worrms

Project Status: Active – The project has reached a stable, usable state and is being actively developed. cran checks Build Status Build status codecov rstudio mirror downloads cran version

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

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 rows

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