
notepad or some text editor:



1- A TPS file with data look like (open in a text editor)

*LM=5 *

*252.0 1000.0 *

*341.0 943.0 *

*651.0 917.0 *

*834.0 851.0 *

*735.0 679.0 *

*IMAGE=AMac2F01_l.jpg *

*ID=0 *



To use the IMAGE= keyword, it is therefore helpful to disable the ID=
keyword. This can be done easily with your text editor by changing every
occurrence of "ID=" into something else, for instance "@ID=" (in this way,
the change is reversible if you want to use the same TPS file for something
else...). If this is done, MorphoJ will use the IMAGE= keyword instead.

Therefore, just in the text editor, go to edit / replace / replace ALL: ID
to @ID or *ID accept and all the ID will now have this new sign that MophoJ
will not recognize and will use the IMAGE name.  Save your new file
“file.tps”  and open it now with MorphoJ.



I hope that helps.



Best wishes

Hugo



2015-06-10 10:25 GMT+01:00 Patrick Arnold :

> Dear all,
>
> I am having a tiny problem when combining tps series and MorphoJ. I
> created tps file with tpsutil, digitized landmarks with tpsdig2 and import
> the dataset into MorphoJ. Unfortunately, image names are not included in
> MorphoJ and thus I am not able to extract classifiers from ID. I thought
> image names are automatically included when creating tps file and I cannot
> find to option to do this manually.
> How to solve this? Thanks in advance.
>
> Patrick
>
>
> --
> Patrick Arnold, M.Sc.
>
> Institut für Spezielle Zoologie und Evolutionsbiologie
> mit Phyletischem Museum
> Friedrich-Schiller-Universität Jena
> Germany
>
> 
> This message was sent through https://webmail.uni-jena.de
>
> --
> 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.
>



-- 
Hugo A. Benítez
   Biologist
  MSc in Zoology
PhD (c) Evolutionary Biology
University of Manchester
http://www.hugoabenitez.com

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