The Taxonomic Name Resolution Service (TNRS) is a tool for automated standardization of plant scientific names.
The TNRS corrects spelling errors and alternative spellings to a standard list of names, and converts out of date names (synonyms) to the current accepted name. The TNRS can process many names at once, saving hours of tedious and error-prone manual name correction. For names that cannot be resolved automatically, the TNRS present a list of possibilities and provides tools for researching and selecting the preferred name.
The TNRS takes as input either a vector of scientific names, or a data.frame containing two columns: row number and scientific name.
library(TNRS)
#First, we'll grab an example dataset containing two columns: row number and scientific name.
fulldata <- tnrs_testfile
head(fulldata,n = 20) ## ID
## 1 1
## 2 2
## 3 3
## 4 4
## 5 5
## 6 6
## 7 7
## 8 8
## 9 9
## 10 10
## 11 11
## 12 12
## 13 13
## 14 14
## 15 15
## 16 16
## 17 17
## 18 18
## 19 19
## 20 20
## taxon
## 1 Arecaceae Mauritia
## 2 Solanaceae Solanum bipatens Dunal
## 3 HYPOPTERYGIACEAE Hypopterygium incrassatolimbatum Ma^sA‰A¬Aºll. Hal.
## 4 Helotiaceae Diplothrix juniperifolia
## 5 Arecaceae Leopoldinia pulchra Mart.
## 6 Melastomataceae Leandra schenckii
## 7 Hydnocarpus macrocarpa
## 8 Campyliaceae Warnstorfia trichophylla (Warnst. ) Tuom. & T. J. Kop.
## 9 Piper arboreum Aubl.
## 10 Poaceae Pseudochaetochloa australiensis Hitchc.
## 11 Juglandaceae Engelhardia spicata var. colebrookeana (Lindl. ex Wall. ) Koord. & Valeton
## 12 Malvaceae Hibiscus 'Old Yella'
## 13 Fabaceae Mimosa vepres Lindm.
## 14 Berberidaceae Epimedium xpurpureum Bailly
## 15 Asteraceae Senecio beguei Humbert
## 16 Coelogyne fragrans
## 17 Cyperaceae Rhynchospora cephalotes (L. ) Vahl
## 18 Pteridophyte Nephrolepis mollis Rosenst.
## 19 Piperaceae Piper crassipeduncullum
## 20 Asteraceae Hieracium billyanum var. parvulum B. de Retz#Note that there are a variety of formats represented here, sometimes including
# scientific name only
# genus only
# family and genus
# family, scientific name, and author
results <- TNRS(taxonomic_names = fulldata)
