View source: R/treeManipulation.R
getRoot | R Documentation |
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 node labels 'support' values (edges), 'label' or should labels get '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$node.labels)) to convert them. midpoint
so far does not transform node.labels properly.
pruneTree
and midpoint
a tree. getRoot
returns
the root node.
Klaus Schliep klaus.schliep@gmail.com
consensus
, root
,
multi2di
tree <- rtree(10, rooted = FALSE) tree$node.label <- c("", round(runif(tree$Nnode-1), digits=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)
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