[MORPHMET] Updated list of references on Arthropoda morphometrics

2014-08-08 Thread Mauro Cavalcanti 
Dear ALL,

I am taking this opportunity of unveiling the new Morphometrics discussion
list to announce that an updated list of the bibliographic database on
arthropods is available for browsing and downloading from the MorphoLib
website (http://morpholib.eu.pn). This specific list is compiled and
managed by Ivan Huber.

Hope this helps!

Cheers,

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

-- 
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Re: [MORPHMET] Re: Updated list of references on Arthropoda morphometrics

2014-08-08 Thread Mauro Cavalcanti 
Dennis,

Thank you very much!

BTW Congratulations for the new Morpheus, which looks great!

Cheers,


2014-08-08 14:25 GMT-03:00 dslice dsl...@morphometrics.org:

 I have added the link to this to the Other Online Morphometric Resources
 section at www.morphometrics.org -ds

 On Friday, August 8, 2014 1:22:57 PM UTC-4, maurobio wrote:

 Dear ALL,

 I am taking this opportunity of unveiling the new Morphometrics
 discussion list to announce that an updated list of the bibliographic
 database on arthropods is available for browsing and downloading from the
 MorphoLib website (http://morpholib.eu.pn). This specific list is
 compiled and managed by Ivan Huber.

 Hope this helps!

 Cheers,

 --
 Dr. Mauro J. Cavalcanti
 E-mail: mauro...@gmail.com
 Web: http://sites.google.com/site/maurobio

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

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-- 
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Re: [MORPHMET] Morphometric and leaf ontogeny

2014-08-24 Thread Mauro Cavalcanti 
Hi,

Visit the MorphoLib website (http://morpholib.eu.pn/), a list of references
on leaf morphometrics is now available there.

Hope this helps.

Cheers,


2014-08-24 3:42 GMT-03:00 d...@walla.co.il d...@walla.co.il:

 Dear All,

 I am looking for papers on morphometric and leaf ontogeny, does any one
 has a good reference list or pdf's to share?

 Thanks

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Web: http://sites.google.com/site/maurobio

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[MORPHMET] MorphoLib updates

2014-09-03 Thread Mauro Cavalcanti 
Dear ALL,

This is to announce the availability of updates to the Morphometrics
Library at http://morpholib.eu.pn

A new section on Links has been added, with a (non-exaustive!) list of
websites on morphometrics.

An entirely new list of bibliographic references, on plant geometric
morphometrics, has been added.

The list of references on mollusk morphometrics has been updated.

Thanks to Simon Mayo, Emma Sherrard, Ingo Schindler, and Corrado Costa for
sending me references. Thanks also to the Morpmetrics.org The Management
(;-)) for the excellent job in setting up the new, much improved,
Morphomet-L discussion list and overall inspiration

More soon...

Cheers,

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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[MORPHMET] MorphoLib access problems

2014-09-04 Thread Mauro Cavalcanti 
Dear ALL,

A few visitors have reported that they have not been able to access the
MorphoLib website at http://morpholib.eu.pn, even suggesting that the URL
may not be valid. In fact, it is. What seems to happen is that some people
maybe behind a firewell that prevents access to websites with 'unusual'
domain names like '.pn' (which refers to the Pitcairn Islands!). In such
cases, I can only suggest trying access the site from a different location
(and a different ISP) and see if the problem persists.

MorphoLib is maintained entirely on the basis of my volunteer work, as a
service to the morphometrics community that for so many years has been so
helpful and resourceful to me. This means that I do not have any available
funds to maintain a domain and therefore resort to a free (but really very
reliable) hosting service which also offers me a free domain name (in this
case, morpholib (dot) eu (dot) pn.

In a world where violence (both against people and the natural environment)
seems to prevail, it is my deepest conviction that we, scientists, should
be strongly commited to openness and the free (both as free speech and,
when possible, also as 'free beer') sharing of information (which includes
ideas, data, and tools to process and and share them).

With warmest regards, :-)

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

-- 
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Re: [MORPHMET] Recent site outage

2014-09-11 Thread Mauro Cavalcanti 
Dear Management,

Here, I have been able to access Morphometrics.org without any trouble.

Hope this helps.

Cheers,

2014-09-11 18:19 GMT-03:00 MORPHMET morphmet@morphometrics.org:

 Yesterday, the website and MORPHMET went down. The reason was that I asked
 to cancel account with the original (more expensive) service provider. When
 they did this, it wiped out something called the Zone File. I spent a
 significant part of today getting that restored. I think it works, now, but
 I cannot be certain about access to non-owners - I am, of course, the owner
 and it works perfectly for me. I think, but am not certain, that it should
 now be accessible to all as before: http://www.morphometrics.org.

 -The Management

 --
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-- 
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E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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[MORPHMET] New version of The Morphometrics Library website

2014-09-30 Thread Mauro Cavalcanti 
Dear ALL,

Just as Microsoft announced the shift from Windows 8.1 to Windows 10 (a
giant leap for mankind, no doubt!), I am pleased to announce that a new and
improved version of The Morphometrics Library (MorphoLib) website is now
available from http://morpholib.eu.pn/

All materials from the former version are of course available, but now much
better organized and accessible in a PHP-based content management system
which will make mantainence much easier and faster than the previous
version using simple plain HTML pages.

