Dear Waldir, There are both philosophical and practical reasons we do not now or will not offer options for choice of sums of squares in procD.lm. First the practical reasons. It is not trivial to offer such an option. The various sums of squares (types 1, 2, 3, etc.) all involve a paradigm of model comparisons. (We have a couple of blog posts about this on www.geomorph.net<http://www.geomorph.net>.). If one understands the paradigms, advanced.procD.lm allows one to calculate any type of sums of squares (SS). If you are determined to use type 3 SS, I recommend using advanced.procD.lm.
As for the philosophical reason that type 3 SS is not something we offer, it is a paradigm we choose not to acknowledge as valid. The reason for this is simple. With type 3 SS the sum of the parts exceeds the total. Type 3 SS, as a paradigm, involves removing effects from the "full" model, one by one, and calculating the changes in summed squared residuals as the effect SS. For unbalanced designs, the sum of SS across effects will exceed the model SS. This does not make much sense. Furthermore, the process involves removing main effects but retaining any interaction with these effects for calculating SS. This is a bit silly. Type 2 SS avoids this problem, and again, advanced.procD.lm can accommodate the type 2 approach. By contrast, type 1 SS involves sequentially adding model effects and calculating the change in summed squared residuals as the effect SS. The sum of SS across the effects is the same as the full model SS. The order of effects is important, but we feel the biologist should have some cognizance of the appropriate order. Because geomorph is an R package, users are free to manipulate functions. Thus, it is possible to augment the R script to provide type 3 SS. But this not something we will do as a permanent fixture, for the reasons above. Good luck! Mike Collyer Sent from my iPhone On Jul 9, 2015, at 9:35 AM, Waldir Miron <noreply-comm...@blogger.com<mailto:noreply-comm...@blogger.com>> wrote: Waldir Miron<http://www.blogger.com/profile/10564967218097034020> has left a new comment on your post "ANOVAs and Geomorph<http://www.geomorph.net/2015/04/anovas-and-geomorph.html>": Dear (s), I am investigating fish shape variaton from different rivers basins and habitats within river basins. However, I have an unbalaced samples for both factors, it is recommended to do an Anova with SS error type III (marginal), to avoid some sampling bias. Unfortunately, I tried several times but I was not able to calculate SS type III using the Procrustes coordinates with the procD.lm function from geomorph package. It seems that the default type error of the function is the type I, and I would like to know if there is any argument to change that or a way to do it. I would appreciate any help. Regards. Posted by Waldir Miron to geomorph<http://www.geomorph.net/> at July 9, 2015 at 9:35 AM -- 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 morphmet+unsubscr...@morphometrics.org.
