Ari, If you are using geomorph, you might want to update it via GitHub. Just a few days ago we updated the software with some bug fixes for surface points (one bug fix was for assuring non-arbitrary directions in PC planes for tangents of surface points). If you are unsure how to do that, look at the post by Dean Adams on 15 February 2016.
Beyond that, you are asking for assistance without defining (1) how you are sliding your landmarks (minimizing Procrustes Distance or Bending Energy) or (2) other specifics that might be important (package within R, maybe other inputs that might be important, such as the relative numbers of fixed landmarks and semilandmarks, etc.). Contrary to your logic, subsetting your sample could have an effect. Your mean configuration would change in each of the subsamples, from the mean of your original sample, thus changing the reference configuration used in the separate GPAs performed. The reference configuration has a prominent role in the sliding of landmarks. With the information you provided, t is not possible to discern among user error, program error, or analytical artifact. Mike Michael Collyer Associate Professor Biostatistics Department of Biology Western Kentucky University 1906 College Heights Blvd. #11080 Bowling Green, KY 42101-1080 Phone: 270-745-8765; Fax: 270-745-6856 Email: [email protected]<mailto:[email protected]> On Feb 18, 2016, at 9:43 AM, Ariadne Schulz <[email protected]<mailto:[email protected]>> wrote: Hello all, I'm having a bit of a semilandmark problem. I'm working on 3D surfaces with semilandmarks. (Profuse thank yous to Emma for writing the scripts for that.) The issue I'm having I think is occurring in the sliding. When I do populations alone everything seems normal. The semilandmarks do not appear to be going off the surface defined for them, but if I try to do more than one population at once several of the semilandmarks slide off the surface so my PCs get rather distorted. Based on the few individuals from different populations I've looked at I think I do have interpopulation variation but I wouldn't expect that to influence the sliding of semilandmarks. Has anyone else encountered an issue like this with either 2D or 3D semilandmarks? As with all things R I expect the answer will be something like me omitting a comma somewhere so any suggestions you might have are welcome. Best, Ari -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org<http://www.morphometrics.org/> --- 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]<mailto:[email protected]>. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- 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].
