worrms
is an R client for the World Register of Marine Species (https://www.marinespecies.org/)
See the taxize book (https://taxize.dev) for taxonomically focused work in this and similar packages.
Stable version from CRAN
install.packages("worrms")
Development version from GitHub
install.packages("remotes") remotes::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 919684 http… Flintina serr… Cuvillie… accep… NA 220 #> 8 906465 http… Verneuilinoid… Bartenst… accep… NA 220 #> 9 903640 http… Quinqueloculi… Hussey, … accep… NA 220 #> 10 917580 http… Orbitolina ra… Sahni & … 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 = 'Leucophaeus scoresbii') #> # A tibble: 1 x 27 #> AphiaID url scientificname authority status unacceptreason taxonRankID rank #> <int> <chr> <chr> <chr> <chr> <lgl> <int> <chr> #> 1 344089 http… Leucophaeus s… Traill, … accep… NA 220 Spec… #> # … with 19 more variables: 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>
by many names
wm_records_names(name = c('Leucophaeus scoresbii', 'Coryphaena')) #> [[1]] #> # A tibble: 1 x 27 #> AphiaID url scientificname authority status unacceptreason taxonRankID rank #> <int> <chr> <chr> <chr> <chr> <lgl> <int> <chr> #> 1 344089 http… Leucophaeus s… Traill, … accep… NA 220 Spec… #> # … with 19 more variables: 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> #> #> [[2]] #> # A tibble: 2 x 27 #> AphiaID url scientificname authority status unacceptreason taxonRankID rank #> <int> <chr> <chr> <chr> <chr> <chr> <int> <chr> #> 1 125960 http… Coryphaena Linnaeus… accep… <NA> 180 Genus #> 2 843430 <NA> <NA> <NA> quara… synonym NA <NA> #> # … with 19 more variables: 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 rank #> <int> <chr> <chr> <chr> <chr> <lgl> <int> <chr> #> 1 141919 http… Mercenaria me… (Linnaeu… accep… NA 220 Spec… #> 2 140431 http… Mya truncata Linnaeus… accep… NA 220 Spec… #> 3 141936 http… Venus verruco… Linnaeus… accep… NA 220 Spec… #> 4 575771 http… Verpa penis (Linnaeu… accep… NA 220 Spec… #> # … with 19 more variables: 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 = 'Leucophaeus scoresbii') #> [[1]] #> # A tibble: 1 x 27 #> AphiaID url scientificname authority status unacceptreason taxonRankID rank #> <int> <chr> <chr> <chr> <chr> <lgl> <int> <chr> #> 1 344089 http… Leucophaeus s… Traill, … accep… NA 220 Spec… #> # … with 19 more variables: 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>
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 rank #> <int> <chr> <chr> <chr> <chr> <chr> <int> <chr> #> 1 148832 http… Rhiniodontidae Müller &… unacc… synonym 140 Fami… #> # … with 19 more variables: 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>
attribute definition by ID
wm_attr_def(id = 1) #> # A tibble: 1 x 4 #> measurementTypeID measurementType CategoryID children #> <int> <chr> <int> <list> #> 1 1 IUCN Red List Category 1 <df[,4] [2 × 4]>
attribute data by AphiaID
wm_attr_data(id = 127160) #> # A tibble: 24 x 10 #> AphiaID measurementType… measurementType measurementValue source_id reference #> <chr> <int> <chr> <chr> <int> <chr> #> 1 127160 23 Species import… FAO-ASFIS: Spec… 197354 "FAO Fis… #> 2 127160 23 Species import… MSFD indicators 197546 "Daniel … #> 3 127160 23 Species import… MSFD indicators 197549 "ICES. 2… #> 4 127160 23 Species import… MSFD indicators 197615 "List of… #> 5 127160 23 Species import… MSFD indicators 197615 "List of… #> 6 127160 23 Species import… MSFD indicators 197615 "List of… #> 7 127160 23 Species import… MSFD indicators 197615 "List of… #> 8 127160 23 Species import… MSFD indicators 197616 "List of… #> 9 127160 23 Species import… MSFD indicators 197616 "List of… #> 10 127160 23 Species import… MSFD indicators 197549 "ICES. 2… #> # … with 14 more rows, and 4 more variables: qualitystatus <chr>, #> # AphiaID_Inherited <int>, CategoryID <int>, children <list>
attributes grouped by a CategoryID
wm_attr_category(id = 7) #> # A tibble: 6 x 4 #> measurementValueID measurementValue measurementValueCode children #> <int> <chr> <chr> <list> #> 1 183 benthos <NA> <df[,4] [8 × 4]> #> 2 184 plankton <NA> <df[,4] [7 × 4]> #> 3 194 nekton <NA> <df[,0] [0 × 0]> #> 4 323 neuston <NA> <df[,0] [0 × 0]> #> 5 378 edaphofauna <NA> <df[,4] [2 × 4]> #> 6 331 not applicable N/A <df[,0] [0 × 0]>
AphiaIDs by attribute definition ID
wm_attr_aphia(id = 4) #> # A tibble: 50 x 2 #> AphiaID Attributes #> <int> <list> #> 1 11 <df[,10] [1 × 10]> #> 2 55 <df[,10] [2 × 10]> #> 3 57 <df[,10] [2 × 10]> #> 4 58 <df[,10] [2 × 10]> #> 5 59 <df[,10] [2 × 10]> #> 6 63 <df[,10] [2 × 10]> #> 7 64 <df[,10] [2 × 10]> #> 8 69 <df[,10] [2 × 10]> #> 9 90 <df[,10] [2 × 10]> #> 10 91 <df[,10] [2 × 10]> #> # … with 40 more rows
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