A new Software section has been added, listing just a few of the more
comprehensive program packages for geometric morphometrics analysis (plus
the available R libraries, as I think that is the way to go).

Also, a new reference list, on amphibians and reptiles (herptiles)
morphometrics has just been started; but notice that this is still quite
rudimentary and I have plenty of references on the subject (having an
interest in these critters myself), which I will add as time allows. This
list is also more eclectic in that it includes papers dealing with more
traditional morphometrics too. Many thanks to Dany Adams for providing the
initial stimulus for me to starting this yet another reference list.

Other lists have been updated, especially the list of references on
arthropods mantained by Ivan Huber with the inclusion of a lot of citations
sent to us by Hugo Benítez. Thanks a lot to Ivan and Hugo for their great
help!

Well, it looks like what started as a simple way to share my reference
lists on morphometrics has evolved by itself into an information portal
(well, sort of ;-))  on geometric morphometrics literature.

Hope it is useful.

With warmest regards,

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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[MORPHMET] A question about PCA in geomorph

2015-04-11 Thread Mauro Cavalcanti 
Dear ALL,

I have a number of questions about the geomorph R package, that I will post
here in separate messages.

First one concerns Principal Components Analysis, using the
plotTangentSpace routine. It requires a 3D matrix as argument, however my
data (on fishes) are 2D and I could not figure out how to convert my data
to the required format; the explanation of the arrayspecs routine in the
Quick Guide to Geomorph was not clear for me (and it lacks a workin
exemple).

My data are read from a NTSYSpc file containing 2D coordinates for 10
landmarks for a number of fish specimens, using the readland.nts routine. I
have been able to perform a PCA on these data using the shapepca routine in
Ian Dryden's shapes R package, but would like to perfom the entire analysis
using geomorph.

Thanks in advance for any hints!

Best regards,

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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

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Re: [MORPHMET] A question about PCA in geomorph

2015-04-12 Thread Mauro Cavalcanti 
Dear Emma  ALL,

Indeed, when reading my data with readland.nts I get the data in the format
required by the geomorph analytical routines. The problem is that I was
calling by mistake a routine from Ian Dryden's shapes package (procGPA) to
generate the Procrustes-aligned coordinates, instead of the gpagen routine.
Fixed this and now everything works fine.

I take this opportunity to ask another question, this time relating to the
plots generated by geomorph. Is there a way to customize them, including
for example axis labels in the PCA plots? In fact, the Quick Guide shows
these plots with labels, but I could not figure out how to include them in
my plots. Calling the R par function (as one should have done when using
the usual plot command) did not work.

Again, thanks for your help.

Best regards,.

2015-04-12 1:39 GMT-03:00 Emma Sherratt emma.sherr...@gmail.com:

 Mauro,

 If you read in your NTS data file using readland.nts, it will
 automatically be in the 3D array format required by plotTangentSpace (after
 you use gpagen to do a Procrustes Superimposition).

 If you have your data as a 2D matrix, you simply use arrayspecs to make it
 a 3D array.

 Emma

 On Sunday, April 12, 2015, Mauro Cavalcanti mauro...@gmail.com wrote:

 Dear ALL,

 I have a number of questions about the geomorph R package, that I will
 post here in separate messages.

 First one concerns Principal Components Analysis, using the
 plotTangentSpace routine. It requires a 3D matrix as argument, however my
 data (on fishes) are 2D and I could not figure out how to convert my data
 to the required format; the explanation of the arrayspecs routine in the
 Quick Guide to Geomorph was not clear for me (and it lacks a workin
 exemple).

 My data are read from a NTSYSpc file containing 2D coordinates for 10
 landmarks for a number of fish specimens, using the readland.nts routine. I
 have been able to perform a PCA on these data using the shapepca routine in
 Ian Dryden's shapes R package, but would like to perfom the entire analysis
 using geomorph.

 Thanks in advance for any hints!

 Best regards,

 --
 Dr. Mauro J. Cavalcanti
 E-mail: mauro...@gmail.com
 Web: maurobio http://sites.google.com/site/maurobio

 --
 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.



