View source: R/phylomatic_local.R
phylomatic_local | R Documentation |
Use Phylomatic locally - ideal for large queries
phylomatic_local( taxa, taxnames = TRUE, storedtree = "R20120829", db = "apg", lowercase = FALSE, nodes = FALSE, verbose = TRUE )
taxa |
(character) Phylomatic format input of taxa names. required |
taxnames |
If |
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 |
db |
(character) One of "ncbi", "itis", or "apg". Default: apg |
lowercase |
(logical) Convert all chars in taxa file to lowercase.
Default: |
nodes |
(logical) label all nodes with default names.
Default: |
verbose |
(logical) Print messages. Default: |
uses phylocomr::ph_phylomatic()
under the hood
This function uses Phylomatic via Phylocom using the
phylocomr package. The interface is slightly different from
phylomatic()
: there's no tree by URL available, and some of the
parameters are not included here.
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
## Not run: library('ape') # Input taxonomic names taxa <- c("Poa annua", "Phlox diffusa", "Helianthus annuus") (tree <- phylomatic_local(taxa)) plot(collapse.singles(tree), no.margin=TRUE) taxa <- c("Poa annua", "Collomia grandiflora", "Lilium lankongense", "Phlox diffusa", "Iteadaphne caudata", "Gagea sarmentosa", "Helianthus annuus") (tree <- phylomatic_local(taxa)) plot(collapse.singles(tree), no.margin=TRUE) library("taxize") spp <- names_list("species", 500) length(spp) (tree <- phylomatic_local(spp)) ## End(Not run)
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