matrix classes for phylobase
Classes representing phylogenies as matrices
from |
a |
... |
optional arguments, to be passed to |
These are square matrices (with rows and columns corresponding to tips, and internal nodes implicit) with different meanings depending on the type (variance-covariance matrix, distance matrix, etc.).
Ben Bolker
tree_string <- "(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);"
tree.owls <- ape::read.tree(text=tree_string)
o2 <- as(tree.owls,"phylo4")
ov <- as(o2,"phylo4vcov")
o3 <- as(ov,"phylo4")
## these are not completely identical, but are
## topologically identical ...
## edge matrices are in a different order:
## cf. edges(o2) and edges(o3)
## BUT the edge matrices are otherwise identical
o2edges <- edges(o2)
o3edges <- edges(o3)
identical(o2edges[order(o2edges[,2]),],
o3edges[order(o3edges[,2]),])
## There is left/right ambiguity here in the tree orders:
## in o2 the 5->6->7->1 lineage
## (terminating in Strix aluco)
## is first, in o3 the 5->6->3 lineage
## (terminating in Athene noctua) is first.Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.