taxize (version 0.0.5)

phylomatic_tree: Format tree string, submit to Phylomatic, get newick tree.

Description

Format tree string, submit to Phylomatic, get newick tree.

Usage

phylomatic_tree(taxa, taxnames = TRUE, get = "GET",
    informat = "newick", method = "phylomatic",
    storedtree = "R20120829", taxaformat = "slashpath",
    outformat = "newick", clean = "true", parallel = TRUE)

Arguments

taxa

Phylomatic format input of taxa names.

taxnames

If true, we get the family names for you to attach to your species names to send to Phylomatic API. If FALSE, you have to provide the strings in the right format.

get

'GET' or 'POST' format for submission to the website.

informat

One of newick, nexml, or cdaordf. If using a stored tree, informat should always be newick.

method

One of phylomatic or convert

storedtree

One of R20120829 (Phylomatic tree R20120829 for plants), smith2011 (Smith 2011, plants), or binindaemonds2007 (Bininda-Emonds 2007, mammals).

taxaformat

Only option is slashpath for now. Leave as is.

outformat

One of newick, nexml, or fyt.

clean

Return a clean tree or not.

parallel

Run in parallel or not.

Value

• Newick formatted tree.

Details

Use the web interface here http://phylodiversity.net/phylomatic/

Examples

# Input taxonomic names
taxa <- c("Poa annua", "Abies procera", "Helianthus annuus")
tree <- phylomatic_tree(taxa=taxa, get = 'POST', informat='newick', method = "phylomatic",
		storedtree = "R20120829", taxaformat = "slashpath", outformat = "newick", clean = "true")
plot(tree)

# Lots of names
taxa <- c("Poa annua", "Abies procera", "Helianthus annuus", "Collomia grandiflora",
		"Ribes latifolium", "Arctostaphylos manzanita", "Phlox glabriflora", "Phlox diffusa",
		"Datura wrightii", "Nicotiana glauca", "Nicotiana tomentosa", "Mimulus bicolor")
tree <- phylomatic_tree(taxa=taxa, get = 'POST', informat='newick', method = "phylomatic",
		storedtree = "R20120829", taxaformat = "slashpath", outformat = "newick", clean = "true")
plot(tree, no.margin=T)

# In parallel with parallel=TRUE speeds up dramatically by doing the gathering of
# family names from NCBI in parallel
registerDoMC(cores=4)  # I have a mac, so using doMC package, use whatever you like
phylomatic_tree(taxa=taxa, get = 'POST', informat='newick', method = "phylomatic",
		storedtree = "R20120829", taxaformat = "slashpath", outformat = "newick", clean = "true", parallel=FALSE)