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.


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.

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

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.

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News

worrms 0.2.8

NEW FEATURES

  • Integration with vcr and webmockr packages for unit test stubbing

worrms 0.2.0

NEW FEATURES

  • Added additional sister functions to most exported functions in the package, all with trailing underscore. For example, wm_children and wm_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.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("worrms")

0.3.2 by Scott Chamberlain, 2 months ago


https://github.com/ropensci/worrms


Report a bug at https://github.com/ropensci/worrms/issues


Browse source code at https://github.com/cran/worrms


Authors: Scott Chamberlain [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports crul, tibble, jsonlite, data.table

Suggests roxygen2, knitr, testthat, vcr


Imported by taxize.


See at CRAN