Description Usage Arguments Details Value Examples
Query Phylomatic for a phylogenetic tree.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
taxa |
Phylomatic format input of taxa names. |
taxnames |
If |
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: |
db |
One of "ncbi", "itis", or "apg". Default: apg |
mssgs |
Print messages. Default: |
... |
curl options passed on to crul::HttpClient |
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"
Newick formatted tree as phylo
object or
nexml character string
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | ## 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.