 --

 ~~~

 Emma Sherratt, PhD.

 Lecturer in Zoology,
 Zoology Division, School of Environmental and Rural Science,
 Room L120 Bldg C02,
 University of New England,
 Armidale, NSW, Australia, 2351
 Tel: +61 2 6773 5041
 email: emma.sherr...@une.edu.au
 Twitter: @DrEmSherratt

 Caecilians are legless amphibians...

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

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







-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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

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Re: [MORPHMET] A question about PCA in geomorph

2015-04-12 Thread Mauro Cavalcanti 
Michael,

Thanks for your helpful message. Indeed, after posting my question about
plot customization, I was able to generate a PCA plot from plotTangentSpace
with axes labels, using the par function immediately before calling the
plotTangentSpace routine, as follows: par(xlab=PC 1, ylab=PC 2).
Obviously, the solution you suggested is even more generic and flexible and
it also works fine.

When means are available to customize the display of deformation grids,
then geomorph will be near perfection!

Thanks again for your help.

With best regards,

2015-04-12 11:19 GMT-03:00 Collyer, Michael michael.coll...@wku.edu:

  Mauro,

  The extractable parts from prcomp() are also extractable from
 plotTangentSpace.  One can make custom plots, relabel axes, change symbols,
 etc.  Example:

  myplot = plotTangentSpace(mydata)
 attributes(myplot) # shows extractable parts

  PC.scores = myplot$x

  par(…)
 plot(PC.scores, …)

  Keep in mind with plotTangentSpace, the product is actually multiple
 plots, as the transformation grids are also plots.  Therefore, it is not
 easy to pass on par() input to the result.  But because users can extract
 the scores, all base R plotting functions are available.

  Cheers!
 -Mike

  Michael Collyer

 Assistant Professor
 Department of Biology
 Western Kentucky University
 1906 College Heights Blvd. #11080
 Bowling Green, KY 42101-1080
 Phone: 270-745-8765; Fax: 270-745-6856
 Email: michael.coll...@wku.edu

  On Apr 12, 2015, at 8:05 AM, Mauro Cavalcanti mauro...@gmail.com wrote:

   Dear Emma  ALL,

  Indeed, when reading my data with readland.nts I get the data in the
 format required by the geomorph analytical routines. The problem is that I
 was calling by mistake a routine from Ian Dryden's shapes package (procGPA)
 to generate the Procrustes-aligned coordinates, instead of the gpagen
 routine. Fixed this and now everything works fine.

  I take this opportunity to ask another question, this time relating to
 the plots generated by geomorph. Is there a way to customize them,
 including for example axis labels in the PCA plots? In fact, the Quick
 Guide shows these plots with labels, but I could not figure out how to
 include them in my plots. Calling the R par function (as one should have
 done when using the usual plot command) did not work.

  Again, thanks for your help.

  Best regards,.

 2015-04-12 1:39 GMT-03:00 Emma Sherratt emma.sherr...@gmail.com:

 Mauro,

  If you read in your NTS data file using readland.nts, it will
 automatically be in the 3D array format required by plotTangentSpace (after
 you use gpagen to do a Procrustes Superimposition).

  If you have your data as a 2D matrix, you simply use arrayspecs to make
 it a 3D array.

  Emma

 On Sunday, April 12, 2015, Mauro Cavalcanti mauro...@gmail.com wrote:

Dear ALL,

  I have a number of questions about the geomorph R package, that I will
 post here in separate messages.

  First one concerns Principal Components Analysis, using the
 plotTangentSpace routine. It requires a 3D matrix as argument, however my
 data (on fishes) are 2D and I could not figure out how to convert my data
 to the required format; the explanation of the arrayspecs routine in the
 Quick Guide to Geomorph was not clear for me (and it lacks a workin
 exemple).

  My data are read from a NTSYSpc file containing 2D coordinates for 10
 landmarks for a number of fish specimens, using the readland.nts routine. I
 have been able to perform a PCA on these data using the shapepca routine in
 Ian Dryden's shapes R package, but would like to perfom the entire analysis
 using geomorph.

  Thanks in advance for any hints!

  Best regards,

 --
 Dr. Mauro J. Cavalcanti
 E-mail: mauro...@gmail.com
 Web: maurobio http://sites.google.com/site/maurobio

  --
 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.



 --

 ~~~

 Emma Sherratt, PhD.

 Lecturer in Zoology,
 Zoology Division, School of Environmental and Rural Science,
 Room L120 Bldg C02,
 University of New England,
 Armidale, NSW, Australia, 2351
 Tel: +61 2 6773 5041
 email: emma.sherr...@une.edu.au
 Twitter: @DrEmSherratt

  Caecilians are legless amphibians...

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

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







 --
 Dr. Mauro J. Cavalcanti
 E-mail: mauro...@gmail.com
 Web: http://sites.google.com/site/maurobio

  --
 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

-- 
MORPHMET may be accessed via its webpage at http

Re: [MORPHMET] Problem with tpsRelw v1.56

2015-06-20 Thread Mauro Cavalcanti 
Dear Jim,

Thanks for your message. I have been attempting to run the latest version
of tpsRelw on an older machine under Windows XP SP3. Have not yet tried it
on a newer computer with 64-bit Windows 7, but can do it soon. Let me know
if any futher information is required.

With warmest regards,



2015-06-20 18:47 GMT-03:00 F. James Rohlf ro...@life.bio.sunysb.edu:

 Sorry for the problems with tpsRelw. Unfortunately i an in Equador now and
 soon will be in Peru.  I will  probably not be able to upload a fix until i
 return on the 26th.  I would appreciate info about those computers with a
 problem as i cannot get it to fail on any of my computers using win7 or
 win8.1.

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


  Original message 
 From: Mauro Cavalcanti mauro...@gmail.com
 Date: 06/19/2015 9:20 AM (GMT-05:00)
 To: Nico Posnien nico.posn...@gmail.com
 Cc: MORPHMET morphmet@morphometrics.org
 Subject: Re: [MORPHMET] Problem with tpsRelw v1.56

 Dear Nico  ALL,

 Running the program in administrador mode does not solve the problem for
 me, under WinXP. And I insist -- this problem does *not* appear in any
 other program from Jim Rohlf's TPS Series. It affects only the latest
 version of tpsRelw.

