A programmatic interface to the web service methods provided by Global Biotic Interactions (GloBI). GloBI provides access to spatial-temporal species interaction records from sources all over the world. rglobi provides methods to search species interactions by location, interaction type, and taxonomic name. In addition, it supports Cypher, a graph query language, to allow for executing custom queries on the GloBI aggregate species interaction data set.
R library to access species interaction data of http://globalbioticinteractions.org
To install rglobi
from CRAN:
install.packages("rglobi")
Or install development version:
install.packages("devtools")devtools::install_github("ropensci/rglobi")
library(rglobi)# find all unique prey names of Homo sapiensprey_of("Homo sapiens")$target_taxon_name# is a shortcut ofget_interactions_by_taxa(sourcetaxon='Homo sapiens', interactiontype='preysOn')$target_taxon_name # list of supported interactions typesget_interaction_types() # all known prey names and locations (latitude, longitude) where birds (Aves) preyed on rodents (Rodentia) in Californiaobs <- get_interactions_by_taxa(sourcetaxon = "Aves", bbox=c(-125.53344800000002,32.750323,-114.74487299999998,41.574361), targettaxon = "Rodentia", returnobservations=T)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 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.
roxygen2 is used to generate .Rd and NAMESPACE by running:
library(roxygen2) roxygenize(".")
Vignettes are generated using knitr
and markdown
packages.
Please report any issues or bugs.
This package is part of the rOpenSci project.
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GloBI data services are not available at [api.globalbioticinteractions.org]. Are you connected to the internet?
when internet resources are not available. Suggested by Brian D. Ripley . Also see https://github.com/ropensci/rglobi/issues/31 .BUG FIXES
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get_interactions_by_type
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get_interactions_by_type
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