originr tutorial

for v0.1.0

Species Origin Data

Data sources:

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:

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 0.1.0. https://cran.rstudio.com/package=originr

License and bugs

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