World Register of Marine Species R client
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README.md

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

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  894298 http://w… Parapachyphloi… Miklukho… accep… NA             Spec…
#>  2  894301 http://w… Ovulina radiata Seguenza… accep… NA             Spec…
#>  3  894297 http://w… Parapachyphloi… Miklukho… accep… NA             Spec…
#>  4  894302 http://w… Paleopolymorph… Vasilenk… accep… NA             Spec…
#>  5  894296 http://w… Parapachyphloi… Miklukho… accep… NA             Spec…
#>  6  894299 http://w… Parafissurina … Petri, 1… accep… NA             Spec…
#>  7  894303 http://w… Anomalina nodu… Terquem,… accep… NA             Spec…
#>  8  901957 http://w… Gaudryinella e… Moullade… accep… NA             Spec…
#>  9  916899 http://w… Gavelinella pu… Porthaul… accep… NA             Spec…
#> 10  925289 http://w… Textularia yat… Murata, … 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://w… Platanista gang… (Lebeck,… accep… NA             Spec…
#> 2  383571 http://w… Platanista gang… Roxburgh… accep… NA             Subs…
#> 3  254969 http://w… Platanista gang… 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://ww… Platanista gan… (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://www… 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: 2 x 25
#>   AphiaID url        scientificname  authority status unacceptreason rank 
#> *   <int> <chr>      <chr>           <chr>     <chr>  <lgl>          <chr>
#> 1  141919 http://ww… Mercenaria mer… (Linnaeu… accep… NA             Spec…
#> 2  141936 http://ww… Venus verrucosa Linnaeus… 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://ww… Platanista gan… (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 measurementTypeID measurementType  measurementValue   source_id
#>  * <chr>               <int> <chr>            <chr>                  <int>
#>  1 127160                 23 Species importa… FAO-ASFIS: Specie…    197354
#>  2 127160                 23 Species importa… MSFD indicators       197546
#>  3 127160                 23 Species importa… MSFD indicators       197549
#>  4 127160                 23 Species importa… MSFD indicators       197615
#>  5 127160                 23 Species importa… MSFD indicators       197615
#>  6 127160                 23 Species importa… MSFD indicators       197615
#>  7 127160                 23 Species importa… MSFD indicators       197615
#>  8 127160                 23 Species importa… MSFD indicators       197616
#>  9 127160                 23 Species importa… MSFD indicators       197616
#> 10 127160                 23 Species importa… 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: 5 x 4
#>   measurementValueID measurementValue measurementValueCode 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                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

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for worrms in R doing citation(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.