rglobi
R Interface to Global Biotic Interactions
A programmatic interface to the web service methods provided by Global Biotic Interactions (GloBI) (< https://www.globalbioticinteractions.org/>). 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 0.2.19
NEW FEATURES
IMPROVEMENT
- show informative messages like
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
rglobi 0.2.18
NEW FEATURES
IMPROVEMENT
BUG FIXES
- Update cypher query endpoint after server upgrade to neo4j v2.3.12
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.