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.
Install
Stable version from CRAN
install.packages("worrms")Development version from GitHub
install.packages("remotes")
remotes::install_github("ropensci/worrms")Get records
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>APHIA ID <–> name
wm_name2id(name = "Rhincodon")
#> [1] 105749
wm_id2name(id = 105706)
#> [1] "Rhincodontidae"Get AphiaID via an external ID
wm_external(id = 1080)
#> [1] 85257
wm_external(id = 105706)
#> [1] 159854Get vernacular names from an AphiaID
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 EnglishChildren
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 RhincodontidaeClassification
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 RhincodontidaeSynonyms
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>attributes (i.e., traits)
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