Hi All,
I am trying to do ancestral state reconstruction in R using the packages {ape}
and {phytools}, but these two packages do not seem to handle reconstruction to
include data at internal nodes.
I was able to run the code for ancestral reconstruction using {Phytools} using
a sample tree with 6 terminal tips and 3 internal node names. But, the
reconstruction using this package is not representing internal node states.
I also tried using {ape}, but this package will not run the function due to
differences between the number of terminal tips and the data (additional data
for internal nodes).
Do these packages not support this function? I have attached my matrix and tree
files for reference.
I have used the following script for {phytools}:
simmap <- make.simmap(phylo, matrix, nsim=100)
cols <- cols(�blue�, �red�); names(cols) <- c(�present�, �absent�)
plotSimmap(simmap[[1]], lwd=3, fsize=1, cols)
add.simmap.legend(leg=sort(unique(matrix)), colors=cols, fsize=1)
And the following for {ape}:
anc <- ace(matrix, phylo, type=�d�)
*Which gives an error of "length of phenotypic and phylogenetic data do not
match", that I am guessing is due to the data for the internal node taxa.
Any help with this would be greatly appreciated!
-Laura
---
Laura Jackson
PhD Student
Department of Biology
185 Churchill Haines
University of South Dakota
414 E. Clark St.
Vermillion SD 57069-1746
Email: [email protected]<mailto:[email protected]>
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