classification_paths_from_taxonomy: Gets classification paths for a vector of taxa

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Gets classification paths for a vector of taxa

Description

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

Usage

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

Arguments

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

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 names.zip

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/clemens.zip

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

82. BioLib.cz

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

Value

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

phylotastic/datelife documentation built on June 9, 2024, 6:50 p.m.