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. Silviriashe/her/hersThe Last King of the JungleDepartment of Earth & Space ScienceUniversity of WashingtonSeattle, WA, [email protected], [email protected] profileSent from my iPhoneOn 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)
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