# [R-sig-phylo] [corHMM reconstruction not estimating internal node states]

```Hello,
```
```

I'm running some precursor models in corHMM to understand the evolution of
a discrete binary character.  Some example code using data(primates) below,
but what happens is the internal nodes are not being estimated (\$States =
NaN).  Also, when I unclass(precursor2.primates), the internal Node labels
are all "NA".  Still solves the optimization, but I can't plot the
reconstruction!

library(corHMM)

data(primates)

#write precursor matrix (Marazzi et al., 2012):

precursor2.matrix <- matrix(data = c(NA, NA, 2, NA,

NA, NA, NA, NA,

1, NA, NA, 4,

NA, NA, 3, NA ),

nrow = 4, ncol = 4,

byrow = TRUE

)

rownames(precursor2.matrix) <- c("(0,R1)", "(1,R1)", "(0,R2)", "(1,R2)")

rownames(precursor2.matrix)

colnames(precursor2.matrix) <- c("(0,R1)", "(1,R1)", "(0,R2)", "(1,R2)")

colnames(precursor2.matrix)

#running the precursor-2 model:

precursor2.primates <- corHMM(primates\$tree,primates\$trait,rate.cat
=2,rate.mat=precursor2.matrix,node.states="marginal",diagn=FALSE)

unclass(precursor2.primates)

Am I neglecting something in the corHMM() function, or is there something
else going on?  I run into the same NaN when running the precursor matrices
Beaulieu wrote into the corHMM notes.

Any help is appreciated!  Thank you!

,  Michael Foisy

MSc. Student

University of Toronto

michael.fo...@mail.utoronto.ca

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