‘rglobi’

R library to access species interaction data of http://globalbioticinteractions.org

install

To install rglobi from CRAN:

install.packages("rglobi")

Or install development version:

install.packages("devtools")
devtools::install_github("ropensci/rglobi")

examples

library(rglobi)
# find all unique prey names of Homo sapiens
prey_of("Homo sapiens")$target_taxon_name
# is a shortcut of
get_interactions_by_taxa(sourcetaxon='Homo sapiens', interactiontype='preysOn')$target_taxon_name

# list of supported interactions types
get_interaction_types()

# all known prey names and locations (latitude, longitude) where birds (Aves) preyed on rodents (Rodentia) in California
obs <- get_interactions_by_taxa(sourcetaxon = "Aves", bbox=c(-125.53344800000002,32.750323,-114.74487299999998,41.574361), targettaxon = "Rodentia", returnobservations=TRUE)
locations <- cbind(obs$target_taxon_name, obs$latitude, obs$longitude)

Please see R help pages (e.g. ?get_interactions_by_taxa and vignettes for more information.

tests

Tests can be executed using devtools package.

# workdir should be rglobi repo root directory (check with getwd())
# install dependencies 
devtools::install('.')
devtools::test()

This should reload the library, executes the test_that testcases and show test reports.

documentation

roxygen2 is used to generate .Rd and NAMESPACE by running:

 library(roxygen2)
 roxygenize(".")

Vignettes are generated using knitr and markdown packages.

meta

Please report any issues or bugs.

This package is part of the rOpenSci project.