Dear All,
I am working on reconstruction of ancestral character state with a trait of
three states (0,1, 2) of a specific organ from 100 taxa.
Per tutorials on
http://blog.phytools.org/2015/09/primer-on-estimating-ancestral-states.html and
http://blog.phytools.org/2013/04/estimating-ancestral-states-when.html,
I set 1/3 as prior probability of being in any of the states for taxa with the
organ but no trait data (missing data).
For the three taxa which don't have this organ, I had to set 1/3 instead of 0
as prior probability for each state, in order to running rerootingMethod or
make.simmap functions in phytools properly. I tried to set 0 as prior
probability for all states of these three taxa in the matrix, and I got the
following error messages by runing rerooting Method or make.simmap:
rerootingMethod:
Error in fitMk(tt, yy, model = model, fixedQ = Q, output.liks =
TRUE)$lik.anc[1, :
incorrect number of dimensions
make.simmap:
Error in 1:nrow(L) : argument of length 0
I thought about deleting the three taxa without such organ from my dataset, but
they are critical in the phylogeny.
May I ask for advice on solution for this issue?
Thanks,
Cheng-Chiang
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