ZooBank R client
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README.md

zbank

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

ZooBank API Client

ZooBank API Docs

See http://zoobank.org/Api

High vs. Low level package APIs

High level API

High level functions do the HTTP request and parse data to a data.frame for ease of downstream use. The high level functions have no underscore on the end of the function name, e.g., zb_name_usages

Low level API

The parsing to data.frame in the high level API does take extra time. The low level API only does the HTTP request, and gives back JSON without doing any more parsing. The low level functions DO have an underscore on the end of the function name, e.g., zb_name_usages_

Install

CRAN version

install.packages("zbank")

Development version

devtools::install_github("ropenscilabs/zbank")
library("zbank")

Examples

Name usages

zb_name_usages(name = "Pseudanthias carlsoni")
#> # A tibble: 1 x 14
#>   tnuuuid originalreferen… protonymuuid label value lsid  parentname
#> * <chr>   <chr>            <chr>        <chr> <chr> <chr> <chr>     
#> 1 ""      427D7953-E8FC-4… 6EA8BB2A-A5… carl… carl… urn:… ""        
#> # ... with 7 more variables: namestring <chr>, rankgroup <chr>,
#> #   usageauthors <chr>, taxonnamerankid <chr>, parentusageuuid <chr>,
#> #   cleanprotonym <chr>, nomenclaturalcode <chr>

Publications

zb_publications(query = "pyle")
#> # A tibble: 153 x 22
#>    referenceuuid label value authorlist year  title citationdetails volume
#>  * <chr>         <chr> <chr> <chr>      <chr> <chr> <chr>           <chr> 
#>  1 A91FACC3-F39… <Uns… <Uns… <Unspecif… ""    [Ori… ""              ""    
#>  2 24689AE4-C77… Alon… Alon… Alonso-Za… 2016  Manu… <em>ZooKeys</e… 550   
#>  3 913BB1FB-1C2… Asgh… Asgh… Asghari, … 2015  Desc… <em>Zootaxa</e… 3986  
#>  4 F8ECE6CE-E77… Bald… Bald… Baldwin, … 1998  <i>B… <I>Ichthyologi… 45    
#>  5 72D9641B-2A9… Bass… Bass… Basset, Y… 1997  Para… <em>AMBIO: A J… ""    
#>  6 5CB7EE8B-042… Bass… Bass… Basset, Y… 2000  Quan… <em>Bioscience… 50    
#>  7 A06A8B51-46B… Bass… Bass… Bassett, … 1997  Para… <em>AMBIO: A J… ""    
#>  8 FAFE53C6-FDD… Bous… Bous… Boustany,… 2002  Sate… <em>Nature</em… 415   
#>  9 18985DB2-CC5… Bush… Bush… Bush, Eli… 1997  Taxo… <em>Harvard Pa… 2     
#> 10 180454B5-D0C… Cid … Cid … Cid Del P… 2016  Five… <em>Zootaxa</e… 4109  
#> # ... with 143 more rows, and 14 more variables: number <chr>,
#> #   edition <chr>, publisher <chr>, placepublished <chr>,
#> #   pagination <chr>, startpage <chr>, endpage <chr>, language <chr>,
#> #   languageid <chr>, referencetype <chr>, lsid <chr>,
#> #   parentreferenceid <chr>, parentreference <chr>, authors <list>

Authors

zb_authors(query = "Schmutz")
#> # A tibble: 3 x 9
#>   agentnameid label value zblsid familyname givenname preferreduuid agentid
#> * <chr>       <chr> <chr> <chr>  <chr>      <chr>     <chr>         <chr>  
#> 1 F16D374C-5… Achi… Achi… urn:l… Achitte-S… Helga C.  F16D374C-531… F16D37…
#> 2 EC923CC6-E… Schm… Schm… urn:l… Schmutz    Karl      EC923CC6-E5E… EC923C…
#> 3 2E04A84F-4… Schm… Schm… ""     Schmutzler Clarence… 2E04A84F-459… 2E04A8…
#> # ... with 1 more variable: isuser <chr>

Get info by any ZooBank identifier

zb_id(id = "6EA8BB2A-A57B-47C1-953E-042D8CD8E0E2")
#> # A tibble: 3 x 10
#>   identifier identifierdomain abbreviation identifierurl registeringagen…
#> * <chr>      <chr>            <chr>        <chr>         <chr>           
#> 1 66491      CAS Ichthy Spec… CAS_SPC      http://resea… ""              
#> 2 643345     Taxonomic Seria… ITIS-TSN     http://www.i… ""              
#> 3 urn:lsid:… ZooBank Nomencl… ZB-Act       http://zooba… William N.      
#> # ... with 5 more variables: registeringagentfamilyname <chr>,
#> #   registeringagentorganizationname <chr>, identifieruuid <chr>,
#> #   domainlogourl <chr>, resolutionnote <chr>

Matching taxon name service

zb_matching(id = "FFF7160A-372D-40E9-9611-23AF5D9EAC4C")
#> # A tibble: 36 x 8
#>    protonymuuid acceptedprotony… protonymuuidarr… fullnamestring
#>    <chr>        <chr>            <chr>            <chr>         
#>  1 FFF7160A-37… FFF7160A-372D-4… FBDC898C-F1EA-4… Cheilodipteru…
#>  2 FFF7160A-37… FFF7160A-372D-4… 97CE20CD-4D6E-4… Gasterosteus …
#>  3 FFF7160A-37… FFF7160A-372D-4… 97CE20CD-4D6E-4… Gaſteroſteus …
#>  4 FFF7160A-37… FFF7160A-372D-4… 4D4EC609-D241-4… Pomatomus sal…
#>  5 FFF7160A-37… FFF7160A-372D-4… 4D4EC609-D241-4… Pomatomus sal…
#>  6 FFF7160A-37… FFF7160A-372D-4… 67D18558-763F-4… Temnodon salt…
#>  7 FFF7160A-37… FFF7160A-372D-4… FBDC898C-F1EA-4… Cheilodipteru…
#>  8 FFF7160A-37… FFF7160A-372D-4… 97CE20CD-4D6E-4… Gasterosteus …
#>  9 FFF7160A-37… FFF7160A-372D-4… 97CE20CD-4D6E-4… Gaſteroſteus …
#> 10 FFF7160A-37… FFF7160A-372D-4… 4D4EC609-D241-4… Pomatomus sal…
#> # ... with 26 more rows, and 4 more variables: nomenclaturalcodeid <int>,
#> #   taxonrank <chr>, synonymtype <int>, referencecount <int>

ZooBank usage stats

zb_stats(start_date = "2018-03-01", end_date = "2018-04-01")
#> # A tibble: 96 x 3
#>    identifierdomain day        recordcount
#>    <chr>            <chr>      <chr>      
#>  1 ZooBank Author   2018-03-01 39         
#>  2 ZooBank Author   2018-03-02 25         
#>  3 ZooBank Author   2018-03-03 9          
#>  4 ZooBank Author   2018-03-04 6          
#>  5 ZooBank Author   2018-03-05 23         
#>  6 ZooBank Author   2018-03-06 17         
#>  7 ZooBank Author   2018-03-07 28         
#>  8 ZooBank Author   2018-03-08 20         
#>  9 ZooBank Author   2018-03-09 19         
#> 10 ZooBank Author   2018-03-10 3          
#> # ... with 86 more rows

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for zbank in R doing citation(package = 'zbank')
  • 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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