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]

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rphylotastic.pdf |rphylotastic.html✨
rphylotastic/json (API)

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

Peer review:

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

Datasets:

On CRAN:

2.28 score 19 scripts 22 downloads 26 exports 145 dependencies

Last updated 1 years agofrom:1cd60f2d99. Checks:ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 01 2024
R-4.5-winERRORNov 01 2024
R-4.5-linuxERRORNov 01 2024
R-4.4-winERRORNov 01 2024
R-4.4-macERRORNov 01 2024
R-4.3-winERRORNov 01 2024
R-4.3-macERRORNov 01 2024

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:ade4apeaskpassassertthatbackportsbase64encbitbit64boldbrranchingbslibcachemcheckmateclicliprclusterclusterGenerationcodacodetoolscolorspacecombinatconditionzcpp11crayoncrulcurldata.tableDEoptimdigestdoParalleldplyrevaluateexpmfansifarverfastmapfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrmapsMASSMatrixmemoisemgcvmimemnormtmunsellnatservnlmennetnumDerivopenssloptimParallelpbapplyphangornphylobasephylocomrphytoolspillarpixmappkgconfigplotrixplyrprettyunitsprogresspurrrquadprogR6rappdirsratelimitrRColorBrewerRcppRcppArmadilloreadrrentrezreshape2rexritisrlangrmarkdownrnclRNeXMLrotlrpartrredlistrstudioapisassscalesscatterplot3dsolriumspstringistringrsystaxizetibbletidyrtidyselecttinytextriebeardtzdburltoolsutf8uuidvctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrworrmsxfunXMLxml2yamlzoo

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