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.


Build Status codecov rstudio mirror downloads cran version

worrms is a R client for the World Register of Marine Species

More stable CRAN version

install.packages("worrms")

Development version

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

get records

by date

wm_records_date('2016-12-23T05:59:45+00:00')
#> # A tibble: 50 x 25
#>    AphiaID                                                           url
#>  *   <int>                                                         <chr>
#>  1  894298 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894298
#>  2  894301 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894301
#>  3  894297 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894297
#>  4  894302 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894302
#>  5  894296 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894296
#>  6  894299 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894299
#>  7  894303 http://www.marinespecies.org/aphia.php?p=taxdetails&id=894303
#>  8  915236 http://www.marinespecies.org/aphia.php?p=taxdetails&id=915236
#>  9  897486 http://www.marinespecies.org/aphia.php?p=taxdetails&id=897486
#> 10  901957 http://www.marinespecies.org/aphia.php?p=taxdetails&id=901957
#> # ... with 40 more rows, and 23 more variables: scientificname <chr>,
#> #   authority <chr>, status <chr>, unacceptreason <lgl>, rank <chr>,
#> #   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
#> *   <int>                                                         <chr>
#> 1  254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967
#> 2  383571 http://www.marinespecies.org/aphia.php?p=taxdetails&id=383571
#> 3  254969 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254969
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <lgl>, rank <chr>, 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
#> *   <int>                                                         <chr>
#> 1  254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <lgl>, rank <chr>, 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
#> *   <int>                                                         <chr>
#> 1  125960 http://www.marinespecies.org/aphia.php?p=taxdetails&id=125960
#> 2  843430                                                          <NA>
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <chr>, rank <chr>, 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 <lgl>, isExtinct <lgl>, match_type <chr>, modified <chr>

by common name

wm_records_common(name = 'clam')
#> # A tibble: 2 x 25
#>   AphiaID                                                           url
#> *   <int>                                                         <chr>
#> 1  141919 http://www.marinespecies.org/aphia.php?p=taxdetails&id=141919
#> 2  141936 http://www.marinespecies.org/aphia.php?p=taxdetails&id=141936
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <lgl>, rank <chr>, 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
#> *   <int>                                                         <chr>
#> 1  254967 http://www.marinespecies.org/aphia.php?p=taxdetails&id=254967
#> # ... with 23 more variables: scientificname <chr>, authority <chr>,
#> #   status <chr>, unacceptreason <lgl>, rank <chr>, 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>

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.

News

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")

0.2.0 by Scott Chamberlain, 9 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


Imported by taxize.


See at CRAN