Introduction to the worrms package

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.

Install

Stable version from CRAN

install.packages("worrms")

Development version from GitHub

install.packages("devtools")
devtools::install_github("ropensci/worrms")
library("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  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

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] 159854

Get 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           English

Children

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

Classification

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

Synonyms

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>