 Best regards,

 2015-06-19 6:34 GMT-03:00 Nico Posnien nico.posn...@gmail.com:

 Dear all,



 Same problem here. Same error message. For me it is not even possible to
 do any analysis.



 Does not seem to be a Windows XP specific problem since I run Windows 8.1.



 Is it possible to re-upload a previous version of tpsRelw?



 Thanks a lot!



 Cheers,

 Nico



 *Von:* Mauro Cavalcanti [mailto:mauro...@gmail.com]
 *Gesendet:* Mittwoch, 17. Juni 2015 23:28
 *An:* MORPHMET
 *Betreff:* [MORPHMET] Problem with tpsRelw v1.56



 Dear ALL,

 I just installed the latest version of tpsRelw (v1.56) on my old (but
 faithful) Windows XP computer but stumbled upon a strange problem: Every
 time I attempt to close either the program's  main window or the About
 dialog box, I got the error message: Unable to write to C:\Documents and
 Settings\Mauro Cavalcanti\tps\tpsRelw.ini. This means that I cannot exit
 the program except by killing the running process using Windows task
 manager. I do not have such problem with any other program in the
 tpsSeries, installed on the same machine.

 Any hints?

 Best regards,


 --

 Dr. Mauro J. Cavalcanti
 E-mail: mauro...@gmail.com
 Web: http://sites.google.com/site/maurobio

 --
 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. Mauro J. Cavalcanti
 E-mail: mauro...@gmail.com
 Web: http://sites.google.com/site/maurobio

 --
 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

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

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[MORPHMET] Problem with tpsRelw v1.56

2015-06-17 Thread Mauro Cavalcanti 
Dear ALL,

I just installed the latest version of tpsRelw (v1.56) on my old (but
faithful) Windows XP computer but stumbled upon a strange problem: Every
time I attempt to close either the program's  main window or the About
dialog box, I got the error message: Unable to write to C:\Documents and
Settings\Mauro Cavalcanti\tps\tpsRelw.ini. This means that I cannot exit
the program except by killing the running process using Windows task
manager. I do not have such problem with any other program in the
tpsSeries, installed on the same machine.

Any hints?

Best regards,

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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

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

Re: [MORPHMET] Re: Using ImageJ for digitizing on Mac OS X

2015-06-15 Thread Mauro Cavalcanti 
Dear Emma,

Thanks, very helpful indeed.

Best regards,

2015-06-15 18:56 GMT-03:00 Emma Sherratt emma.sherr...@gmail.com:

 Dear Edouard,

 You can find a comprehensive guide by David Polly here:
 http://www.indiana.edu/~g562/Handouts/Collecting%20Landmarks.pdf

 And a few tips on digitizing 2D data can be found here:
 http://www.emmasherratt.com/morphometrics/-goal-gathering-two-dimensional-landmark-coordinates-to-describe-the-shape-of-my-favourite-structure

 Best,

 Emma

 On Tuesday, 16 June 2015 03:26:05 UTC+10, Edouard Masson-MacLean wrote:

 Hello,

 Is there a guide for the complete beginner on how to use ImageJ instead
 of tpsdig, especially on how to set the scale before digitizing?

 Many thanks

 Edouard


 -
 Edouard Masson-MacLean
 PhD Candidate
 Room 119
 Department of Archaeology
 School of Geosciences
 University of Aberdeen
 St. Mary's, Elphinstone Road
 Aberdeen, AB24 3UF
 Scotland, UK

  --
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-- 
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Web: http://sites.google.com/site/maurobio

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Re: [MORPHMET] tpsUtil update 1.63

2015-09-08 Thread Mauro Cavalcanti 
Jim,

This looks really great. tpsUtil is truly *useful*.

Best regards,

2015-09-08 12:49 GMT-03:00 F. James Rohlf :

> I have just uploaded tpsUtil 1.63 to the life.bio.sunysb.edu/morph
> server. It adds a feature recently suggested by Andrea Cardini. There is
> now a plot that shows which landmarks are being deleted or retained and
> what their new numbers of the retained landmarks will be.
>
>
>
> Note: this module works for *both* 2D and 3D data though the plot only
> uses the X & Y coordinates.
>
>
>
> --
>
> F. James Rohlf *New email: f.james.ro...@stonybrook.edu
> *
>
> Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.
>
> & Research Professor. Dept. of Anthropology
>
> Stony Brook University 11794-4364
>
> The much revised 4th editions of Biometry and Statistical Tables are now
> available:
>
> http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
>
>
> http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf
>
> P Please consider the environment before printing this email
>
>
>
> --
> 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
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[MORPHMET] Complaints about 'geomorph' R package

2015-12-16 Thread Mauro Cavalcanti 
Dear members of the R geomorph Development Team,

As you surely know, I am a big fan of the 'geomorph' R package, which I
have been using since its inception (as part of a larger personal move to
do every possible analysis, morphometric or not, using R). Several times, I
have provided tentative bug reports and humble suggestions for improvements
(that sometimes have been incorporated into new releases of the package).

