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‘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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.