Marianna I think Gmshiny would be a good first approach for you to geomorph. Maybe it has what you need for your analyses. https://www.gmshiny.com/video-tutorials https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13723
El mar., 7 ene. 2025, 1:56 a. m., alcardini <[email protected]> escribió: > Dear All, > R has many advantages, but I am very sympathetic with Ann's point: in > theory we can and should check the software and, if open source, one has > the code; in practice most of us, users, don't do it, as, if we had those > advanced skills, we would probably program the functions ourselves in the > first place. > I tend to double check results with at least two independent software, > whenever possible. That has limitations and cannot of course exclude errors > in both. Over the years, I've found bugs (including in R) in almost all the > programs I have used. Often they were minor ones, but sometimes they were > serious. In a small field, I do wonder how many independent validations are > done and that means both the theory and code behind functions in any type > of software. As I wrote, with open source software in theory one can check > everything, but even peer-reviewed functions are not always checked by > reviewers. > I suspect there is literature on this type of issues in science, but > haven't had time to search. > > For the Procrustes ANOVA, if Marianna looks for an alternative to MorphoJ > with the same identical design, that is difficult in my clearly limited > experience. > PAST has a permutational ANOVA but at least the version I use requires a > perfectly balanced design and cannot replicate, for instance, the > symmetry/asymmetry analysis (if that's Marianna's case). > R packages have functions for Procrustes ANOVA and the like, but they > (again in my limited experience as a basic R user) use type II sum of > squares, unlike MorphoJ which, I believe, uses type I. To avoid > misunderstandings on this, I am not advocating one or the other type of SSQ > but simply stating that different programs may use different types and that > usually matters unless the design is perfectly balanced. > > R is a great tool and has been a revolution. However, as Ann pointed out > in a context such as forensics, where errors can have dramatic > consequences, most users, like me, probably have to trust the statisticians > and coders. I may be wrong and surprisingly discover that the vast majority > of R users can and do check carefully the functions (and theory) they use. > To avoid unnecessary discussions on an obvious point, I completely agree > that, at the very least, R provides the option, unlike proprietary > software. I admire those who use it routinely and wish I could do the same. > However, as a biologist without expertise in numerical methods, I find most > of the underlying theory and code well beyond my understanding. > > All the best > > Andrea > > On Mon, 6 Jan 2025 at 04:47, 'Ann Ross' via Morphmet < > [email protected]> wrote: > >> Dear Murat, >> Exactly, the point. When dealing with black box and invalidated code to >> determine if said code is doing what it’s supposed to do such as >> permutations is an issue. So many untested and invalidated GUI’s exist that >> do not meet forensic practice standards. I guess ok in general research >> perhaps fine. And should not fall on the user. However, in forensic >> practice validation and testing required. I will respectfully disagree. >> A >> Ann H. Ross, Ph.D., D-ABFA >> >> >> On Jan 5, 2025, at 10:04 PM, Murat Maga <[email protected]> wrote: >> >> >> Dear Ann, >> Not sure what you mean by not validated? What is the validation of a >> t-test function in R or any other software library? Validation is the >> responsibility of the person using the tools, not the developers. >> Open-source tools make this validation for more simple, since if you have >> any concern you can look under the hood. Evaluate the code line by line and >> then if you find an issue you can easily take it up with the developers. >> >> In closed-source software this is almost near impossible. I would argue >> this is a far more superior