[MORPHMET] Your opinion + a tiny piece of your exotic data

[Vincent Bonhomme]

Dear morphmet,

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

I write to you today to ask you if you:
1- think I have forgotten a case in the current five rules

2- are keen to share some data. A very small fraction of datasets or even a
single complete shape would be perfect. I'm particularly interested in
exotic format. Being a newbie to everything outside outlines, all
text-based formats including .tps, .nts, .xml and others are exotic to me
so every single contribution will be warmly welcomed. Unless if you're keen
to do it and explicitely write it to me, I won't, of course, don't share
them, not even for tests or whatever.

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

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

All the best from southern France,

Vincent




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Re: [MORPHMET] Method to study outline data suffered from the 'Pinocchio effect'?

[Vincent Bonhomme]

Hi there,

As concerns outline analysis w/ EFT, my package Momocs does the job (last
version , CRAN
, vignette
,
doc ) and I'll be happy to help.

As concerns the Pinocchio effect, it once happened to me on exotic shapes,
but the 'nose' wasn't so Pinocchio so that was fine. You should have a try.

All the best,

vincent


2016-07-24 7:13 GMT+02:00 wongjinyung :

> Dear community,
>
> I'm studying outlines that have spines on them and the spines (especially
> some extreme cases with very long spines relative to the rest) affect the
> result of superimposition of the semi-landmarks quite a lot (a.k.a. the
> 'Pinocchio effect'), I hope I can get some suggestion on the method to use,
> as well as the software implementation. (I work on 2D outlines, currently
> using sliding semi-landmark method / elliptic Fourier analysis in R).
>
> I'm wondering whether there is an implementation of resistant-fit
> superimposition (with sliding) for semi-landmarks to deal with data like
> this? Or is there any other method that will not be affected by the
> 'Pinocchio' effect (as much)? Literature or experience on similar issue?
>
> Thanks,
> Wong Jin Yung
>
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Re: [MORPHMET] Crowdsourced GM Bibliography

[Vincent Bonhomme]

hi there,

that's a great idea!
I think simplicity and ease of adding stuff is key. I love tex but not sure
it's not a shared feeling among my colleagues. Why not using a simple
GitHub repository and list papers there in (simpler) Markdown? that would
not be binded to someone/some structure in particular but built/share by
all of us. and combined with pandoc we would still be able to generate
html, tex, whatever we want.

by the way, I think we could (should?) do the same for data. I'd be very
happy to discuss it with anyone interested.

all the best,

vincent



2016-03-09 16:57 GMT+01:00 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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Re: [MORPHMET] Using ImageJ for digitizing on Mac OS X

[Vincent Bonhomme]

hi there,

Analyze  Set Scale...

+
http://microscopy.berkeley.edu/courses/dib/sections/04IPIII/IJsetscale.html

hth
best,

v

2015-06-15 14:59 GMT+02:00 Edouard Masson-MacLean e.massonmacl...@gmail.com
:

 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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Re: [MORPHMET] Suggestions for geomorph

[Vincent Bonhomme]

Hi Mauro and all,

StereoMorph http://cran.r-project.org/web/packages/StereoMorph/index.html
is a brand new alternative, shiny-powered to cope with common weaknesses of
R in terms of graphical/interactions

hth

v


2015-06-08 22:58 GMT+02:00 Mauro Cavalcanti mauro...@gmail.com:

 Dear members of the geomorph Development Team,

 I have been using the digitize2d() function of the geomorph R package to
 obtain landmark coordinates from my fish specimens.It works fine, but I
 respectfully have two suggestions for its improvement.

 First one is quite simple: when end of file is reached and the last
 specimen has been digitized, the function stops with one of those ugly and
 arcane error messages (well, all programming languages generate ugly and
 arcane error messages! ;-)). This should not happen; instead, the function
 should issue a user-friendly warning, like End of file, Last specimen
 (or perhaps something less friendly, like Can't you see you have reached
 the end of file, you moron? ;-))

 Second suggestion may be more difficult to implement, but if it can be
 done, it would provide a great improvement: the ability to edit a
 previoulsly created file. Currently, the function detects the specimens
 without landmark coordinates and starts digitizing from this specimen on;
 if all specimens have already landmark coordinates, then the function stops
 with the same ugly error messages referred to above. It would be really
 great if one could see each specimen with the superimposed digitized
 landmarks, one by one, so that landmarks could be checked, added, or
 deleted.

 Hope this helps!

 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] Go-to Program of Elliptical Fourier Analysis

[Vincent Bonhomme]

Hi Karl,

Try import_jpg in Momocs on segmented images ie black shape on a white
background.
Be sure to get the last version (https://github.com/vbonhomme/Momocs/ ) ,
the one on CRAN and published in JSS is completeley obsolete now
New vignettes are being rewritten, so feel free to contact me for the
hotline.

All the best,
Vincent

2015-02-15 21:52 GMT+01:00 Karl Fetter karl.fet...@gmail.com:

 Hi Everyone,

 I'd like to find out what the 'go-to' program is for collecting elliptical
 fourier descriptors? Is there a favorite? I like to analyze data in R, are
 there programs that are easier to integrate into R than others?

 I see that the R package Momocs has a lot of tools for analyzing EFA data,
 but can one also collect data with Momocs?

 I'm pretty familiar with Landmark GMM workflows, is the EFA workflow
 similar in concept? I.e., image a leaf, collect the data (with some
 program), do some kind of superimposition, work with the data.

 Thanks for the tips,

 Karl Fetter
 UVM - Plant Biology

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