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/>).

Readme

originr

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Species Origin Data

Data sources:

Install

Stable CRAN version

install.packages("originr")

Development version

remotes::install_github("ropensci/originr")
library("originr")

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")
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.

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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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Details

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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