But with due respect, today I have a few severe complaints, that I am
posting here because they may have been of concern for other
morphometricians working with the geomorph package.

My first -- and biggest -- complaint concern the way landmark coordinates
captured by the 'digitize2d' routine are  stored in the latest version of
geomorph. There seems to have been some change in the code (undocumented as
far as I could see) which altered the scaling of the coordinates -- as a
result, I lost weeks of work on a file with more than 70 fish specimens
because when I opened the file in geomorph 2.17 to re-start digitizing the
remaining specimens (after having digitized about 50 in geomorph 2.15), all
coordinates were unexpectedly changed and the file became even unreadable
by Jim Rohlf's tps programs (but before this change in geomorph I could
have the tps programs read files digitized in geomorph without trouble).

Well, at first I solved this by simply downgrading my version of geomorph,
returning to the old 2.15 version and everything worked fine. Since I use
RStudio, i just had to remember to unckeck geomorph in the list of packages
to be updated.

But today, to my dismay and further annoyance, when I upgraded several
packages in my R installation -- even unckecking as usual the geomorphy
entry -- I got a strange error message which turned geomorph (whatever the
installed version) useless! Here it is:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :
  there is no package called 'Biostrings'
ERROR: lazy loading failed for package 'geomorph'
* removing 'C:/Program Files/R/R-3.1.3/library/geomorph'


The geomorph package depends on other two packages, 'ape' and 'rgl', but
none of them have been upgraded recently and both load fine and without any
error messages, therefore I suppose the above error is generated by
geomorph itself.

Right, the error message about a missing package may be a minor (and easily
fixed) issue. But so is not the changes done to the digitize2d function,
which lead to data loss and waste of time and resources! Even if there are
some good reason (as surely does!) for changing the scaling of landmark
coordinates, such change should no tbe done without at least providing
users with the option of using the previous mode of operation of the
routine. Besides, such change should be carefully documented (and I could
not fund any mention to it in the "NEWS" file of the latest versions of
geomorph).

I hope you understand my reasons for complaining, and I look forward to
obtaining directions on how to get out of this mess (currently, I cannot
even use geomorph, whatever the version, because as a a result of the
"misisng package" error, the entire package was automatically wiped out of
my R installation...)

Life is short (so we need R)!

With best regards,

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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[MORPHMET] Yet another sequel to complaints about 'geomorph' R package

2015-12-16 Thread Mauro Cavalcanti 
Dear members of the geomorph R package Development Team,

I at least have been able to track down the "missing library" error when
attempting to install even previous versions of geopmorph.

It turns out that geomorph depends upon a package called 'phangorn' --
which has just been updated to make use of "Biostrings". At least one other
R package (phytools) is also dependent upon phangorn Iand therefore upon
Biostrings too).

The fact that the Biostrings package has not been installed as a depedency
of the latest phangorn is due to the fact that the Bioconductor Project
(and associated packages) is not on CRAN. A big mess, indeed...

Hope this helps!

It seems that these complaints about geomorph are turning to become a
series with many sequels as "Star Wars"...

May the Force Be With You! ;-)

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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[MORPHMET] A sequel to complaints about 'geomorph' R package

2015-12-16 Thread Mauro Cavalcanti 
Dear members of the geomorph R package Development Team,

After posting my complaints about the current problems in the geomorph R
package I have just stumbled upon, I have been able to at least find a
workaround to the annoying message about the missing "Biostrings" package.

I found out that "Biostrings" is part of the huge "Bioconductor" project
which aims to develop a large set of tools for bioinformatics. Following
the directions here (
https://bioconductor.org/packages/release/bioc/html/Biostrings.html) I have
been able to install the required library (plus several other packages of
ehich Biostrings depends) and afterwards could re-install version 2.15 of
geomorph. Now everything works as before!

But this is a makeshift solution. I have no idea why even previous versions
of geomorph are now requiring "Biostrings" (which are part of Bioconductor,
that I have never had in my R installation). Furthermore, the problem with
the scaling of landmark coordinates in the current version of geomorph
still stands and should be properly treated by offering an option to keep
the 'old' mode in the digitize2d function.

Hope this helps.

With best regards,

-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

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Re: [MORPHMET] Crowdsourced GM Bibliography

2016-03-10 Thread Mauro Cavalcanti 
Dear Robert & ALL,

I have, for some years already, keeping lists of GM bibliographies
(selected groups of organisms), as part of the MorphoLib project (
http://morpholib.netai.net). All references are ket in downloadable files
in BiBTeX format and seachable interfaces are provided (automatically
generated from the bibliography files using the Jabref manager).

Hope this helps.

