Dear R-sig-phylo community,
>
> I'm an MA student in NY working on his thesis and am relatively new to
> phytools. I have two questions. My first question concerns a methods
> issue for ancestral reconstruction and my second question is a coding
> issue with inputting my data.
>
> *Question 1:* Ace (from Paradis et al., ape package) uses a "Felsenstein's
> pruning algorithm & compute the likelihood" that may have issues for my
> research and make.simmap has had known errors for the conditional
> likelihoods of the root nodes - is there a recommended method for
> recovering the ancestral character states for a character evolution of
>
> a global population?
>
> *Question 2:*
> I'm attempting to use the make.simmap(tree, x, model="SYM", nsim=1, ...)
> function
> in phytools but have had difficulty in inputting my discrete character data.
>
>
I know "x" can be a "vector containing the tip states for a discretely
> valued character".
>
> My code in R is listed below with some thoughts on where I went wrong. I
> would appreciate any advice or help to get me in the right direction. Thank
> you.
>
> Best regards,
> Fernando L.
>
>
> *library(phytools) *
>
>
> *tree<-read.nexus("test_tree.nexus")*
>
>
> # Resolving polytomies in my tree in order to use ace and estimate the
> ancestral state of discrete data.
>
>
> *dichot_tree = multi2di(tree) *
>
> *dichot_tree$edge.length<-runif(n=nrow(dichot_tree$edge),min=0,max=1)*
>
>
>
> * dichot_tree$edge.length[dichot_tree$edge.length<1]<-1*
>
#My binary discrete character traits is within my nexus file
> *traits = read.nexus.data("**test_tree.nexus** ")*
>
> *x<-as.matrix(traits)*
>
> # making a matrix for my data. It contains 262 species samples with
> discrete binary states of 0 or 1.
>
>
> [image: Inline image 4]
>
>
>
> # I attempt to use the make.simmap function and get the following
> error.
>
>
> *xsimm <- make.simmap(dichot_tree, x, model = "ARD")*
>
> *Error in xx[tree$tip.label, ] : subscript out of bounds*
>
>
>
>
>
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