method of "validation" then to appeal to the >> authority. >> >> On Sunday, January 5, 2025 at 6:46:15 PM UTC-8 Ann Ross wrote: >> >>> 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 < >>> [email protected]> 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 <(515)%20294-3834> >>> >>> >>> >>> *From:* [email protected] <[email protected]> *On Behalf >>> Of *Murat Maga >>> *Sent:* Sunday, January 5, 2025 12:29 PM >>> *To:* Morphmet <[email protected]> >>> *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 [email protected] 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 >>> >>> >>> >>> Get Outlook for Android <https://aka.ms/AAb9ysg> >>> ------------------------------ >>> >>> *From:* [email protected] <[email protected]> on behalf >>> of alcardini <[email protected]> >>> *Sent:* Friday, January 3, 2025 11:56:13 PM >>> *To:* [email protected] <[email protected]>; morphmet2 < >>> [email protected]> >>> *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, [email protected] <[email protected]> >>> 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. >>> >>> -- >>> 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 [email protected]. >>> To view this discussion visit >>> https://groups.google.com/d/msgid/morphmet2/549e6df3-2eaf-46cc-9b34-f30f5caf2777n%40googlegroups.com >>> <https://groups.google.com/d/msgid/morphmet2/549e6df3-2eaf-46cc-9b34-f30f5caf2777n%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >>> >>> >>> -- >>> >>> E-mail address: [email protected], [email protected] >>> WEBPAGE: https://sites.google.com/view/alcardini2/ >>> or https://tinyurl.com/andreacardini >>> >>> -- >>> 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 [email protected]. >>> >>> To view this discussion visit >>> https://groups.google.com/d/msgid/morphmet2/CAJ__j7O9uG-7sAMvKFZVmm3EgojQU-o-Hs_oZSbVMhTE9zLsQw%40mail.gmail.com >>> <https://groups.google.com/d/msgid/morphmet2/CAJ__j7O9uG-7sAMvKFZVmm3EgojQU-o-Hs_oZSbVMhTE9zLsQw%40mail.gmail.com?utm_medium=email&utm_source=footer> >>> . >>> >>> -- >>> 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 [email protected]. >>> To view this discussion visit >>> https://groups.google.com/d/msgid/morphmet2/5a1598a7-96b9-4cd4-9a1e-ec45c61fcc64n%40googlegroups.com >>> <https://groups.google.com/d/msgid/morphmet2/5a1598a7-96b9-4cd4-9a1e-ec45c61fcc64n%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >>> -- >>> 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 [email protected]. >>> >>> To view this discussion visit >>> https://groups.google.com/d/msgid/morphmet2/CO6PR04MB84274559E14A8D833235AD6FA2102%40CO6PR04MB8427.namprd04.prod.outlook.com >>> <https://groups.google.com/d/msgid/morphmet2/CO6PR04MB84274559E14A8D833235AD6FA2102%40CO6PR04MB8427.namprd04.prod.outlook.com?utm_medium=email&utm_source=footer> >>> . >>> >>> -- >> 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 [email protected]. >> To view this discussion visit >> https://groups.google.com/d/msgid/morphmet2/27206e9b-5373-4c01-8a80-99a007c8e8c4n%40googlegroups.com >> <https://groups.google.com/d/msgid/morphmet2/27206e9b-5373-4c01-8a80-99a007c8e8c4n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> >> -- >> 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 [email protected]. >> To view this discussion visit >> https://groups.google.com/d/msgid/morphmet2/EE95733E-EEF5-4073-ACD7-F5EBE0F8CA70%40ncsu.edu >> <https://groups.google.com/d/msgid/morphmet2/EE95733E-EEF5-4073-ACD7-F5EBE0F8CA70%40ncsu.edu?utm_medium=email&utm_source=footer> >> . >> > > > -- > E-mail address: [email protected], [email protected] > WEBPAGE: https://sites.google.com/view/alcardini2/ > or https://tinyurl.com/andreacardini > > -- > 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 [email protected]. > To view this discussion visit > https://groups.google.com/d/msgid/morphmet2/CAJ__j7OOMdDodm-7V46VC7MpTZ420YYk%2BNqPXwOUA6qP5n1vyA%40mail.gmail.com > <https://groups.google.com/d/msgid/morphmet2/CAJ__j7OOMdDodm-7V46VC7MpTZ420YYk%2BNqPXwOUA6qP5n1vyA%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "Morphmet" group. 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