Summary for phylo4/phylo4d objects
Summary of information for the tree (phylo4 only) and/or the
associated data (phylo4d).
summary(object, ...) ## S4 method for signature 'phylo4' summary(object, quiet = FALSE) ## S4 method for signature 'phylo4d' summary(object, quiet = FALSE) nodeType(object) ## S4 method for signature 'phylo4' nodeType(object)
object |
a phylo4d object |
... |
optional additional elements (not in use) |
quiet |
Should the summary be displayed on screen? |
The nodeType method returns named vector which has
the type of node (internal, tip, root) for value, and the node number
for name
The summary method invisibly returns a list with the
following components:
list("name") |
the name of the object |
list("nb.tips") |
the number of tips |
list("nb.nodes") |
the number of nodes |
list("mean.el") |
mean of edge lengths |
list("var.el") |
variance of edge lengths (estimate for population) |
list("sumry.el") |
summary (i.e. range and quartiles) of the edge lengths |
list("degree") |
(optional) type of polytomy for each node: ‘node’, ‘terminal’ (all descendants are tips) or ‘internal’ (at least one descendant is an internal node); displayed only when there are polytomies |
list("sumry.tips") |
(optional) summary for the data associated with the tips |
list("sumry.nodes") |
(optional) summary for the data associated with the internal nodes |
Ben Bolker, Thibaut Jombart, Francois Michonneau
phylo4d-methods constructor and
phylo4d class.
tOwls <- "(((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=tOwls)
P1 <- as(tree.owls, "phylo4")
P1
summary(P1)
nodeType(P1)
## summary of a polytomous tree
E <- matrix(c(
8, 9,
9, 10,
10, 1,
10, 2,
9, 3,
9, 4,
8, 11,
11, 5,
11, 6,
11, 7,
0, 8), ncol=2, byrow=TRUE)
P2 <- phylo4(E)
nodeLabels(P2) <- as.character(nodeId(P2, "internal"))
plot(P2, show.node.label=TRUE)
sumryP2 <- summary(P2)
sumryP2Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.