Client for World Register of Marine Species (< http://www.marinespecies.org/>). Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification.
worrms
is a R client for the World Register of Marine Species
See the taxize book for taxonomically focused work in this and similar packages.
More stable CRAN version
install.packages("worrms")
Development version
devtools::install_github("ropensci/worrms")
library("worrms")
by date
wm_records_date('2016-12-23T05:59:45+00:00')#> # A tibble: 50 x 25#> AphiaID url scientificname authority status unacceptreason rank #> <int> <chr> <chr> <chr> <chr> <lgl> <chr>#> 1 894302 http… Paleopolymorp… Vasilenk… accep… NA Spec…#> 2 894296 http… Parapachyphlo… Miklukho… accep… NA Spec…#> 3 894298 http… Parapachyphlo… Miklukho… accep… NA Spec…#> 4 894301 http… Ovulina radia… Seguenza… accep… NA Spec…#> 5 894299 http… Parafissurina… Petri, 1… accep… NA Spec…#> 6 894297 http… Parapachyphlo… Miklukho… accep… NA Spec…#> 7 894303 http… Anomalina nod… Terquem,… accep… NA Spec…#> 8 901957 http… Gaudryinella … Moullade… accep… NA Spec…#> 9 916899 http… Gavelinella p… Porthaul… accep… NA Spec…#> 10 902959 http… Valvulineria … Kicinski… accep… NA Spec…#> # … with 40 more rows, and 18 more variables: valid_AphiaID <int>,#> # valid_name <chr>, valid_authority <chr>, 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')#> # A tibble: 3 x 25#> AphiaID url scientificname authority status unacceptreason rank #> <int> <chr> <chr> <chr> <chr> <lgl> <chr>#> 1 254967 http… Platanista ga… (Lebeck,… accep… NA Spec…#> 2 383571 http… Platanista ga… Roxburgh… accep… NA Subs…#> 3 254969 http… Platanista ga… Owen, 18… accep… NA Subs…#> # … with 18 more variables: valid_AphiaID <int>, valid_name <chr>,#> # valid_authority <chr>, kingdom <chr>, phylum <chr>, class <chr>,#> # order <chr>, family <chr>, genus <chr>, citation <chr>, lsid <chr>,#> # isMarine <int>, isBrackish <lgl>, isFreshwater <int>,#> # isTerrestrial <int>, isExtinct <lgl>, match_type <chr>, modified <chr>
by many names
wm_records_names(name = c('Platanista gangetica', 'Coryphaena'))#> [[1]]#> # A tibble: 1 x 25#> AphiaID url scientificname authority status unacceptreason rank #> <int> <chr> <chr> <chr> <chr> <lgl> <chr>#> 1 254967 http… Platanista ga… (Lebeck,… accep… NA Spec…#> # … with 18 more variables: valid_AphiaID <int>, valid_name <chr>,#> # valid_authority <chr>, kingdom <chr>, phylum <chr>, class <chr>,#> # order <chr>, family <chr>, genus <chr>, citation <chr>, lsid <chr>,#> # isMarine <lgl>, isBrackish <lgl>, isFreshwater <int>,#> # isTerrestrial <lgl>, isExtinct <lgl>, match_type <chr>, modified <chr>#> #> [[2]]#> # A tibble: 2 x 25#> AphiaID url scientificname authority status unacceptreason rank #> <int> <chr> <chr> <chr> <chr> <chr> <chr>#> 1 125960 http… Coryphaena Linnaeus… accep… <NA> Genus#> 2 843430 <NA> <NA> <NA> quara… synonym <NA> #> # … with 18 more variables: valid_AphiaID <int>, valid_name <chr>,#> # valid_authority <chr>, 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 25#> AphiaID url scientificname authority status unacceptreason rank #> <int> <chr> <chr> <chr> <chr> <lgl> <chr>#> 1 141919 http… Mercenaria me… (Linnaeu… accep… NA Spec…#> 2 140431 http… Mya truncata Linnaeus… accep… NA Spec…#> 3 141936 http… Venus verruco… Linnaeus… accep… NA Spec…#> 4 575771 http… Verpa penis (Linnaeu… accep… NA Spec…#> # … with 18 more variables: valid_AphiaID <int>, valid_name <chr>,#> # valid_authority <chr>, 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')#> [[1]]#> # A tibble: 1 x 25#> AphiaID url scientificname authority status unacceptreason rank #> <int> <chr> <chr> <chr> <chr> <lgl> <chr>#> 1 254967 http… Platanista ga… (Lebeck,… accep… NA Spec…#> # … with 18 more variables: valid_AphiaID <int>, valid_name <chr>,#> # valid_authority <chr>, kingdom <chr>, phylum <chr>, class <chr>,#> # order <chr>, family <chr>, genus <chr>, citation <chr>, lsid <chr>,#> # isMarine <lgl>, isBrackish <lgl>, isFreshwater <int>,#> # 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 <data.frame [2 × 4]>
attribute data by AphiaID
wm_attr_data(id = 127160)#> # A tibble: 24 x 10#> AphiaID measurementType… measurementType measurementValue source_id#> <chr> <int> <chr> <chr> <int>#> 1 127160 23 Species import… FAO-ASFIS: Spec… 197354#> 2 127160 23 Species import… MSFD indicators 197546#> 3 127160 23 Species import… MSFD indicators 197549#> 4 127160 23 Species import… MSFD indicators 197615#> 5 127160 23 Species import… MSFD indicators 197615#> 6 127160 23 Species import… MSFD indicators 197615#> 7 127160 23 Species import… MSFD indicators 197615#> 8 127160 23 Species import… MSFD indicators 197616#> 9 127160 23 Species import… MSFD indicators 197616#> 10 127160 23 Species import… MSFD indicators 197549#> # … with 14 more rows, and 5 more variables: reference <chr>,#> # 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 measurementValueCo… children #> <int> <chr> <chr> <list> #> 1 183 benthos <NA> <data.frame [6 ×…#> 2 184 plankton <NA> <data.frame [2 ×…#> 3 194 nekton <NA> <data.frame [0 ×…#> 4 323 neuston <NA> <data.frame [0 ×…#> 5 378 edaphofauna <NA> <data.frame [2 ×…#> 6 331 not applicable N/A <data.frame [0 ×…
AphiaIDs by attribute definition ID
wm_attr_aphia(id = 4)#> # A tibble: 50 x 2#> AphiaID Attributes #> <int> <list> #> 1 11 <data.frame [1 × 10]>#> 2 55 <data.frame [2 × 10]>#> 3 57 <data.frame [2 × 10]>#> 4 58 <data.frame [2 × 10]>#> 5 59 <data.frame [2 × 10]>#> 6 63 <data.frame [2 × 10]>#> 7 64 <data.frame [2 × 10]>#> 8 69 <data.frame [2 × 10]>#> 9 90 <data.frame [2 × 10]>#> 10 91 <data.frame [2 × 10]>#> # … with 40 more rows
worrms
in R doing citation(package = 'worrms')
vcr
and webmockr
packages for unit test stubbingwm_attr_aphia
, wm_attr_aphia_
, wm_attr_category
, wm_attr_category_
, wm_attr_data
, wm_attr_data_
, wm_attr_def
, wm_attr_def_
(#3)wm_children
and
wm_children_
. These underscore methods take in many inputs, typically
of a AphiaID or a taxonomic or vernacular name. We decided to make
separate functions so that we minimize any disturbance to the existing
package API. (#4) (#6)