[R] Ancestral state reconstruction under a split-tree for BiSSE

KRAmazon sjdavid at alumni.uci.edu
Tue Jun 11 22:30:45 CEST 2013


I am trying to do ancestral reconstruction under a split BiSSE model. 

#phy is my tree
nodes<-c(755,620,602,448,6,340) #vector of nodes at which to split the
pars.b<-c(428.597,  90.777, 421.878,  81.815, 0.201, 2.900)  #pars were
taken from the non-split model

All of that performs as expected, but when I try to perform ancestral
reconstruction on my split model, I get this error:

> asr.split<-asr.marginal(lik.split,coef(fit.split))
Error in check.pars.nonnegative(pars, 6) : 
  Incorrect parameter length: expected 6, got 42

Why does it expect 6 parameters for my split model instead of the 42? Am I
using the wrong
function for the ancestral reconstruction, or is the code incorrect? The
updates for version 0.9-1 
of diversitree state that reconstruction under split models is availabe. 

It was also suggested to me that I could average the parameters from
fit.split and do asr with an unsplit tree. 
Is this viable?

Thank you for your time!

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