classification_paths_from_taxonomy: Gets classification paths for a vector of taxa

View source: R/tree_from_taxonomy.R

classification_paths_from_taxonomyR Documentation

Gets classification paths for a vector of taxa


This uses the taxize package's wrapper of the Global Names Resolver to get taxonomic paths for the vector of taxa you pass in. Sources is a vector of source labels in order (though it works best if everything uses the same taxonomy, so we recommend doing just one source). You can see options by doing taxize::gnr_datasources(). Our default is Catalogue of Life


classification_paths_from_taxonomy(taxa, sources = "Catalogue of Life")



Vector of taxon names


Vector of names of preferred sources; see taxize::gnr_datasources(). Currently supports 100 taxonomic resources, see details.


Taxonomies supported by taxize::gnr_datasources()

  1. Catalogue of Life

  2. Wikispecies

  3. ITIS

  4. NCBI

  5. Index Fungorum

  6. GRIN Taxonomy for Plants

  7. Union 4

  8. The Interim Register of Marine and Nonmarine Genera

  9. World Register of Marine Species

  10. Freebase

  11. GBIF Backbone Taxonomy

  12. EOL

  13. Passiflora vernacular names

  14. Inventory of Fish Species in the Wami River Basin

  15. Pheasant Diversity and Conservation in the Mt. Gaoligonshan Region

  16. Finding Species

  17. Birds of Lindi Forests Plantation

  18. Nemertea

  19. Kihansi Gorge Amphibian Species Checklist

  20. Mushroom Observer

  21. TaxonConcept

  22. Amphibia and Reptilia of Yunnan

  23. Common names of Chilean Plants

  24. Invasive Species of Belgium

  25. ZooKeys

  26. COA Wildlife Conservation List

  27. AskNature

  28. China: Yunnan, Southern Gaoligongshan, Rapid Biological Inventories Report No. 04

  29. Native Orchids from Gaoligongshan Mountains, China

  30. Illinois Wildflowers

  31. Coleorrhyncha Species File

  32. /home/dimus/files/dwca/zoological

  33. Peces de la zona hidrogeográfica de la Amazonia, Colombia (Spreadsheet)

  34. Eastern Mediterranean Syllidae

  35. Gaoligong Shan Medicinal Plants Checklist

  36. birds_of_tanzania

  37. AmphibiaWeb

  38. tanzania_plant_sepecimens

  39. Papahanaumokuakea Marine National Monument

  40. Taiwanese IUCN species list

  41. BioPedia

  42. AnAge

  43. Embioptera Species File

  44. Global Invasive Species Database

  45. Sendoya S., Fernández F. AAT de hormigas (Hymenoptera: Formicidae) del Neotrópico 1.0 2004 (Spreadsheet)

  46. Flora of Gaoligong Mountains

  47. ARKive

  48. True Fruit Flies (Diptera, Tephritidae) of the Afrotropical Region

  49. 3i - Typhlocybinae Database

  50. CATE Sphingidae

  51. ZooBank

  52. Diatoms

  53. AntWeb

  54. Endemic species in Taiwan

  55. Dermaptera Species File

  56. Mantodea Species File

  57. Birds of the World: Recommended English Names

  58. New Zealand Animalia

  59. Blattodea Species File

  60. Plecoptera Species File

  61. /home/dimus/files/dwca/

  62. Coreoidea Species File

  63. Freshwater Animal Diversity Assessment - Normalized export

  64. Catalogue of Vascular Plant Species of Central and Northeastern Brazil

  65. Wikipedia in EOL

  66. Database of Vascular Plants of Canada (VASCAN)

  67. Phasmida Species File

  68. OBIS

  69. USDA NRCS PLANTS Database

  70. Catalog of Fishes

  71. Aphid Species File

  72. The National Checklist of Taiwan

  73. Psocodea Species File

  74. FishBase

  75. 3i - Typhlocybinae Database

  76. Belgian Species List

  77. EUNIS

  78. CU*STAR

  79. Orthoptera Species File

  80. Bishop Museum

  81. IUCN Red List of Threatened Species


  83. Tropicos - Missouri Botanical Garden

  84. nlbif

  85. The International Plant Names Index

  86. Index to Organism Names

  87. uBio NameBank

  88. Arctos

  89. Checklist of Beetles (Coleoptera) of Canada and Alaska. Second Edition.

  90. The Paleobiology Database

  91. The Reptile Database

  92. The Mammal Species of The World

  93. BirdLife International

  94. Checklist da Flora de Portugal (Continental, Açores e Madeira)

  95. FishBase Cache

  96. Silva

  97. Open Tree of Life Reference Taxonomy

  98. iNaturalist

  99. The Interim Register of Marine and Nonmarine Genera

  100. Gymno


A list with resolved taxa (a tibble, from taxize::gnr_resolve) and a vector of taxa not resolved

OpenTreeChronograms documentation built on June 22, 2022, 9:08 a.m.