ComTreeOpt: Enhance user-specific community trees

In iantrotter/ComTreeOpt: Community Tree Optimizer using Open Tree of Life

Description

Based on an interface with Open Tree of Life, the Community Tree Optimizer (ComTreeOpt) classifies families from user-specific lists into resolvable and non-resolvable families, builds resolved subtrees for resolvable families and inserts them in the megatree R20160415.new (Gastauer & Meira-Neto, 2017) previously pruned to species from non-resolvable families.

Usage

ComTreeOpt(family, genus, species,
  megatree.uri = "https://www.dropbox.com/s/rc8jtmb6b2hdweo/R20160415.new?dl=0")

Arguments

family	A list of families.
genus	A list of genuses.
species	A list of species. The list of families, genus and species must have the same number of entries.
megatree.uri	URI to a megatree. The default value is the R20160415.new megatree (Gastauer & Meira-Neto, 2017).

Value

A phylogenetic tree containing the user-specified species, based on the Open Tree of Life.

References

Gastauer, M. & Meira-Neto, J. A. A. (2017) Updated angiosperm family tree for analyzing phylogenetic diversity and community structure. Acta Botanica Brasília, vol.31, n.2, pp.191-198. DOI: http://dx.doi.org/10.1590/0102-33062016abb0306.

Examples

data(FSN_species);
tree <- ComTreeOpt(family, genus, species);
plot(tree, show.node.label=T)

iantrotter/ComTreeOpt documentation built on May 15, 2019, 3:18 p.m.