Example of using the Global Names Resolver API to check species names

Load required packages

# If you don't have them already
# install.packages(c('RJSONIO','plyr','devtools')) require(devtools)
# install_github('taxize_','ropensci')
require(RJSONIO)

## Loading required package: RJSONIO

require(plyr)

## Loading required package: plyr

require(taxize)

## Loading required package: taxize

Get the data sources available

# Get just id's and names of sources in a data.frame
tail(gnr_datasources(todf = T))

##     id                                title
## 82 164                            BioLib.cz
## 83 165 Tropicos - Missouri Botanical Garden
## 84 166                                nlbif
## 85 167                                 IPNI
## 86 168              Index to Organism Names
## 87 169                        uBio NameBank

# give me the id for EOL (Encyclopedia of Life)
out <- gnr_datasources(todf = T)
out[out$title == "EOL", "id"]

## [1] 12

# Fuzzy search for sources with the word 'zoo'
out <- gnr_datasources(todf = T)
out[agrep("zoo", out$title, ignore.case = T), ]

##     id
## 20 100
## 25 105
## 32 113
## 33 114
## 51 132
##                                                                         title
## 20                                                          Mushroom Observer
## 25                                                                    ZooKeys
## 32                                /home/dimus/files/dwca/zoological names.zip
## 33 Peces de la zona hidrogeogr\xe1fica de la Amazonia, Colombia (Spreadsheet)
## 51                                                                    ZooBank

Resolve some names

# Search for Helianthus annuus and Homo sapiens, return a data.frame
gnr(names = c("Helianthus annuus", "Homo sapiens"), returndf = TRUE)

##    data_source_id    submitted_name       name_string score
## 1               4 Helianthus annuus Helianthus annuus 0.988
## 3              10 Helianthus annuus Helianthus annuus 0.988
## 4              12 Helianthus annuus Helianthus annuus 0.988
## 7             110 Helianthus annuus Helianthus annuus 0.988
## 10            159 Helianthus annuus Helianthus annuus 0.988
## 12            166 Helianthus annuus Helianthus annuus 0.988
## 14            169 Helianthus annuus Helianthus annuus 0.988
## 2               4      Homo sapiens      Homo sapiens 0.988
## 5              12      Homo sapiens      Homo sapiens 0.988
## 6             107      Homo sapiens      Homo sapiens 0.988
## 8             122      Homo sapiens      Homo sapiens 0.988
## 9             123      Homo sapiens      Homo sapiens 0.988
## 11            159      Homo sapiens      Homo sapiens 0.988
## 13            168      Homo sapiens      Homo sapiens 0.988
## 15            169      Homo sapiens      Homo sapiens 0.988
##                      title
## 1                     NCBI
## 3                 Freebase
## 4                      EOL
## 7     Illinois Wildflowers
## 10                 CU*STAR
## 12                   nlbif
## 14           uBio NameBank
## 2                     NCBI
## 5                      EOL
## 6                AskNature
## 8                 BioPedia
## 9                    AnAge
## 11                 CU*STAR
## 13 Index to Organism Names
## 15           uBio NameBank

# Search for the same species, with only using data source 12 (i.e., EOL)
gnr(names = c("Helianthus annuus", "Homo sapiens"), data_source_ids = "12", 
    returndf = TRUE)

##   data_source_id    submitted_name       name_string score title
## 1             12 Helianthus annuus Helianthus annuus 0.988   EOL
## 2             12      Homo sapiens      Homo sapiens 0.988   EOL

That's it. Have fun! And put bugs/comments/etc. here.