Hello,
I'm trying to use the package Diversitree to perform an ancestral
reconstruction using a constrained Mk2 model.
Unfortunately, after running the model and plotting the results I saw that
most of the internal nodes did not get any state (NaN).
Doing exactly the same without the constrain works fine and assigns a state
for all internal nodes.
Any idea why this happens?
Here is the relevant part of code I was using:
lik<-make.mk2(tree,states)
lik.m <- constrain( lik, q10 ~ 0 )
fit.m <- find.mle(lik.m, .1)
st <- asr.marginal(lik.m, coef(fit.m)) #same if I use joint reconstruction
And this is what I got for 31 nodes:
> st
[,1] [,2] [,3].............................[,23] [,24] [,25]
[1,] 1 NaN NaN .................... NaN NaN NaN
[2,] 0 NaN NaN ................... NaN NaN NaN
[,26] [,27] [,28] [,29] [,30] [,31]
[1,] 0.1770124 0.02323889 0.001580509 0.0003160667 0.05889347 0.002819436
[2,] 0.8229876 0.97676111 0.998419491 0.9996839333 0.94110653 0.997180564
Thanks,
Anna
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