Tree manipulation
midpoint performs midpoint rooting of a tree. pruneTree
produces a consensus tree.
getRoot(tree) midpoint(tree, node.labels = "support", ...) ## S3 method for class 'phylo' midpoint(tree, node.labels = "support", ...) ## S3 method for class 'multiPhylo' midpoint(tree, node.labels = "support", ...) pruneTree(tree, ..., FUN = ">=")
tree |
an object of class |
node.labels |
are nodel labels 'support' values, 'label' or should be 'deleted' |
... |
further arguments, passed to other methods. |
FUN |
a function evaluated on the nodelabels, result must be logical. |
pruneTree prunes back a tree and produces a consensus tree, for trees
already containing nodelabels. It assumes that nodelabels are numerical or
character that allows conversion to numerical, it uses
as.numeric(as.character(tree$node.labels)) to convert them. midpoint
so far does not transform node.labels properly.
pruneTree and midpoint a tree. getRoot returns
the root node.
Klaus Schliep klaus.schliep@gmail.com
tree <- rtree(10, rooted = FALSE)
tree$node.label <- c("", round(runif(tree$Nnode-1), 3))
tree2 <- midpoint(tree)
tree3 <- pruneTree(tree, .5)
old.par <- par(no.readonly = TRUE)
par(mfrow = c(3,1))
plot(tree, show.node.label=TRUE)
plot(tree2, show.node.label=TRUE)
plot(tree3, show.node.label=TRUE)
par(old.par)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.