Sarah, As far as I am aware, MorphoJ estimates a set of PICs one dimension at a time. Thus, for a multivariate dataset of N species and p-trait dimensions, this will return a matrix of N-1 by p. Here, each of the N-1 rows (nodes of the bifurcating tree) contains a vector of PICs, one per trait dimension. This approach is simple to replicate in R: just use the pic function and loop across trait dimensions.
Note that this differs from McPeek's formulation of multivariate independent contrasts (see e.g., McPeek et al. 2008: Am. Nat.). For this approach, differences in each of the p-dimensions of data are combined in the numerator of his equation, resulting in a a single PIC for each of the N-1 nodes. As you mentioned, these are equivalent to the Euclidean distance between taxa standardized by branch lengths. While the math of McPeek's procedure is simple enough, I am unaware of a function in R that estimates these directly. I also do not believe these are found in MorphoJ, but someone who uses that program could better respond to that query. Hope this helps. Dean Dr. Dean C. Adams Director of Graduate Education, EEB Program Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University www.public.iastate.edu/~dcadams/ phone: 515-294-3834 -----Original Message----- From: Sarah Friedman <sarahtfr...@gmail.com> Sent: Monday, March 19, 2018 2:24 PM To: MORPHMET <morphmet@morphometrics.org> Subject: [MORPHMET] Multivariate PICs? Hi all, Primarily, I'm wondering if there is a way to calculate phylogenetic independent contrasts on multivariate shape data in R. However if no R method exists, I know a method to do this is implemented in MorphoJ, and I could possibly code an analogous method in R but I'm unsure how the contrasts are calculated. Does anybody know if the independent contrasts are calculated using the method described in McPeek (1994), the Euclidean distances between contrasts on each branch, or another method? Thanks, Sarah -- 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. -- 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.
