originr tutorial
for v0.2.0
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/
Installation
Stable version from CRAN
install.packages("originr")
Development version from GitHub
if (!require("devtools")) install.packages("devtools")
devtools::install_github("ropenscilabs/originr")
library("originr")
Usage
EOL invasive species datasets
Datasets included:
gisd100- 100 of the World’s Worst Invasive Alien Species (Global Invasive Species Database) http://eol.org/collections/54500gisd- Global Invasive Species Database 2013 http://eol.org/collections/54983isc- Centre for Agriculture and Biosciences International Invasive Species Compendium (ISC) http://eol.org/collections/55180daisie- Delivering Alien Invasive Species Inventories for Europe (DAISIE) Species List http://eol.org/collections/55179i3n- IABIN Invasives Information Network (I3N) Species http://eol.org/collections/55176mineps- 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
#> 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
Citing
Scott Chamberlain and Ignasi Bartomeus (2016). originr: Fetch Species Origin Data from the Web. R package version 0.2.0. https://cran.rstudio.com/package=originr
License and bugs
- License: MIT
- Report bugs at our GitHub repo for originr
