pez (version 1.0-0)

phy.build: Build a novel phylogeny from existing data (based on phyloGenerator)

Description

Build a novel phylogeny from existing data (based on phyloGenerator)

Usage

congeneric.merge(tree, species, split = "_", ...)
bind.replace(backbone, donor, replacing.tip.label, donor.length = NA)

Arguments

tree

phylo phylogeny to have those species inserted into it

species

vector of species names to be bound into the tree if missing from it

split

the character that splits genus and species names in your phylogeny. Default is _, i.e. Quercus_robur.

...

ignored

backbone

backbone phylogeny (phylo) into which the donor is to be bound

donor

phylogeny (phylo) to bound into the backbone phylogeny

replacing.tip.label

the species in the donor phylogeny that's being replaced by the donor phylogeny

donor.length

how deep the donor phylogeny should be cut into the backbone phylogeny. If NA (default), then the bladj algorithm is followed (or, in plain English, it's put half-way along the branch)

Value

• phylo phylogeny

  phylogeny (phylo)

Details

congeneric.merge Binds missing species into a phylogeny by replacing all members of the clade it belongs to with a polytomy. Assumes the tip.labels represent Latin binomials, split by the split argument. This code was originally shipped with phyloGenerator - this is the merge method in that program.

bind.replace Binds a phylogeny (donor) into a bigger phylogeny ('backbone'); useful if you're building a phylogeny a la Phylomatic. A version of this R code was shipped with phyloGenerator (Pearse & Purvis 2013). This is really an internal function for congeneric.merge, but hopefully it's of some use to you!

References

Pearse W.D. & Purvis A. phyloGenerator: an automated phylogeny generation tool for ecologists. Methods in Ecology and Evolution 4(7): 692--698.

Examples

tree <- read.tree(text="((a_a:1,b_b:1):1, c_c:2):1;")
tree <- congeneric.merge(tree, c("a_nother", "a_gain", "b_sharp"))