worrms
World Register of Marine Species (WoRMS) Client
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")records
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>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 <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 rowsMeta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
worrmsin R doingcitation(package = 'worrms') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
News
worrms 0.3.2
MINOR IMPROVEMENTS
- add link to taxize book in vignette and README (#12)
BUG FIXES
- fix bug in test regarding date (#19)
worrms 0.3.0
MINOR IMPROVEMENTS
- fix to most functions throughout the package (those that have two versions, with and without an underscore): underscore versions of functions now do not error when an input is not found, but instead warn the user and move on - to facilitate working with many inputs. the non-underscore version of each function still only accepts 1 input and errors if you give more than 1 (#14) (#18)
BUG FIXES
- make sure that functions that accept only 1 input for the first parameter error well with an informative message (#15)
worrms 0.2.8
NEW FEATURES
- Integration with
vcrandwebmockrpackages for unit test stubbing - gains new functions for getting WORMS traits data (they call them "attributes"):
wm_attr_aphia,wm_attr_aphia_,wm_attr_category,wm_attr_category_,wm_attr_data,wm_attr_data_,wm_attr_def,wm_attr_def_(#3)
worrms 0.2.0
NEW FEATURES
- Added additional sister functions to most exported functions in the
package, all with trailing underscore. For example,
wm_childrenandwm_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)
MINOR IMPROVEMENTS
- Moved to using markdown docs (#5)
- All functions now state what they return (#9)
worrms 0.1.0
NEW FEATURES
- Released to CRAN.