[Phylobase-devl] edge data?

[Brian O'Meara]

On Mar 24, 2008, at 3:50 PM, Peter Cowan wrote:
> Hi all,
>
> I've been trying to write up an example function for the vignette.  I
> thought that I would do a brownian trait simulator, because they are
> so popular.  I was basing the S4 version on the one by David Ackerly
> in the picante package [^1] called evolve.trait().  This nifty
> function keeps track of the trait value for each unit of branch
> length.  That is, if a branch has length 5, there will be five values
> along the branch.  This data seems most logically stored as edge data.
>
> As of now the phylo4d class does not have an edge data slot.
> Furthermore, the commented out version suggests a data frame, which
> would not work with the variable length data described above, trees
> with differing branch lengths.
>
> I forget why we decided against edge data, is this too esoteric of a
> use case?  Any suggestions of a better way to handle the above case?

Stochastic character mapping, where a discrete character is simulated  
up a tree including where it changes state (done in Mesquite and  
SIMMAP), and evolutionary pathway likelihood (estimating ancestral  
states along edges as well as at nodes) (done in the unreleased  
version of Brownie) also involve mapping of data on edges. SIMMAP  
stores this in files as a modification of the Nexus branch length  
format (has starting state: time in that state, next state : time in  
that state, etc. in brackets) but I don't know how it does it  
internally (closed source); Brownie uses SIMMAP style input;  
internally, I think I set it up to store states and times as two  
vectors per edge. I don't know how Mesquite stores stochastically- 
mapped characters.

The Huelsenbeck et al 2003 article about stochastic mapping has been  
cited 52 times, according to Google scholar; SIMMAP (Bollback, 2006)  
has been cited 17 times, so there is some interest in it, at least  
for discrete characters.

Brian


>
> [1] <https://r-forge.r-project.org/projects/picante/>
>
> Peter
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