[Phylobase-devl] edge data?

Peter Cowan pdc at berkeley.edu
Mon Mar 24 20:50:06 CET 2008


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?

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

Peter


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