Hi everyone, This is a very interesting discussion and very close to something I've been thinking about...
If I understand the question correctly, this isn't necessarily about replacing Procrustes alignment or to point out problems, but to understand potential effects on downstream phylogenetic comparative analyses? In that perspective, if one were to simulate shapes under Brownian motion, then it would be of interest if the post-Procrustes aligned variables (Procrustes coordinates, residuals, etc) still conform to Brownian. I think this would be important but maybe someone's done this already and it would probably answer the OPs question. best wishes, Manabu Manabu Sakamoto, PhD 坂本 学 [email protected] On Tue, 9 Sept 2025 at 13:43, 'F. James Rohlf' via Morphmet < [email protected]> wrote: > What is your alternative? Preserve in the analysis the arbitrary > positioning of specimens in a photo or scan? Procrustes does have biases > but it would have to be replaced with some other procedure. Perhaps one has > some known reference points but then variation in those points will become > very important. > > Jim > > __________________ > F. James Rohlf, Distinguished Prof. Emeritus > Dept. Anthropology and Ecology & Evolution > Stonybrook University > > > -------- Original message -------- > From: [email protected] > Date: 9/9/25 2:49 AM (GMT-05:00) > To: Jacqueline Silviria <[email protected]> > Cc: [email protected] > Subject: Re: [MORPHMET2] Effect of Procrustes alignment on parameter > estimates > > Dear Jacqueline > > Yes it could be for instance for ancestral state reconstruction. What I am > thinking about is whether anybody has done a simulation study where they > simulate shape data, procrustes align the data, infer some quantity of > interest (could be ancestral state, or something else) and then look at how > the estimated quantity compares to the true quantity (the one used for > simulation) with or without procrustes alignment. I would expect procrustes > alignment to have an effect as it is not really a part of any of the > stochastic models I am aware of. > > I am sorry if my question is very odd, I do not have a strong background > in geometric morphometrics so I might have misunderstood something. > > Thank you! > > Best regards, > Sofia > > On 9 Sep 2025, at 03.45, Jacqueline Silviria <[email protected]> > wrote: > > Just to be clear, by parameter estimation for stochastic models, you mean > for the purpose of ancestral state reconstruction? > > *Jacqueline S. Silviria* > *she/her/hers* > *The Last King of the Jungle* > <https://protect.checkpoint.com/v2/r01/___https://discord.gg/m7KKkuKW___.YzJ1OnN0b255YnJvb2s6YzpnOmJiYjFlOWU2ZDE1YzNkOTg0NjllNjZmMmQzOGI5NTg1Ojc6NWE2Yzo1ZTc1Mzg1OWFjNDZlZDhhNmE3NjFjOTQyMmE4ZjZkNmRmMGI2ZDhlY2U3OTBmMDY4Mjk3YzJjNzc4YzYwNDc0Omg6VDpG> > > > > > *Department of Earth & Space ScienceUniversity of WashingtonSeattle, WA, > [email protected] <[email protected]>, [email protected] > <[email protected]>* > > *ResearchGate profile > <https://protect.checkpoint.com/v2/r01/___https://www.researchgate.net/profile/J_Silviria___.YzJ1OnN0b255YnJvb2s6YzpnOmJiYjFlOWU2ZDE1YzNkOTg0NjllNjZmMmQzOGI5NTg1Ojc6OGMxYzo2NTI2YWIyNzM4NTYzNGUxYjA1ZmZiOTRiODcwYTBmOWQ4NTViOGEyMDMwOGU2MTk5NDlhMWU0MDVkOTU4ZjkyOmg6VDpG>* > > Sent from my iPhone > > On Sep 8, 2025, at 6:02 AM, Sofia Stroustrup <[email protected]> > wrote: > > Dear all, > > I am wondering whether any of you are aware of a study that investigates > the effect of Procrustes alignment on parameter estimation for instance > under a Brownian motion or Ornstein-Uhlenbeck process? What I am thinking > about is, if we simulate data under a stochastic model, procrustes align > the data and then do parameter estimation how does Procrustes alignment > affect the estimates. I have not been able to find any study investigating > this. > > Thank you very much for your help! > > Best regards, > Sofia > (PhD student at University of Copenhagen) > > -- > 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/morphmet2/695dcdb1-5844-420f-82ce-881a6ffe81f2n%40googlegroups.com > <https://protect.checkpoint.com/v2/r01/___https://groups.google.com/d/msgid/morphmet2/695dcdb1-5844-420f-82ce-881a6ffe81f2n*40googlegroups.com?utm_medium=email&utm_source=footer___.YzJ1OnN0b255YnJvb2s6YzpnOmJiYjFlOWU2ZDE1YzNkOTg0NjllNjZmMmQzOGI5NTg1Ojc6NGQ4MTozMGNmZGZiMGY4ZWQzZjgzNDllODA4NDU3ZDExMDAyMzgyMTRkNTVjNDU4ZDRkNjMxMDhjYjRiNGRjMzM0YjA0Omg6VDpG> > . > > > > -- > 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/morphmet2/7F159313-FA85-45F7-93E6-611EBD78DADF%40gmail.com > <https://protect.checkpoint.com/v2/r01/___https://groups.google.com/d/msgid/morphmet2/7F159313-FA85-45F7-93E6-611EBD78DADF*40gmail.com?utm_medium=email&utm_source=footer___.YzJ1OnN0b255YnJvb2s6YzpnOmJiYjFlOWU2ZDE1YzNkOTg0NjllNjZmMmQzOGI5NTg1Ojc6ZjAxYzpkYjVmZGU0Y2EyNTQ0NzU1YjQ3ODViZTU2YjA5MmE0MWNmNjBhNTZkZDA3NjAxOGE3ZmQ1ZDBkOTk2YmY3ZjZhOmg6VDpG> > . > > -- > 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/morphmet2/68c020e8.050a0220.379554.2b88%40mx.google.com > <https://groups.google.com/d/msgid/morphmet2/68c020e8.050a0220.379554.2b88%40mx.google.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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