Best regards,

2016-03-09 12:57 GMT-03:00 Robert Z. Selden, Jr. :

> In an attempt to centralize the large wealth (and breadth) of knowledge
> generated through studies of geometric morphometrics, I thought that we
> might all collaborate on a working bibliography. And since geometric
> morphometrics is comprised of a fairly tight-knit international community, 
> *why
> not* make this a crowdsourced project?
>
>
>
> Since the great majority of practitioners are familiar–at least
> peripherally–with scripting, the bibliography is maintained in BibTeX, and
> can be edited in Overleaf. Additionally, using the field “annote,” the
> abstracts for each paper can be included. Further still, the BibTeX text in
> the GMBib.bib file can be cut, then pasted into a text file, where it can
> be imported to a number of reference and .pdf managers.
>
>
>
> I do ask that if you add a citation, you follow the current (BibTeX)
> format, and also place each new reference in alphabetical order (let
> Overleaf refresh after each entry to ensure there are no errors). This will
> help us to ensure that we are not duplicating citations that have already
> been added. Additionally, if you have more information (abstract, DOI,
> etc.) for a reference in the bibliography that is currently posted, please
> add that information.
>
>
>
> The goal of this endeavor is to maintain an active (and accurate) list of
> publications related to geometric morphometrics that can be used in
> classrooms, laboratories, and–yes–your own personal reference manager, and
> to have it maintained by the community of practitioners. So please add your
> new publications as soon as they’re available!
>
>
>
> To begin adding references to the current bibliography, click here
> .
>
>
>
> To generate a searchable .pdf of the current bibliography, simply click on
> the PDF tab at the top of the screen in Overleaf. Feel free to share the *Read
> and Edit* link (
> https://wordpress.com/page/crhrarchaeology.wordpress.com/89371) with
> colleagues and co-workers.
>
>
>
> Any and all users can add new references and edit existing references
> using this link
> .
>
>
>
> If you run into any issues, or just have questions, please forward those
> along.
>
>
>
> I’ve also added a link to my blog (
> https://crhrarchaeology.wordpress.com/morphometrics/gm-bibliography-project/)
> where this same text is posted (archaeologists are nothing if not
> redundant). Many thanks in advance for your contributions—I think that this
> can be a great resource.
>
>
>
> Best,
>
> Zac
>
>
>
>
>
>
>
> --
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-- 
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Web: http://sites.google.com/site/maurobio

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Re: [MORPHMET] model II regression statistics PAST

2016-03-12 Thread Mauro Cavalcanti 
Patrick,

PAST is "free" as in "free beer", not as in *free speech*. It is gratis,
but not open. The problem you have is just typical of such black box
approach to scientific software development -- since one cannot see the
source code, it is not possible to check how this or that algorithm is
implemented.

Stick to R, where nothing is hidden.

Best regards,

2016-03-12 11:49 GMT-03:00 Patrick Arnold :

> Dear morphometrics,
>
> I am frequently using PAST (paleontological statistics; what a great free
> software) for the analysis of morphometric data (geometric and
> traditional). Now I want to do a reduced major axis regression on bivariate
> data (only one Y for each X). However, I do not found the possibility to
> perform a significance test for the regression (F statistics) or for the
> slope and intercept (t statistics).
> It is provided for least square regression (e.g., under polynomial option)
> but not for model II regression. Does anyone know a possibility to obtain
> regression statistics in PAST for model II regressions?
> Thanks in advance.
>
> Cheers
> Patrick
>
>
> --
> Patrick Arnold, M.Sc.
>
> wissenschaftlicher Mitarbeiter und Doktorand
> Institut für Spezielle Zoologie und Evolutionsbiologie
> mit Phyletischem Museum
> Friedrich-Schiller-Universität Jena
> Erbertstraße 1
> 07743 Jena
> Germany
>
> Phone:  +49 (0)3641 9-49165
> Fax:+49 (0)3641 9-49142
> E-mail: patrick.arn...@uni-jena.de
>
> --
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Web: http://sites.google.com/site/maurobio

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Re: [MORPHMET] Measurements to Landmarks

2016-11-09 Thread Mauro Cavalcanti 
Dear Edgar,

Back in the 1990's, I have used this procedure to convert several datasets
of  measurements into landmark coordinates. I used a program which
implemented the method devised by Carpenter et al. written in Basic for
MS-DOS (a long gone programming language for a long gone operating system).
The algorithm has been subsequently implemented by Dennis Slice in earlier
versions of the Morpheus software.

The method works quite well and I have published a few studies using it. If
you are interested, I can provide you with a copy of the program I used,
although using an earlier version of Morpheus would perhaps be a better
idea as this software runs on more recent machines.

Salud!

--
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

Em 08/11/2016 23:27, "Edgar Esteban Herrera Collazos" <
edgaresteba...@gmail.com> escreveu:

> Hey everyone,
>
> Just wondering, I have a sets of measurements, and I was wondering if
> there is a way to turn those measurements into landmarks?
>
> Best regards,
>
> --
> Edgar Esteban Herrera Collazos B.Sc.
> Cel: 319 379 0213
>
> Postgraduate Student at Pontificia Universidad Javeriana
> Ichthyology Laboratory 108B Ed 53 - 3208320 Ext 4127
> ---
> Estudiante de Posgrado en la Pontificia Universidad Javeriana
> Laboratorio de Ictiología 108B Ed 53 - 3208320 Ext 4127
>
>
> --
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Re: [MORPHMET] Digital morphology data survey: ethics on data generation & use

2017-07-28 Thread Mauro Cavalcanti 
Hi,

Done! Interesting initiative, hope to see the results of the survey.

