Fetch Species Origin Data from the Web

Get species origin data (whether species is native/invasive) from the following sources on the web: Encyclopedia of Life (< http://eol.org>), Flora 'Europaea' (< http://rbg-web2.rbge.org.uk/FE/fe.html>), Global Invasive Species Database (< http://www.iucngisd.org/gisd>), the Native Species Resolver (< http://bien.nceas.ucsb.edu/bien/tools/nsr/nsr-ws/>), Integrated Taxonomic Information Service (< http://www.itis.gov/>), and Global Register of Introduced and Invasive Species (< http://www.griis.org/>).


Species Origin Data

Data sources:

Stable CRAN version

install.packages("originr")

Development version

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

Datasets included:

An example using mineps

eol(name='Ciona intestinalis', dataset='mineps')
#>        searched_name                                name eol_object_id
#> 1 Ciona intestinalis Ciona intestinalis (Linnaeus, 1767)        512629
#>       db
#> 1 mineps
nsr("Pinus ponderosa", "United States")
#>     family genus         species       country native_status
#> 1 Pinaceae Pinus Pinus ponderosa United States             P
#>                                                 native_status_reason
#> 1 Present in one or more checklists for region, status not indicated
#>   native_status_sources isIntroduced isCultivated
#> 1                  usda            0            0
sp <- c("Carpobrotus edulis", "Rosmarinus officinalis")
gisd(sp)
#> $`Carpobrotus edulis`
#> $`Carpobrotus edulis`$species
#> [1] "Carpobrotus edulis"
#> 
#> $`Carpobrotus edulis`$alien_range
#>  [1] "albania"          "argentina"        "australia"       
#>  [4] "bermuda"          "chile"            "croatia"         
#>  [7] "france"           "french polynesia" "germany"         
#> [10] "gibraltar"        "greece"           "guernsey"        
#> [13] "ireland"          "italy"            "malta"           
#> [16] "mexico"           "new zealand"      "pitcairn"        
#> [19] "portugal"         "saint helena"     "spain"           
#> [22] "tunisia"          "united kingdom"   "united states"   
#> 
#> $`Carpobrotus edulis`$native_range
#> character(0)
#> 
#> 
#> $`Rosmarinus officinalis`
#> $`Rosmarinus officinalis`$species
#> [1] "Rosmarinus officinalis"
#> 
#> $`Rosmarinus officinalis`$status
#> [1] "Not in GISD"
flora_europaea("Lavandula stoechas")
#> $native
#>  [1] "Islas_Baleares" "Corse"          "Kriti"          "France"        
#>  [5] "Greece"         "Spain"          "Italy"          "Portugal"      
#>  [9] "Sardegna"       "Sicilia"        "Turkey"        
#> 
#> $exotic
#> [1] NA
#> 
#> $status_doubtful
#> [1] NA
#> 
#> $occurrence_doubtful
#> [1] NA
#> 
#> $extinct
#> [1] NA
  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for originr in R doing citation(package = 'originr')
  • 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

originr 0.1.0

NEW FEATURES

  • Released to CRAN.

Reference manual

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install.packages("originr")

0.2.0 by Scott Chamberlain, a year ago


https://github.com/ropensci/originr


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


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


Authors: Scott Chamberlain [aut, cre], Ignasi Bartomeus [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports stats, httr, jsonlite, data.table, xml2, taxize

Suggests testthat, roxygen2, covr


See at CRAN