# Inspect the results
head(results, 10)## ID Name_submitted
## 1 1 Arecaceae Mauritia
## 2 2 Solanaceae Solanum bipatens Dunal
## 3 3 HYPOPTERYGIACEAE Hypopterygium incrassatolimbatum Ma^sAAAll. Hal.
## 4 4 Helotiaceae Diplothrix juniperifolia
## 5 5 Arecaceae Leopoldinia pulchra Mart.
## 6 6 Melastomataceae Leandra schenckii
## 7 7 Hydnocarpus macrocarpa
## 8 8 Campyliaceae Warnstorfia trichophylla (Warnst. ) Tuom. & T. J. Kop.
## 9 9 Piper arboreum Aubl.
## 10 10 Poaceae Pseudochaetochloa australiensis Hitchc.
## Overall_score Name_matched_id Name_matched
## 1 1 1960517 Mauritia
## 2 1 511364 Solanum bipatens
## 3 0.93028 567775 Hypopterygium incrassatolimbatum
## 4 0.59957384396743 55516 Diplothrix juniperifolia
## 5 1 37359 Leopoldinia pulchra
## 6 1 305732 Leandra schenckii
## 7 1 1284586 Hydnocarpus macrocarpa
## 8 0.67965907517394 540191 Warnstorfia trichophylla
## 9 1 363887 Piper arboreum
## 10 1 387911 Pseudochaetochloa australiensis
## Name_score Name_matched_rank Author_submitted
## 1 1 Genus
## 2 1 species Dunal
## 3 1 species Ma^sAAAll. Hal.
## 4 0.59957384396743 species
## 5 1 species Mart.
## 6 1 species
## 7 1 species
## 8 0.59957384396743 species (Warnst. ) Tuom. & T. J. Kop.
## 9 1 species Aubl.
## 10 1 species Hitchc.
## Author_matched Author_score Canonical_author
## 1
## 2 Dunal 1 Dunal
## 3 Müll. Hal. 0.6514 Müll. Hal.
## 4 DC.
## 5 Mart. 1 Mart.
## 6 Cogn.
## 7 Warb.
## 8 (Warnst.) Tuom. & T.J. Kop. 1 (Warnst.) Tuom. & T.J. Kop.
## 9 Aubl. 1 Aubl.
## 10 Hitchc. 1 Hitchc.
## Name_matched_accepted_family Genus_submitted Genus_matched Genus_score
## 1 Arecaceae Mauritia Mauritia 1
## 2 Solanaceae Solanum Solanum 1
## 3 Hypopterygiaceae Hypopterygium Hypopterygium 1
## 4 Asteraceae Diplothrix Diplothrix 1
## 5 Arecaceae Leopoldinia Leopoldinia 1
## 6 Melastomataceae Leandra Leandra 1
## 7 Achariaceae Hydnocarpus Hydnocarpus 1
## 8 Amblystegiaceae Warnstorfia Warnstorfia 1
## 9 Piperaceae Piper Piper 1
## 10 Poaceae Pseudochaetochloa Pseudochaetochloa 1
## Specific_epithet_submitted Specific_epithet_matched Specific_epithet_score
## 1
## 2 bipatens bipatens 1
## 3 incrassatolimbatum incrassatolimbatum 1
## 4 juniperifolia juniperifolia 1
## 5 pulchra pulchra 1
## 6 schenckii schenckii 1
## 7 macrocarpa macrocarpa 1
## 8 trichophylla trichophylla 1
## 9 arboreum arboreum 1
## 10 australiensis australiensis 1
## Family_submitted Family_matched Family_score Infraspecific_rank
## 1 Arecaceae Arecaceae 1
## 2 Solanaceae Solanaceae 1
## 3 Hypopterygiaceae Hypopterygiaceae 1
## 4 Helotiaceae
## 5 Arecaceae Arecaceae 1
## 6 Melastomataceae Melastomataceae 1
## 7
## 8 Campyliaceae
## 9
## 10 Poaceae Poaceae 1
## Infraspecific_epithet_matched Infraspecific_epithet_score
## 1
## 2
## 3
## 4
## 5
## 6
## 7
## 8
## 9
## 10
## Infraspecific_rank_2 Infraspecific_epithet_2_matched
## 1
## 2
## 3
## 4
## 5
## 6
## 7
## 8
## 9
## 10
## Infraspecific_epithet_2_score Annotations Unmatched_terms
## 1
## 2
## 3
## 4 Helotiaceae
## 5
## 6
## 7
## 8 Campyliaceae
## 9
## 10
## Name_matched_url
## 1
## 2 http://www.theplantlist.org/tpl1.1/search?q=Solanum+bipatens
## 3 http://www.theplantlist.org/tpl1.1/search?q=Hypopterygium+incrassatolimbatum
## 4 http://www.theplantlist.org/tpl1.1/search?q=Diplothrix+juniperifolia
## 5 http://www.theplantlist.org/tpl1.1/search?q=Leopoldinia+pulchra
## 6 http://www.theplantlist.org/tpl1.1/search?q=Leandra+schenckii
## 7 http://www.tropicos.org/Name/100431320
## 8 http://www.theplantlist.org/tpl1.1/search?q=Warnstorfia+trichophylla
## 9 http://www.theplantlist.org/tpl1.1/search?q=Piper+arboreum
## 10 http://www.tropicos.org/Name/25520644
## Name_matched_lsid Phonetic Taxonomic_status Accepted_name
## 1 Y Accepted Mauritia
## 2 Y No opinion
## 3 Y Synonym Hypopterygium tamarisci
## 4 Y Synonym Zinnia juniperifolia
## 5 Y Accepted Leopoldinia pulchra
## 6 Y Synonym Leandra regnellii
## 7 Y Accepted Hydnocarpus macrocarpa
## 8 Y Accepted Warnstorfia trichophylla
## 9 Y Accepted Piper arboreum
## 10 Y Accepted Pseudochaetochloa australiensis
## Accepted_species Accepted_name_author Accepted_name_id
## 1 1960517
## 2
## 3 Hypopterygium tamarisci (Sw.) Brid. ex Müll. Hal. 567887
## 4 Zinnia juniperifolia (DC.) A.Gray 1941999
## 5 Leopoldinia pulchra Mart. 37359
## 6 Leandra regnellii (Triana) Cogn. 305723
## 7 Hydnocarpus macrocarpa Warb. 1284586
## 8 Warnstorfia trichophylla (Warnst.) Tuom. & T.J. Kop. 540191
## 9 Piper arboreum Aubl. 363887
## 10 Pseudochaetochloa australiensis Hitchc. 