Best regards,

2017-07-27 22:27 GMT-03:00 Christy Anna Hipsley :

> Dear Morphmet Community,
>
> I kindly ask your help in completing a short survey on trends in digital
> morphology data generation and use as part of a perspectives piece on the
> “Ethics of data sharing in the age of digital imaging”, which I will
> present at this year’s BioSyst EU meeting in Gothenburg, Sweden (
> http://www.conferencemanager.se/BiosystEU2017/speakers-and-symposia.html).
>
> While many recommendations have been made on best practices in this field,
> we as a community are still far from a consensus on how our data should be
> managed, both on the side of the people generating it and the people
> requesting it.
>
> Your responses are anonymous, and I will post the results on Morphmet at
> the end of the survey. The questions are focused on 3D digital morphology
> data (CT, laser scanning, etc), but please feel free to answer if you also
> deal with 2D images.
>
> To reach the survey, go here: https://goo.gl/forms/igFKPc376kVn5eI13
>
> The site will remain active for the next 2 weeks, until Friday, 11 August.
>
> Almost every question has the option to enter text, so please give as much
> information and opinions as possible to help us represent your concerns!
>
> Thank you for your time,
> Christy Hipsley & Emma Sherratt
>
>
> --
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-- 
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] Copy of TPS files with 'include path'

2017-05-14 Thread Mauro Cavalcanti 
Gabriel,

TPS files are regular text files with data structured in a certain way.

Just open your TPS file in a plain text editor (Notepad++ is a good choice)
and fix the paths manually using the regular search-and-replace facility.

Hope this helps.

Salud!

--
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E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio

Em 14/05/2017 15:22, "Gabriel Lauziere" 
escreveu:

> Hi everybody,
>
> I'm doing geometric-morphometric on fish pictures. With TPSutil, I built
> my tps files from images and I digitalized landmarks. I let the 'include
> path' option checked for all my TPS files.
>
> Now I want to save a back up of those images with their landmarks.
> Unfortunately, I'm unable to save a copy of my tps files (images +
> landmarks) on another computer (or even a USB stick). I'm only able to
> export the coordinates of those landmarks in a excel file.
>
> I tried to copy all my images and all my tps files on a USB stick, but it
> didn't work...I think it's because the "path" of my tps files is now fixed
> with the original computer. So I'm looking for a solution! Can anyone help
> me?
>
> Thank you very much,
>
> Gabriel Piette-Lauziere
> Master student
> Laval University
>
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Re: [MORPHMET] Phylogenetic tree in MorphoJ-regrading

2019-01-28 Thread Mauro Cavalcanti 
Arvind,

The NEXUS format is used to represent phylogenetic trees, on which MorphoJ
will map your shapes. You don't prepare 2D data in NEXUS format, as the
software does not compute phylogenetic trees itself,  See the MorphoJ
documentation (
http://www.flywings.org.uk/MorphoJ_guide/frameset.htm?index.htm),
specifically the item "Comparison Menu" -> "Map Onto Phylogeny" for details.

By the way, a comprehensive description of the NEXUS format can be found in
the fine paper by Madison et al (1997):

David R. Maddison, David L. Swofford, Wayne P. Maddison. " NEXUS: An
Extensible File Format for Systematic Information".  Systematic Biology,
Vol. 46, No. 4 (Dec., 1997), pp. 590-621.

Hope this helps.

Best wishes,

Em seg, 28 de jan de 2019 às 15:07, Arvind Kumar Dwivedi <
dubeyma...@gmail.com> escreveu:

