phylomatic: Query Phylomatic for a phylogenetic tree.

In ropensci/brranching: Fetch 'Phylogenies' from Many Sources

Query Phylomatic for a phylogenetic tree.

Description

Query Phylomatic for a phylogenetic tree.

Usage

phylomatic(
  taxa,
  taxnames = TRUE,
  get = "GET",
  informat = "newick",
  method = "phylomatic",
  storedtree = "R20120829",
  treeuri = NULL,
  taxaformat = "slashpath",
  outformat = "newick",
  clean = TRUE,
  db = "apg",
  mssgs = TRUE,
  ...
)

Arguments

taxa	Phylomatic format input of taxa names.
taxnames	If TRUE (default), 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' (default) or 'POST' format for submission to the website.
informat	One of newick (default), nexml, or cdaordf. If using a stored tree, informat should always be newick.
method	One of phylomatic (default) or convert
storedtree	One of R20120829 (Phylomatic tree R20120829 for plants), smith2011 (Smith 2011, plants), binindaemonds2007 (Bininda-Emonds 2007, mammals), or zanne2014 (Zanne et al. 2014, plants). Default: R20120829
treeuri	URL for a phylogenetic tree in newick format.
taxaformat	Only option is slashpath for now. Leave as is.
outformat	One of newick, nexml, or fyt.
clean	Return a clean tree or not. Default: TRUE
db	One of "ncbi", "itis", or "apg". Default: apg
mssgs	Print messages. Default: TRUE
...	curl options passed on to crul::HttpClient

Details

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

If you set taxnames = FALSE, you need to pass in a character vector, with each element like this example: "asteraceae/taraxacum/taraxacum_officinale", of the form "family/genus/genus_specfic epithet"

Value

Newick formatted tree as phylo object or nexml character string

Examples

## Not run: 
# Input taxonomic names
taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus")
tree <- phylomatic(taxa=taxa, get = 'POST')
plot(tree, no.margin=TRUE)

# Genus names
taxa <- c("Poa", "Phlox", "Helianthus")
tree <- phylomatic(taxa=taxa, storedtree='R20120829', get='POST')
plot(tree, no.margin=TRUE)

# Lots of names
taxa <- c("Poa annua", "Collomia grandiflora", "Lilium lankongense", "Phlox diffusa",
"Iteadaphne caudata", "Gagea sarmentosa", "Helianthus annuus")
tree <- phylomatic(taxa=taxa, get = 'POST')
plot(tree, no.margin=TRUE)

# Don't clean - clean=TRUE is default
(tree <- phylomatic(taxa=taxa, clean = FALSE))
## with clean=FALSE, you can get non-splitting nodes, which you
## need to collpase before plotting
library('ape')
plot(collapse.singles(tree), no.margin=TRUE)

# Output NeXML format
taxa <- c("Gonocarpus leptothecus", "Gonocarpus leptothecus", "Lilium lankongense")
out <- phylomatic(taxa=taxa, get = 'POST', outformat = "nexml")
cat(out)

# Lots of names, note that when you have enough names (number depends on length of individual
# names, so there's no per se rule), you will get an error when using `get='GET'`,
# when that happens use `get='POST'`
library("taxize")
spp <- names_list("species", 500)
# phylomatic(taxa = spp, get = "GET")
(out <- phylomatic(taxa = spp, get = "POST", db = "itis"))
plot(out)

## End(Not run)

ropensci/brranching documentation built on Dec. 6, 2022, 10:47 a.m.