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rphylotastic

R package to interact with phylotastic web services.

  • Find the available functions of the R library in this documentation

  • See the full description of the API of phylotastic web services here

To install this in R:

library(devtools)
devtools::install_github("phylotastic/rphylotastic")

For help on functions:

library(rphylotastic)
help(package="rphylotastic")

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Version

Install

install.packages('rphylotastic')

Monthly Downloads

2

Version

0.0.4

License

GPL-2

Issues

Pull Requests

Stars

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Maintainer

Brian OMeara

Last Published

February 27th, 2018

Functions in rphylotastic (0.0.4)

newick_compare

Compare two phylogenetic trees
remove_species_from_list

Remove an existing list of species
species_get_info

Get information of a list of species
taxa_get_otol_tree

Get OToL induced subtree
get_base_url

Get Phylotastic base URL return The URL for the phylotastic server
get_list_server_url

Return Species List server URL
taxa_resolve_names_with_gnr

Resolve Scientific Names with GNR TNRS
taxa_resolve_names_with_otol

Resolve Scientific Names with Open Tree TNRS
taxon_get_species

Get all species from a taxon
taxon_get_species_and_country

Get all species filtered by country from a taxon
replace_species_in_list

Replace a list of species
species_get_image_data

Get image metadata of a list of species
taxa_get_phylomatic_tree

Get phylomatic subtree
taxa_get_taxonomic_tree

Get taxonomic tree from the NCBI
get_species_from_list

Get existing list/lists of species
insert_species_in_list

Insert list of species
taxon_separate_dark_taxa_using_otol

Separate dark from known taxa on OpenTree of Life
text_get_scientific_names

Function to pull scientific names from text
update_species_in_list

Update metadata of a list of species
url_get_scientific_names

Function to pull scientific names from web pages
taxon_get_species_with_genome

Get all species that have genome sequence in NCBI from a taxon
taxon_separate_dark_taxa_using_genbank

Separate dark from known taxa on another database