> Dear Sir/Ma'am
>
> Greetings...
>
> I am working on shape variations among fishes.
>
> I have a problem in preparing phylogenetic tree in MorphoJ software.
>
> MorphoJ is asking to upload NEXUS file to prepare phylogenetic tree.
>
> I have two major queries:
>
> 1. Do I have to prepare NEXUS file from the 2D XY coordinate data ???
>
> 2. If this is the case, how I can prepare NEXUS file  I don not how to
> format 2D XY data in NEXUS file.
>
> Here is my data on 2D XY coordinate for 3 species having 3 samples in each
> species:
>
> LM=13
> 122.0 583.0
> 430.0 725.0
> 808.0 778.0
> 1083.0 748.0
> 1653.0 612.0
> 1706.0 523.0
> 1651.0 452.0
> 1489.0 462.0
> 1239.0 361.0
> 843.0 280.0
> 510.0 412.0
> 530.0 467.0
> 263.0 567.0
> IMAGE=TIL 845.JPG
> ID=species1
> SCALE=0.013768
> LM=13
> 144.0 810.0
> 455.0 970.0
> 828.0 1024.0
> 1108.0 985.0
> 1665.0 862.0
> 1712.0 770.0
> 1651.0 692.0
> 1482.0 704.0
> 1264.0 594.0
> 861.0 550.0
> 538.0 658.0
> 562.0 722.0
> 303.0 803.0
> IMAGE=TIL 846.JPG
> ID=species1
> SCALE=0.011780
> LM=13
> 75.0 935.0
> 436.0 1098.0
> 842.0 1140.0
> 1099.0 1092.0
> 1681.0 990.0
> 1735.0 902.0
> 1655.0 836.0
> 1521.0 819.0
> 1298.0 704.0
> 843.0 615.0
> 485.0 755.0
> 520.0 822.0
> 237.0 915.0
> IMAGE=TIL 847.JPG
> ID=species1
> SCALE=0.014137
> LM=13
> 43.0 3131.0
> 110.0 3183.0
> 248.0 3212.0
> 316.0 3203.0
> 550.0 3182.0
> 573.0 3154.0
> 553.0 3123.0
> 497.0 3122.0
> 433.0 3089.0
> 282.0 3046.0
> 147.0 3072.0
> 149.0 3115.0
> 78.0 3138.0
> IMAGE=TIL 402.JPG
> ID=species2
> SCALE=0.037037
> LM=13
> 83.0 3174.0
> 165.0 3222.0
> 278.0 3246.0
> 339.0 3238.0
> 549.0 3209.0
> 568.0 3175.0
> 546.0 3153.0
> 502.0 3162.0
> 434.0 3127.0
> 302.0 3100.0
> 193.0 3122.0
> 197.0 3158.0
> 132.0 3178.0
> IMAGE=TIL 403.JPG
> ID=species2
> SCALE=0.038462
> LM=13
> 84.0 3126.0
> 155.0 3174.0
> 291.0 3205.0
> 347.0 3198.0
> 581.0 3154.0
> 597.0 3119.0
> 587.0 3096.0
> 522.0 3099.0
> 450.0 3066.0
> 304.0 3048.0
> 191.0 3077.0
> 195.0 3107.0
> 126.0 3135.0
> IMAGE=TIL 404.JPG
> ID=species2
> SCALE=0.037037
> LM=13
> 45.0 1452.0
> 227.0 1601.0
> 478.0 1672.0
> 635.0 1656.0
> 1061.0 1568.0
> 1106.0 1508.0
> 1070.0 1452.0
> 840.0 1392.0
> 566.0 1317.0
> 338.0 1341.0
> 286.0 1320.0
> 177.0 1472.0
> 91.0 1469.0
> IMAGE=HKL 14.JPG
> ID=species3
> SCALE=0.014700
> LM=13
> 68.0 1477.0
> 260.0 1605.0
> 494.0 1652.0
> 640.0 1627.0
> 1036.0 1529.0
> 1097.0 1467.0
> 1037.0 1418.0
> 805.0 1358.0
> 541.0 1316.0
> 344.0 1355.0
> 296.0 1332.0
> 203.0 1494.0
> 120.0 1492.0
> IMAGE=HKL 15.JPG
> ID=species3
> SCALE=0.015385
> LM=13
> 56.0 1496.0
> 242.0 1620.0
> 506.0 1666.0
> 666.0 1645.0
> 1094.0 1532.0
> 1141.0 1471.0
> 1074.0 1423.0
> 835.0 1364.0
> 574.0 1315.0
> 341.0 1355.0
> 282.0 1341.0
> 175.0 1508.0
> 103.0 1513.0
> IMAGE=HKL 16.JPG
> ID=species3
> SCALE=0.014284
>
> Kindly suggest.
> Desperately waiting for response from the experts.
>
> regards
> Arvind
>
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Re: [MORPHMET] new paper: elephant seal nose-metrics

2019-03-19 Thread Mauro Cavalcanti 
Dear Andrea,

Absolutely fascinating!

Well, although not using GM methods, the book by William B. Evans & Alexey
V. Yablokov, "Noninvasive Study of Mammalian Populations" (Sofia/Moscow:
Pensoft, 2004) provides a lot of interesting ideas and insights on the use
of analytical techniques for living, non-sedated animals in the field. GM
methods would offer a powerful contribution in this regard.

With warmest regards,

Em seg, 18 de mar de 2019 às 12:01, andrea cardini 
escreveu:

> Dear All,
> this out now: https://onlinelibrary.wiley.com/doi/abs/10./jzs.12276
> “Nose‐metrics” of wild southern elephant seal (Mirounga leonina) males
> using image analysis and geometric morphometrics
> JZSER, online first
>
> As far as I know, it's one of the few applications of GMM on data from
> naturally behaving animals photographed in the field. By the way, if
> anyone has references of this type of work (NB not on sedated animals),
> please I'd appreciate having a pdf.
>
> Thanks also to those who asked me reprints of the Evol. Biol. paper on
> spurious results in integration/modularity tests. Please, write me if
> you have no subscription and need the pdf, as it's not yet in my webpage.
>
> Cheers
>
> Andrea
>
> --
>
> Dr. Andrea Cardini
> Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di
> Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
> tel. 0039 059 2058472
>
> Adjunct Associate Professor, Centre for Forensic Anthropology, The
> University of Western Australia, 35 Stirling Highway, Crawley WA 6009,
> Australia
>
> E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
> WEBPAGE: https://sites.google.com/site/alcardini/home/main
>
> FREE Yellow BOOK on Geometric Morphometrics:
> https://tinyurl.com/2013-Yellow-Book
>
> ESTIMATE YOUR GLOBAL FOOTPRINT:
> http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/
> SUPPORT: secondwarning.org
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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>

-- 
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 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."

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