387911
## Accepted_name_rank
## 1 Genus
## 2
## 3 species
## 4 species
## 5 species
## 6 species
## 7 species
## 8 species
## 9 species
## 10 species
## Accepted_name_url
## 1
## 2
## 3 http://www.theplantlist.org/tpl1.1/search?q=Hypopterygium+tamarisci
## 4 http://www.theplantlist.org/tpl1.1/search?q=Zinnia+juniperifolia
## 5 http://www.theplantlist.org/tpl1.1/search?q=Leopoldinia+pulchra
## 6 http://www.theplantlist.org/tpl1.1/search?q=Leandra+regnellii
## 7 http://www.tropicos.org/Name/100431320
## 8 http://www.theplantlist.org/tpl1.1/search?q=Warnstorfia+trichophylla
## 9 http://www.theplantlist.org/tpl1.1/search?q=Piper+arboreum
## 10 http://www.tropicos.org/Name/25520644
## Accepted_name_lsid Accepted_family Overall_score_order
## 1 Arecaceae 1
## 2 1
## 3 Hypopterygiaceae 1
## 4 Asteraceae 1
## 5 Arecaceae 1
## 6 Melastomataceae 1
## 7 Achariaceae 1
## 8 Amblystegiaceae 1
## 9 Piperaceae 1
## 10 Poaceae 1
## Highertaxa_score_order Source Warnings
## 1 1 tpl 2
## 2 1 tpl 0
## 3 1 tpl 0
## 4 7 tpl 4
## 5 1 tpl 0
## 6 1 tpl 0
## 7 1 tropicos 0
## 8 3 tpl 4
## 9 1 tpl 0
## 10 1 tropicos 0# The output includes information on the name submitted, the match score (how close the match is), the name matched, the status of the matched name, and the accepted name.When using the TNRS, we ask that you cite both the TNRS itself and the data sources that are used by the TNRS. The TNRS couldn’t function without these data sources, and it is important to recognize the work of these data providers by citing their work. Users may also want to report metadata about the version of the TNRS they used in their analyses for the purposes of reproducibility. The function TNRS_metadata facilitates citations and version reporting by providing this information in an easily-used format. This function returns:
metadata <- TNRS_metadata()
#If you want to see the TNRS version information (e.g. to report in an manuscript):
metadata$version## sourceID sourceName sourceNameFull
## 1 1 tropicos Missouri Botanical Gardens Tropicos database
## 2 2 tpl The Plant List (ver. 1.1)
## 3 3 usda USDA Plants
## sourceUrl
## 1 https://www.tropicos.org/
## 2 http://www.theplantlist.org/
## 3 https://plants.sc.egov.usda.gov/java/
## description
## 1 The Missouri Botanical Garden''s Tropicos database links over 1.33M scientific names with over 4.87M specimens and over 685K digital images. The data includes over 150K references from over 52.6K publications offered as a free service to the world''s scientific community.
## 2 The Plant List (TPL) was a working list of all known plant species produced by the botanical community in response to Target 1 of the 2002-2010 Global Strategy for Plant Conservation (GSPC). TPL has been static since 2013, but was used as the starting point for the Taxonomic Backbone of the World Flora Online (WFO), and updated information can be found at www.worldfloraonline.org
## 3 The PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories.
## dataUrl logo_path version
## 1 http://services.tropicos.org/ images/tropicos.png <NA>
## 2 images/tpl.png 1.1
## 3 http://plants.usda.gov/adv_search.html images/usda.png <NA>
## sourceReleaseDate tnrsDateAccessed
## 1 <NA> 2020-05-30
## 2 2013-09-01 2020-06-25
## 3 <NA> 2020-07-03#To see the sources that are used by the TNRS:
metadata$sources## db_version build_date code_version api_version
## 1 4.1.3 2020-10-01 5.0.2 1.1.2#To get the citation information to paste into a reference manager (e.g. paperpile, zotero):
# writeLines(text = metadata$citations$citation)