blueraleigh / mk Goto Github PK

Dear Michael,

I attempted to run the calcTipRates.R script from your paper "The macroevolutionary singularity of snakes" recently in Science, but encountered an error that stated "Error in UseMethod("Ntip"): no applicable method for 'Ntip' applied to an object of class "tree"". Upon inspecting the source code of mk.tiprate, I discovered that the error was a result of the 2nd line of code, where "n = Ntip(phy)" failed to extract tip numbers from the "tree" file. As a resolution, I converted the tree file into a "phylo" format. Nevertheless, another error appeared, which stated "Error in tree.isbinary(phy) : is.tree(phy) is not TRUE". This error originated from the "mpr.fitch" function called by mk.tiprate from the parsimony package. I am uncertain about how to rectify this issue. I would appreciate it immensely if you could provide me with your help. Thank you for your time and consideration.

Sincerely,
Wei