[R-sig-phylo] Transforming a data.frame into a phylogenetic tree

David Bapst dwbapst at uchicago.edu
Tue Jan 26 22:09:16 CET 2010


Hi,
It appears you are keeping track of the ancestor by its character
matrix. (So this is a speciational model of character evolution, I
guess?)  I've coded simulations that produce similar data for
paleobiological comparison, but I just have a single column for the
ancestor ID. (My own functions use that ID to then compare between
anc-desc populations).

I haven't tried it yet, but I believe it should be possible to
transform that data into a more formal bifurcating topology and then
into an ape object (I have transformed it into a bifurcating tree for
use in ouch, though, and that worked). With ancestor-descendent
relationships, you'll need to figure out how to define where internal
nodes occur (i.e. where do species begin and end on the branches).
Without having a column that tracks the ancestor, I'm not certain how
to reconstruct the phylogeny from the data. If anyone else has
actually tried to transform such data into an ape object, I'd be
really interested to hear about it.
-Dave Bapst
Geosci, UChicago

On Tue, Jan 26, 2010 at 2:18 PM, Timothee POISOT <tpoisot at um2.fr> wrote:
>
> Dear users,
>
> I am currently doing a model of community assembly, and I would like to
> integrate phylogenetic information. For each organism, I know its ancestor
> and the time at which speciation occured. These informations are stored in
> a data.frame, an example of which is here :
>
>> PhyloTree
>        Anc   OffSpr TimeApp
> 1       Anc 00000000       1
> 2  00000000 10000000      28
> 3  00000000 00000001      84
> 4  00000000 00000010     101
> 5  10000000 10100000     106
> 6  00000000 00100000     139
> 7  00000000 01000000     160
> 8  00000001 10000001     161
> 9  10000000 11000000     168
> 10 00100000 00110000     177
> 11 10000001 10010001     186
> 12 00000010 00000110     197
>
> Do you have any idea about how I can proceed to transform this object into
> a tree object, such as the one used by APE?
>
> Regards,
>
> Timothée
>
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