Search Catalogue of Life for taxonomic classifications.

Usage

col_classification(name = NULL, id = NULL, format = NULL, start = NULL, checklist = NULL,
  url = "http://www.catalogueoflife.org/col/webservice")

Arguments

name

The string to search for. Only exact matches found the name given will be returned, unless one or wildcards are included in the search string. An * (asterisk) character denotes a wildcard; a character may also be used. The name must be at least 3 characters long, not counting wildcard characters.

id

The record ID of the specific record to return (only for scientific names of species or infraspecific taxa)

format

format of the results returned. Valid values are format=xml and format=php; if the format parameter is omitted, the results are returned in the default XML format. If format=php then results are returned as a PHP array in serialized string format, which can be converted back to an array in PHP using the unserialize command

start

The first record to return. If omitted, the results are returned from the first record (start=0). This is useful if the total number of results is larger than the maximum number of results returned by a single Web service query (currently the maximum number of results returned by a single query is 500 for terse queries and 50 for full queries).

checklist

The year of the checklist to query, if you want a specific year's checklist instead of the lastest as default (numeric).

url

The base COL url for the function (should be left to default).

Examples

# A basic example
col_classification(name="Apis")
$Apis
  classif_id classif_name classif_rank
1   12247828     Animalia      Kingdom
2   12247833   Arthropoda       Phylum
3   12248024      Insecta        Class
4   12248225  Hymenoptera        Order
5   12252115      Apoidea  Superfamily
6   12252157       Apidae       Family



# An example where there is no classification
col_classification(id=11935941)
$`11935941`
  classif_id       classif_name classif_rank
1   12247828           Animalia      Kingdom
2   12247941      Echinodermata       Phylum
3   12249685         Asteroidea        Class
4   12254343        Paxillosida        Order
5   12258012 Porcellanasteridae       Family
6   12437394         Abyssaster        Genus



# Use a specific year's checklist
col_classification(name="Apis", checklist="2012")
$Apis
  classif_id classif_name classif_rank
1    2339542     Animalia      Kingdom
2    2339603   Arthropoda       Phylum
3    2339755      Insecta        Class
4    2339947  Hymenoptera        Order
5    2344123      Apoidea  Superfamily
6    2344165       Apidae       Family


col_classification(name="Apis", checklist="2009")
$Apis
  classif_id classif_name classif_rank
1          1     Animalia      Kingdom
2        134   Arthropoda       Phylum
3        311      Insecta        Class
4        551  Hymenoptera        Order
5        560      Apoidea  Superfamily
6       8597       Apidae       Family



# Pass in many names or many id's
out <- col_classification(name=c("Buteo","Apis","Accipiter","asdf"), checklist="2012")
out$Apis # get just the output you want
  classif_id classif_name classif_rank
1    2339542     Animalia      Kingdom
2    2339603   Arthropoda       Phylum
3    2339755      Insecta        Class
4    2339947  Hymenoptera        Order
5    2344123      Apoidea  Superfamily
6    2344165       Apidae       Family

ldply(out) # or combine to one data.frame
         .id classif_id  classif_name classif_rank
1      Buteo    2339542      Animalia      Kingdom
2      Buteo    2339896      Chordata       Phylum
3      Buteo    2340272          Aves        Class
4      Buteo    2340295 Ciconiiformes        Order
5      Buteo    2346405  Accipitridae       Family
6       Apis    2339542      Animalia      Kingdom
7       Apis    2339603    Arthropoda       Phylum
8       Apis    2339755       Insecta        Class
9       Apis    2339947   Hymenoptera        Order
10      Apis    2344123       Apoidea  Superfamily
11      Apis    2344165        Apidae       Family
12 Accipiter    2339542      Animalia      Kingdom
13 Accipiter    2339896      Chordata       Phylum
14 Accipiter    2340272          Aves        Class
15 Accipiter    2340295 Ciconiiformes        Order
16 Accipiter    2346405  Accipitridae       Family