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.

Installation

More stable CRAN version

Development version

remotes::install_github("ropensci/worrms")
library("worrms")

records

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  908243 http… Linderina kol… Singh, 1… accep… NA                     220
#>  9  901296 http… Pseudoreichel… Ueno, 19… accep… NA                     220
#> 10  901957 http… Gaudryinella … Moullade… 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')
#> # A tibble: 2 x 27
#>   AphiaID url   scientificname authority status unacceptreason taxonRankID rank 
#>     <int> <chr> <chr>          <chr>     <chr>  <lgl>                <int> <chr>
#> 1  343613 http… Leucophaeus    <NA>      accep… NA                     180 Genus
#> 2  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('Platanista gangetica', 'Coryphaena'))
#> [[1]]
#> # A tibble: 0 x 0
#> 
#> [[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')
#> [[1]]
#> # A tibble: 1 x 27
#>   AphiaID url   scientificname authority status unacceptreason taxonRankID rank 
#>     <int> <chr> <chr>          <lgl>     <chr>  <lgl>                <int> <chr>
#> 1  343613 http… Leucophaeus    NA        accep… NA                     180 Genus
#> # … with 19 more variables: valid_AphiaID <int>, valid_name <chr>,
#> #   valid_authority <lgl>, 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>

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] [7 × 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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