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/>).


Build Status codecov.io rstudio mirror downloads cran version

Species Origin Data

Data sources:

Stable CRAN version

install.packages("originr")

Development version

devtools::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
#> 1 Ciona intestinalis Ciona intestinalis (Linnaeus, 1767)        512629
#>       db
#> 1 mineps

Native Species Resolver

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

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"       
#>  [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

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.

rofooter

News

originr 0.3.0

NEW FEATURES

  • replaced HTTP clients, now using crul package (#13)
  • new function eol_invasive_data() to get the global data.frame of invasive species data from EOL.

MINOR IMPROVEMENTS

  • Improved documentation around eol() behavior. dataset="all" does not encompass, or at least does not include data to indicate that it encompasses, the individual EOL invasives datasets. There's no response from EOL on this, so we're stuck with the behavior (#10) (#18)
  • Added internal datasets for nsr() function. Now internally we check whether the country, and state/province name passed in is in the acceptable set, and throw warning if not (#19)

originr 0.2.0

NEW FEATURES

  • Added a new data source: Global Register of Introduced and Invasive Species (GRIIS). See griis() (#5) (#7)

BUG FIXES

  • Fix to flora_europaea() to convert factors to character and to stop with meaningful message when more than one species passed in (#8)

originr 0.1.0

NEW FEATURES

  • Released to CRAN.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("originr")

0.3.0 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 crul, jsonlite, data.table, xml2, taxize

Suggests testthat, roxygen2


See at CRAN