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",
      url = "http://phylodiversity.net/phylomatic/pmws")

Arguments

taxa

Phylomatic format input of taxa names.

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.

url

The base URL for the Phylomatic API service, leave as is.

Examples

# Getting taxonomic information from ITIS, if you already have taxonomic serial numbers (TSNs)
dat_ <- laply(list("36616", "19322", "183327", "36616", "41107", "181835", "25929"), itis_phymat_format, format='isubmit')
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=36616
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=19322
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=183327
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=36616
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=41107
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=181835
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=25929
tree <- phylomatic_tree(taxa=taxa, get = 'POST', informat='newick', method = "phylomatic",
                storedtree = "R20120829", taxaformat = "slashpath", outformat = "newick", clean = "true")
Error in inherits(.data, "split"): object 'taxa' not found
plot(tree)
Error in plot(tree): object 'tree' not found

# 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")

Retrieving data for species ' Poa annua '

Retrieving data for species ' Abies procera '

Retrieving data for species ' Helianthus annuus '

http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=41107
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=181835
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=36616
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")

Retrieving data for species ' Poa annua '

Retrieving data for species ' Abies procera '

Retrieving data for species ' Helianthus annuus '

Retrieving data for species ' Collomia grandiflora '

Retrieving data for species ' Ribes latifolium '

Retrieving data for species ' Arctostaphylos manzanita '

Retrieving data for species ' Phlox glabriflora '

Retrieving data for species ' Phlox diffusa '

Retrieving data for species ' Datura wrightii '

Retrieving data for species ' Nicotiana glauca '

Retrieving data for species ' Nicotiana tomentosa '

Retrieving data for species ' Mimulus bicolor '

http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=41107
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=181835
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=36616
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=31037
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=895213
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=23496
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=504315
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=30930
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=30521
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=30574
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=505846
http://www.itis.gov/ITISWebService/services/ITISService/getFullHierarchyFromTSN?tsn=33245
plot(tree, no.margin=T)