Re: [MORPHMET2] MorphoJ ProcrustesANOVA

Sun, 05 Jan 2025 18:46:20 -0800

Hi All,
The one thing to keep in mind that all this coding is important but not validated. One needs to trust the results and if not validated leaves a lot of questions. This is from a forensic perspective.  
Ann
Ann H. Ross, Ph.D., D-ABFA
Ann H. Ross, Ph.D., D-ABFA


On Jan 5, 2025, at 7:48 PM, 'Adams, Dean [EEOB]' via Morphmet <morphmet2@googlegroups.com> wrote:



Marianna,

 

I completely understand that R and other coding approaches can seem daunting. But I agree 100% with Murat, and encourage you and others to steer into the wind!   Coding is empowering!

 

First, a bit of R-coding allows you to improve your data manipulation and curation. This helps with scientific repeatability, compliance with journal requirements (which increasingly require one to submit curated data and scripts to a public repository), and basically enhances and encourages open-source science. 

 

But more importantly, coding empowers you as a scientist. By moving to R, you remove yourself from the restraints that exist with canned software, whose options are necessarily limited by the buttons and options that the user has available to point-and-click.  In essence, while prepackaged software is easy to use, it limits thinking and creativity by restricting

one’s analysis to those options that the software happens to have.

 

The unfortunate outcome of such canned software is that our GM literature becomes filled with many studies of similar analyses: not because those  biological topics are inherently interesting per se, but because that is what the software happens to allow. This is the analytical version of what one of my mentors (Larry Slobodkin) once called ‘intellectual painting by numbers.’  I seriously hope that our field can do better now in the 21st century.

 

My message: learning a bit of code breaks this cycle, and frees one to investigate the questions that one actually wishes to explore, not just those for which canned software has already provided. I strongly encourage you (and others) to learn a bit of R, Python, or some other language so that your creative science is not restricted!

 

Best of luck in your journey.

 

Dean

 

Dr. Dean C. Adams

Distinguished Professor of Evolutionary Biology

Department of Ecology, Evolution, and Organismal Biology

Iowa State University

https://faculty.sites.iastate.edu/dcadams/

phone: 515-294-3834

 

From: morphmet2@googlegroups.com <morphmet2@googlegroups.com> On Behalf Of Murat Maga
Sent: Sunday, January 5, 2025 12:29 PM
To: Morphmet <morphmet2@googlegroups.com>
Subject: Re: [MORPHMET2] MorphoJ ProcrustesANOVA

 

Dear Marianna,

 

A quick comment: Instead of trying to work this with PAST, I highly encourage you to spend that time trying to do the same in R using geomorph, or other shape analysis libraries. Yes, it will probably take longer, yes it will be somewhat bumpy road initially. But you will be much better set for the next challenge. Graphical user interface applications are good up to a point (for common tasks). And I am telling you as someone who is developing UI based morphometrics analysis. 

 

Most often in biology, you will have to customize your analysis to the specific question you are trying to answer. This is best done via scripting in a flexible programming environment (whether that's R or Python or some other language is irrelevant). There are tons of resources and a very supportive community to help you with your challenges. Going forward, all fields of biology will be more computational not less, and the sooner you start warming up to the idea it will be better for your career. 

 

Your future self will thank you for that decision.

 

M

 

On Sunday, January 5, 2025 at 5:05:47 AM UTC-8 mscer...@gmail.com wrote:

Thanks everyone... I suspected this was the case but wanted to be sure I wasn't missing anything. I'm going to look into using PAST first, since I'm not the most comfortable in R. 

On Saturday, January 4, 2025 at 5:34:57 AM UTC-8 Adams, Dean [EEOB] wrote:

In R use geomorph.

 

Dean

 

From: morp...@googlegroups.com <morp...@googlegroups.com> on behalf of alcardini <alca...@gmail.com>
Sent: Friday, January 3, 2025 11:56:13 PM
To: mscer...@gmail.com <mscer...@gmail.com>; morphmet2 <morp...@googlegroups.com>
Subject: Re: [MORPHMET2] MorphoJ ProcrustesANOVA

 

Dear Marianna,

the tests are parametric in MorphoJ as far as I know. 

One can do the permutations in R. If you have also a main factor, however, it is a bit convoluted to design it (or at least I found only a convoluted way of doing it). You'll find a description in a footnote in Table 1 of https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/2527

If you're analyzing symmetry/asymmetry, the 'trick' I used needs to be reworked and may not work but it should be possible to do an equivalent analysis in one of the morphometric packages (morpho, geomorph, not sure about momocs).

I am sure a skilled R coder will be able to suggest better ways.

Good luck. 

Cheers

 

Andrea

 

On Sat, 4 Jan 2025 at 04:37, mscer...@gmail.com <mscer...@gmail.com> wrote:

Dear morphmet members, 

I expect this will be a relatively easy question. 

Does the Procrustes ANOVA in MorphoJ use permutations? I don't see it as an option, though I see it in regression and in Matrix correlation.
I expect that since there isn't an option for it, then it is not a permutation-based test, but it seems so odd that it wouldn't be. 

I can't find it in the documentation, and I'm convinced it must be there and I'm missing it. If there is something that discusses this, could you kindly point me to it. 

Thanks in advance, 

Marianna C.

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