worrms is an R client for the World Register of Marine Species.
See the taxize book for taxonomically focused work in this and similar packages.
Stable version from CRAN
install.packages("worrms")
Development version from GitHub
install.packages("devtools")
devtools::install_github("ropensci/worrms")
library("worrms")
WoRMS 'records' are taxa, not specimen occurrences or something else.
by date
wm_records_date('2016-12-23T05:59:45+00:00')
#> # A tibble: 50 x 27
#> AphiaID url scientificname authority status unacceptreason taxonRankID
#> <int> <chr> <chr> <chr> <chr> <lgl> <int>
#> 1 894302 http… Paleopolymorp… Vasilenk… accep… NA 220
#> 2 894296 http… Parapachyphlo… Miklukho… accep… NA 220
#> 3 894298 http… Parapachyphlo… Miklukho… accep… NA 220
#> 4 894301 http… Ovulina radia… Seguenza… accep… NA 220
#> 5 894299 http… Parafissurina… Petri, 1… accep… NA 220
#> 6 894297 http… Parapachyphlo… Miklukho… accep… NA 220
#> 7 894303 http… Anomalina nod… Terquem,… accep… NA 220
#> 8 901957 http… Gaudryinella … Moullade… accep… NA 220
#> 9 916899 http… Gavelinella p… Porthaul… accep… NA 220
#> 10 902959 http… Valvulineria … Kicinski… accep… NA 220
#> # … with 40 more rows, and 20 more variables: rank <chr>,
#> # valid_AphiaID <int>, valid_name <chr>, valid_authority <chr>,
#> # parentNameUsageID <int>, kingdom <chr>, phylum <chr>, class <chr>,
#> # order <chr>, family <chr>, genus <chr>, citation <chr>, lsid <chr>,
#> # isMarine <int>, isBrackish <lgl>, isFreshwater <lgl>,
#> # isTerrestrial <lgl>, isExtinct <int>, match_type <chr>, modified <chr>
by a taxonomic name
wm_records_name(name = 'Platanista gangetica')
#> Error: (204) No Content - Platanista gangetica
by many names
wm_records_names(name = c('Platanista gangetica', 'Coryphaena'))
#> [[1]]
#> # A tibble: 0 x 0
#>
#> [[2]]
#> # A tibble: 2 x 27
#> AphiaID url scientificname authority status unacceptreason taxonRankID
#> <int> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 125960 http… Coryphaena Linnaeus… accep… <NA> 180
#> 2 843430 <NA> <NA> <NA> quara… synonym NA
#> # … with 20 more variables: rank <chr>, valid_AphiaID <int>,
#> # valid_name <chr>, valid_authority <chr>, parentNameUsageID <int>,
#> # kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> # genus <chr>, citation <chr>, lsid <chr>, isMarine <int>,
#> # isBrackish <int>, isFreshwater <int>, isTerrestrial <int>,
#> # isExtinct <lgl>, match_type <chr>, modified <chr>
by common name
wm_records_common(name = 'clam')
#> # A tibble: 4 x 27
#> AphiaID url scientificname authority status unacceptreason taxonRankID
#> <int> <chr> <chr> <chr> <chr> <lgl> <int>
#> 1 141919 http… Mercenaria me… (Linnaeu… accep… NA 220
#> 2 140431 http… Mya truncata Linnaeus… accep… NA 220
#> 3 141936 http… Venus verruco… Linnaeus… accep… NA 220
#> 4 575771 http… Verpa penis (Linnaeu… accep… NA 220
#> # … with 20 more variables: rank <chr>, valid_AphiaID <int>,
#> # valid_name <chr>, valid_authority <chr>, parentNameUsageID <int>,
#> # kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> # genus <chr>, citation <chr>, lsid <chr>, isMarine <int>,
#> # isBrackish <lgl>, isFreshwater <lgl>, isTerrestrial <lgl>,
#> # isExtinct <lgl>, match_type <chr>, modified <chr>
using the TAXMATCH algorithm
wm_records_taxamatch(name = 'Platanista gangetica')
#> Error: (204) No Content - AphiaRecordsByMatchNames
wm_name2id(name = "Rhincodon")
#> [1] 105749
wm_id2name(id = 105706)
#> [1] "Rhincodontidae"
wm_external(id = 1080)
#> [1] 85257
wm_external(id = 105706)
#> [1] 159854
wm_common_id(id = 156806)
#> # A tibble: 2 x 3
#> vernacular language_code language
#> <chr> <chr> <chr>
#> 1 gilded wedgeclam eng English
#> 2 Turton's wedge clam eng English
Get direct taxonomic children for an AphiaID
wm_classification(id = 105706)
#> # A tibble: 11 x 3
#> AphiaID rank scientificname
#> <int> <chr> <chr>
#> 1 2 Kingdom Animalia
#> 2 1821 Phylum Chordata
#> 3 146419 Subphylum Vertebrata
#> 4 1828 Superclass Gnathostomata
#> 5 11676 Superclass Pisces
#> 6 10193 Class Elasmobranchii
#> 7 368407 Subclass Neoselachii
#> 8 368408 Infraclass Selachii
#> 9 368410 Superorder Galeomorphi
#> 10 10208 Order Orectolobiformes
#> 11 105706 Family Rhincodontidae
Get classification for an AphiaID
wm_classification(id = 105706)
#> # A tibble: 11 x 3
#> AphiaID rank scientificname
#> <int> <chr> <chr>
#> 1 2 Kingdom Animalia
#> 2 1821 Phylum Chordata
#> 3 146419 Subphylum Vertebrata
#> 4 1828 Superclass Gnathostomata
#> 5 11676 Superclass Pisces
#> 6 10193 Class Elasmobranchii
#> 7 368407 Subclass Neoselachii
#> 8 368408 Infraclass Selachii
#> 9 368410 Superorder Galeomorphi
#> 10 10208 Order Orectolobiformes
#> 11 105706 Family Rhincodontidae
Get synonyms for an AphiaID
wm_synonyms(id = 105706)
#> # A tibble: 1 x 27
#> AphiaID url scientificname authority status unacceptreason taxonRankID
#> <int> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 148832 http… Rhiniodontidae Müller &… unacc… synonym 140
#> # … with 20 more variables: rank <chr>, valid_AphiaID <int>,
#> # valid_name <chr>, valid_authority <chr>, parentNameUsageID <int>,
#> # kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> # genus <lgl>, citation <chr>, lsid <chr>, isMarine <lgl>,
#> # isBrackish <lgl>, isFreshwater <lgl>, isTerrestrial <lgl>,
#> # isExtinct <lgl>, match_type <chr>, modified <chr>