Hi Wesley,
You are right: this definition is out-dated. Have a look at:
http://ape-package.ird.fr/
in the 'Development' section, there is a document explaining the
structure of the class "phylo". Also the second edition of APER has been
updated on this point.
Best,
Emmanuel
Le 12/05/2014 10:10, Wesley Goi a écrit :
Hi all,
I've search quite around for methods of converting from a edgelist (from
igraph) to a phylo class
taken from the 2006: Analysis of Phylogenetics and Evolution with R
the instructions for building an object of the "phylo" class seems to have
been changed. Please correct me if I'm mistaken.
An object of class "phylo" is a list with the following components.
edge
a two-column matrix where each row represents a branch (or edge) of the
tree; the nodes and the tips are symbolized with numbers; the nodes are
represented with negative numbers (the root being "-1"), and the tips are
represented with positive numbers. For each row, the first column gives the
ancestor. This representation allows an easy manipulation of the tree.
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