Hi Michelle, One problem might be misinterpreting what R displays when you use a function rather than what R might save as an object if you create an object based on the function.
For example, you could input the following gpagen(mylandmarks, curves = mycurves, PrinAxes = T) and R would return presumably return the landmarks and centroid sizes… up to a point where it might stop the display because of lots of values. Alternative, and preferably (and maybe what you did, but you did not specify), if you input mygpa <- gpagen(mylandmarks, curves = mycurves, PrinAxes = T) Then R would return nothing, but it should list your Csize if you ask it to, i.e., mygpa$Csize I’m not sure what you mean by "similar unsatisfactory results”. Unsatisfactory because the module produces no results or because it produces results that are equally unsatisfying? If you want a DIY approach, you can use mshape() to get the consensus configuration, subtract this from your landmarks, square the residuals, sum them by configuration and take the square root of the sum, by configuration. Cheers -Mike Michael Collyer Assistant Professor 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 Dec 4, 2014, at 5:31 PM, Michelle Singleton <[email protected]<mailto:[email protected]>> wrote: Hello All, I am having trouble with the gpagen module in Adam et al.'s Gemorph package, and I am hoping someone here may have encountered the same problem or have some insight into my problem.I am applying gpagen to execute GPA with sliding surface semilandmarks (bending energy criterion). I am running the most recent versions of both R and Geomorph. According to the documentation, gpagen should return a list comprising 1) $coords: the aligned coordinate matrix and 2) $Csize: a vector of centroid sizes. Instead, it is returning aligned, slid configurations in the same 3D array format (p, k, n) as the infile (generated using readland.nts) but no centroid size vector. I have compared the pre- and post-slide configurations to confirm that sliding is occurring. I have tried running the csize module separately and gotten similar unsatisfactory results. Can anyone explain why I am getting partial output or recommend a fix or workaround? Many, many thanks, Michelle Singleton [email protected]<mailto:[email protected]> -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org<http://www.morphometrics.org/> 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 To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].
