Dear all, My goal is to carry out allometry adjustment to produce 'allometry-free' shapes and visualize the result. This has been brought up a lot recently, but I still wish to check whether what I did was correct, both in terms of concepts and implementation.
Currently I'm doing allometry adjustment in R in this way (without taking group into consideration): mod1 <- lm(shape ~ size) mean.shape <- apply(shape, 2, mean) allometry.free.shape <- t(apply(mod1$residuals, 1, `+`, mean.shape)) But I also have a factor (let's call it 'group'). When I run Procrustes ANOVA using procD.lm in geomorph, both group and size:group terms are significant, and HOS test in procD.allometry is significant too. If I want to take this into consideration to get the allometry free shape, what can I do? I came across MorphoJ's procedure of pooled within group regression and I think maybe this is what I am looking for (side note: I'm very confused on the difference between what I read from the discussion on this forum some time ago <https://groups.google.com/a/morphometrics.org/forum/#!topic/morphmet/K7vtiKl2xhI> and MorphoJ's explanation on pooled within group regression, I am not good in stats). Following is the explanation from MorphoJ's user manual <http://www.flywings.org.uk/MorphoJ_guide/frameset.htm?covariation/regression.htm> : *The bottom element is for selecting a pooled within-group regression. This type of regression is suitable, for instance, for removing the effect of within-group variation of a variable such as size, age or environmental factors before comparisons between groups. The analysis is performing a regression using the deviations of the dependent and independent variables from the respective group means (the group means are added back to the residuals and predicted values in the output dataset). * How can I do this in R? This is what I have came out with: mod2 <- lm(shape ~ group) mod3 <- lm(shape ~ size * group) allometry.free.shape <- mod3$residuals + predict(mod2) The output visualization made sense but I am not confident. Did it do what MorphoJ does? If it was wrong, how can I do it? And is it conceptually correct to get allometry free shapes this way for data with significant size:group interaction? Many thanks Cheers, Jin Yung -- 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 morphmet+unsubscr...@morphometrics.org.
