Package: rphylotastic 0.0.8.1

Brian OMeara

rphylotastic: An R Interface to 'Phylotastic' Web Services

This wraps the 'Phylotastic' services APIs described on Web Services at <www.phylotastic.org>. The main use case is to return a phylogenetic tree for a set of species, but the services also include ways to extract species names from web pages, perform taxonomic name resolution, retrieve a list of all descendant species of a taxon, find images of a species, and more.

Authors:Brian O'Meara [aut, cre], Abu Saleh Md Tayeen [aut], Luna L. Sanchez Reyes [aut]

rphylotastic_0.0.8.1.tar.gz
rphylotastic_0.0.8.1.zip(r-4.7)rphylotastic_0.0.8.1.zip(r-4.6)rphylotastic_0.0.8.1.zip(r-4.5)
rphylotastic_0.0.8.1.tgz(r-4.6-any)rphylotastic_0.0.8.1.tgz(r-4.5-any)
rphylotastic_0.0.8.1.tar.gz(r-4.6-any)
rphylotastic_0.0.8.1.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rphylotastic/json (API)

# Install 'rphylotastic' in R:
install.packages('rphylotastic', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/phylotastic/rphylotastic/issues

Datasets:

On CRAN:

Conda:

2.28 score 19 scripts 26 exports 96 dependencies

Last updated from:1cd60f2d99. Checks:8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR167
source / vignettesERROR201
linux-release-x86_64ERROR179
macos-release-arm64ERROR134
macos-oldrel-arm64ERROR125
windows-develERROR107
windows-releaseERROR107
windows-oldrelERROR103
wasm-releaseOK149

Exports:arclabelsfile_get_scientific_namesfile_get_scientific_names_from_GNRDget_base_urlget_species_from_listinsert_species_in_listremove_species_from_listreplace_species_in_listspecies_get_image_dataspecies_get_infotaxa_common_to_scientifictaxa_get_otol_treetaxa_get_phylomatic_treetaxa_resolve_names_with_gnrtaxa_resolve_names_with_otoltaxa_toss_binomialstaxon_get_speciestaxon_get_species_from_countrytaxon_get_species_with_genometaxon_separate_dark_taxa_using_genbanktaxon_separate_dark_taxa_using_otoltext_get_scientific_namestraits_get_treeupdate_species_in_listurl_get_scientific_namesurl_get_scientific_names_from_GNRD

Dependencies:ade4apeaskpassbackportsbrranchingcheckmatecliclusterGenerationcodacodetoolscombinatconditionzcpp11crayoncrulcurldata.tableDEoptimdigestdoParalleldplyrexpmforeachfuturefuture.applygenericsglobalsgluehmshttpcodehttrigraphiteratorsjsonlitelatticelifecyclelistenvmagrittrmapsMASSMatrixmimemnormtnatservnlmenumDerivopenssloptimParallelosqpparallellyphangornphylobasephylocomrphytoolspillarpixmappkgconfigplotrixplyrprettyunitsprogresspurrrR6RcppRcppArmadillorentrezreshape2ritisrlangrnclRNeXMLrotlrredlistS7scatterplot3dsolriumspstringistringrsystaxizetibbletidyrtidyselecttriebeardurltoolsutf8uuidvctrsWikipediRwikitaxawithrworrmsXMLxml2zoo

Readme and manuals

Help Manual

Help pageTopics
rphylotastic: An R Interface to 'Phylotastic' Web Servicesrphylotastic-package rphylotastic
Add arc labels to tips of a phylogeny; works for non-monophyletic groups and single tip lineages.arclabels arclabels.default
Function to pull scientific names from filefile_get_scientific_names
Function to pull scientific names from file using GNRDfile_get_scientific_names_from_GNRD
Flowering plants families from Open Tree Taxonomyflower_plant_fams
Get Phylotastic base URL return The URL for the phylotastic serverget_base_url
Return Species List server URLget_list_server_url
Get existing list/lists of speciesget_species_from_list
Insert list of speciesinsert_species_in_list
Remove an existing list of speciesremove_species_from_list
Replace a list of speciesreplace_species_in_list
Get image metadata of a list of speciesspecies_get_image_data
Get information from Encyclopedia of Life of a list of speciesspecies_get_info
Convert common names to scientific names.taxa_common_to_scientific
Get OToL induced subtreetaxa_get_otol_tree
Get phylomatic subtreetaxa_get_phylomatic_tree
Resolve Scientific Names with GNR TNRStaxa_resolve_names_with_gnr
Resolve Scientific Names with Open Tree TNRStaxa_resolve_names_with_otol
Keep the first part of the binomial from a vector of taxon names that includes species binomial namestaxa_toss_binomials
Get all species from a taxon from Open Tree of Life taxonomy.taxon_get_species
Get all species filtered by country from a taxontaxon_get_species_from_country
Get all species that have genome sequence in NCBI from a taxontaxon_get_species_with_genome
Separate dark from known taxa on another databasetaxon_separate_dark_taxa_using_genbank
Separate dark from known taxa on OpenTree of Lifetaxon_separate_dark_taxa_using_otol
Flowering plants families from Open Tree Taxonomyterrestrial_plant_orders
Function to pull scientific names from texttext_get_scientific_names
Function to get tree for a traits set.traits_get_tree
Update metadata of a list of speciesupdate_species_in_list
Function to pull scientific names from web pagesurl_get_scientific_names