rglobi
R Interface to Global Biotic Interactions
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
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 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
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.
News
rglobi 0.2.17
NEW FEATURES
IMPROVEMENT
BUG FIXES
- Use utils::download.file in an attempt to avoid intermittent download issues on debian.
rglobi 0.2.16
NEW FEATURES
IMPROVEMENT
BUG FIXES
- Enforce utf-8 encoding when reading csv, take 2.
rglobi 0.2.15
NEW FEATURES
IMPROVEMENT
BUG FIXES
- Enforce utf-8 encoding when reading csv.
rglobi 0.2.14
NEW FEATURES
IMPROVEMENT
BUG FIXES
- Fix yet another test error caused by overly restrictive assertion.
rglobi 0.2.13
NEW FEATURES
IMPROVEMENT
BUG FIXES
- Fix another test error caused by overly restrictive assertion.
rglobi 0.2.12
NEW FEATURES
IMPROVEMENT
BUG FIXES
- Fix test error caused by overly restrictive assertion.
rglobi 0.2.11
NEW FEATURES
IMPROVEMENT
BUG FIXES
- After switching to https endpoint for GloBI APIs, the default configuration needed updating to ensure existing functions to continue to work.
rglobi 0.2.10
NEW FEATURES
IMPROVEMENT
- a rglobi user requested to search by interactions type (see https://github.com/ropensci/rglobi/issues/23). The functionality was implemented by adding method
get_interactions_by_type.
BUG FIXES
NEW FEATURES
IMPROVEMENT
- a rglobi user requested to search by interactions type (see https://github.com/ropensci/rglobi/issues/23). The functionality was implemented by adding method
get_interactions_by_type.
BUG FIXES
rglobi 0.2.9
NEW FEATURES
IMPROVEMENT
BUG FIXES
- make get_interaction_matrix use same name matching method as get_interactions . See https://github.com/globalbioticinteractions/globalbioticinteractions.github.io/issues/63 .
rglobi 0.2.8
NEW FEATURES
IMPROVEMENTS
BUG FIXES
- Switch neo4j port from 7474 to 80 following changes to the neo4j endpoint.