Hi Cheng-Chiang.
Yes, you either need to supply a state for each tip or you can instead
supply an ambiguous prior probability distribution. Perhaps it would
make sense to add a fourth state that is the absence of the feature?
Alternatively, you could imagine that an absent feature might have some
trait value if it were observed (like the hair color of a bald man - it
exists even if it cannot be observed), but this trait value is unknown.
In that case it does make sense to supply a flat prior distribution -
then both make.simmap and rerootingMethod can be used to obtain a
posterior trait distribution on the unobserved trait's value.
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 7/1/2016 5:28 PM, Wu, Cheng-Chiang wrote:
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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