Hello all,
(I'm a troublemaker today.)
Sometimes, in ordered discrete data, there are states we know might
exist as intermediary between observed states but aren't observed
themselves. I suppose this is probably common for meristic data. At
least to me, it seems like it should be possible to reconstruct node
states in a scenario with 'missing' states in a ML approach by
defining the corre
Anyway, in a recent conversation with a friend, he noted that he
couldn't get the function for ML ancestral reconstruction of discrete
characters, specifically ace (in ape) or rerootingMethod (in phytools)
to accept data with missing states. I was a little shocked by this,
and I didn't believe him in my foolhardiness and investigated myself.
#################################
library(ape)
data(bird.orders)
#make an ordered matrix for a 4 state trait
model<-matrix(0,4,4)
for(i in 1:4){for(j in 1:4){
if(abs(i-j)<2){
model[i,j]<-0.1
}
}}
rownames(model)<-colnames(model)<-0:3
#simulate data where you have only observed endmembers
trait <- factor(c(rep(0, 5), rep(3, 18)))
names(trait)<-bird.orders$tip.label
ace(trait, bird.orders, type = "discrete")
#works
ace(trait, bird.orders, type = "discrete", model=model)
#fail
library(phytools)
rerootingMethod(tree=bird.orders, x=trait)
#works
rerootingMethod(tree=bird.orders, x=trait, model=model)
#fail
#################################
(And it doesn't look like ancestral.pml in phangorn accepts model matrices.)
So, are these functions rejecting a model with missing states due to a
real analytical issue that I'm blithely ignorant of, or is there some
other function that I've missed that will allow ML reconstruction with
missing states?
Cheers,
-Dave
--
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701
http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html
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