rOpenSci: The originr package

Species Origin Data

Data sources:

• 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
• Native Species Resolver http://bien.nceas.ucsb.edu/bien/tools/nsr/nsr-ws/
• Integrated Taxonomic Information Service http://www.itis.gov/
• Global Register of Introduced and Invasive Species http://www.griis.org/

Install

Stable CRAN version

install.packages("originr")

Development version

remotes::install_github("ropensci/originr")

library("originr")

EOL invasive species datasets

Datasets included:

• gisd100 - 100 of the World’s Worst Invasive Alien Species (Global Invasive Species Database) http://eol.org/collections/54500
• gisd - Global Invasive Species Database 2013 http://eol.org/collections/54983
• isc - Centre for Agriculture and Biosciences International Invasive Species Compendium (ISC) http://eol.org/collections/55180
• daisie - Delivering Alien Invasive Species Inventories for Europe (DAISIE) Species List http://eol.org/collections/55179
• i3n - IABIN Invasives Information Network (I3N) Species http://eol.org/collections/55176
• mineps - Marine Invaders of the NE Pacific Species http://eol.org/collections/55331

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")
gisd(sp)
#> $`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

Meta

• 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.