originr v0.4.0


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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 (<https://bien.nceas.ucsb.edu/bien/tools/nsr/>), Integrated Taxonomic Information Service (<https://www.itis.gov/>), and Global Register of Introduced and Invasive Species (<http://www.griis.org/>).



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Species Origin Data

Data sources:


Stable CRAN version


Development version


EOL invasive species datasets

Datasets included:

An example using mineps

eol(name='Ciona intestinalis', dataset='mineps')
#>        searched_name               name eol_object_id     db
#> 1 Ciona intestinalis Ciona intestinalis           NaN mineps

Native Species Resolver

nsr("Pinus ponderosa", "United States")
#>     family genus         species       country state_province county_parish
#> 1 Pinaceae Pinus Pinus ponderosa United States                             
#>   native_status native_status_reason native_status_sources isIntroduced
#> 1             N     Native to region                                  0
#>   isCultivated
#> 1            0

Global Invasive Species Database

sp <- c("Carpobrotus edulis", "Rosmarinus officinalis")
#> $`Carpobrotus edulis`
#> $`Carpobrotus edulis`$species
#> [1] "Carpobrotus edulis"
#> $`Carpobrotus edulis`$alien_range
#>  [1] "albania"          "argentina"        "australia"        "bermuda"         
#>  [5] "chile"            "croatia"          "france"           "french polynesia"
#>  [9] "germany"          "gibraltar"        "greece"           "guernsey"        
#> [13] "ireland"          "italy"            "malta"            "mexico"          
#> [17] "new zealand"      "pitcairn"         "portugal"         "saint helena"    
#> [21] "spain"            "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

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.


Functions in originr

Name Description
nsr Search the Native Species Resolver
griis Check invasive species status for a species from GRIIS database
flora_europaea Check species status (native/exotic) in Flora Europaea
originr-package originr
gisd Check invasive species status for a set of species from GISD database
eol Search for presence of taxonomic names in EOL invasive species databases.
is_native Check if a species is native somewhere
nsr_pol_divisions NSR political divisions
nsr_countries Vector of country names for use with NSR
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Type Package
License MIT + file LICENSE
URL https://docs.ropensci.org/originr, https://github.com/ropensci/originr
BugReports https://github.com/ropensci/originr/issues
Encoding UTF-8
LazyLoad yes
LazyData yes
RoxygenNote 7.1.0
X-schema.org-applicationCategory Biology
X-schema.org-keywords species, native, invasive, origin, web, API, eol, gisd, nsr, itis, griis
X-schema.org-isPartOf https://ropensci.org
NeedsCompilation no
Packaged 2020-06-12 01:01:52 UTC; sckott
Repository CRAN
Date/Publication 2020-06-12 05:20:02 UTC

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