A phytools user recently reported discrepant results between phylANOVA in phytools and aov.phylo in geiger. Both functions conduct the simulation-based method of Garland et al. (2013). In theory, the only difference is that phylANOVA performs post-hoc comparison of means. It turns out, however, that phylANOVA contains the implicit assumption that y is in the order of tree$tip.label. This assumption is now only true if names(y) is NULL, in which case a warning is also issued. Updated code is here and in the latest version of phytools.
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