Description Usage Arguments Details Value Examples
View source: R/phylomatic_local.R
Use Phylomatic locally - ideal for large queries
1 2 3 4 5 6 7 8 9 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## 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)
|
preparing names...
processing with phylomatic...
Phylogenetic tree with 3 tips and 3 internal nodes.
Tip labels:
[1] "poa_annua" "phlox_diffusa" "helianthus_annuus"
Node labels:
[1] "euphyllophyte" "poales_to_asterales" "ericales_to_asterales"
Rooted; includes branch lengths.
preparing names...
processing with phylomatic...
Phylogenetic tree with 7 tips and 7 internal nodes.
Tip labels:
poa_annua, lilium_lankongense, gagea_sarmentosa, collomia_grandiflora, phlox_diffusa, helianthus_annuus, ...
Node labels:
euphyllophyte, magnoliales_to_asterales, poales_to_asterales, , liliaceae, ericales_to_asterales, ...
Rooted; includes branch lengths.
[1] 500
preparing names...
processing with phylomatic...
Phylogenetic tree with 443 tips and 253 internal nodes.
Tip labels:
alkanna_cappadocica, lithospermum_purpurascens, myosotis_adpressa, bourreria_rinconensis, plagiobothrys_hispidus, cestrum_zarucchianum, ...
Node labels:
euphyllophyte, seedplants, nymphaeales_to_asterales, magnoliales_to_asterales, poales_to_asterales, eudicots, ...
Rooted; includes branch lengths.
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