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

Build Status rstudio mirror downloads cran version cran checks

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=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.

rOpenSci footer

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

BUG FIXES

NEW FEATURES

IMPROVEMENT

BUG FIXES

rglobi 0.2.9

NEW FEATURES

IMPROVEMENT

BUG FIXES

rglobi 0.2.8

NEW FEATURES

IMPROVEMENTS

BUG FIXES

  • Switch neo4j port from 7474 to 80 following changes to the neo4j endpoint.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("rglobi")

0.2.19 by Jorrit Poelen, 4 months ago


https://github.com/ropensci/rglobi


Report a bug at https://github.com/ropensci/rglobi/issues


Browse source code at https://github.com/cran/rglobi


Authors: Jorrit Poelen [aut, cre] , Stephen Gosnell [aut] , Sergey Slyusarev [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports rjson, RCurl, curl

Suggests testthat, knitr


See at CRAN