phylomat-class {phylobase} | R Documentation |
Classes representing phylogenies as matrices
as_phylo4vcov(from, ...)
from |
a phylo4 object |
... |
optional arguments, to be passed to vcov.phylo in
ape (the main useful option is cor , which can be set
to TRUE to compute a correlation rather than a
variance-covariance matrix) |
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.).
.Data
:edge.label
:order
:Ben Bolker
tree.owls <- read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);") 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. o2@edge and o3@edge ## BUT the edge matrices are otherwise identical identical(o2@edge[order(o2@edge[,2]),], o3@edge[order(o3@edge[,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.