| as.phylo.formula {ape} | R Documentation |
Conversion from Taxonomy Variables to Phylogenetic Trees
Description
The function as.phylo.formula (short form as.phylo)
builds a phylogenetic tree (an object of class phylo) from
a set of nested taxonomic variables.
Usage
## S3 method for class 'formula'
as.phylo(x, data = parent.frame(), collapse = TRUE, ...)
Arguments
x |
a right-side formula describing the taxonomic relationship:
|
data |
the data.frame where to look for the variables (default to user's workspace). |
collapse |
a logical value specifying whether to collapse single nodes in the returned tree (see details). |
... |
further arguments to be passed from other methods. |
Details
Taxonomic variables must be nested and passed in the correct order:
the higher clade must be on the left of the formula, for instance
~Order/Family/Genus/Species. In most cases, the resulting tree
will be unresolved and will contain polytomies.
The option collapse = FALSE has for effect to add single nodes
in the tree when a given higher level has only one element in the
level below (e.g., a monospecific genus); see the example below.
Value
an object of class "phylo".
Author(s)
Julien Dutheil dutheil@evolbio.mpg.de, Eric Marcon and Klaus Schliep
See Also
as.phylo, read.tree for a
description of "phylo" objects, multi2di
Examples
data(carnivora)
frm <- ~SuperFamily/Family/Genus/Species
tr <- as.phylo(frm, data = carnivora, collapse=FALSE)
tr$edge.length <- rep(1, nrow(tr$edge))
plot(tr, show.node.label=TRUE)
Nnode(tr)
## compare with:
Nnode(as.phylo(frm, data = carnivora, collapse = FALSE))