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ALA4R

ALA4R is deprecated and will be removed from CRAN at the end of 2021. The package to replace ALA4R, galah, is now available on CRAN. galah provides an improved interface to ALA data, while providing the same core functionality as ALA4R. For an introduction to galah, visit the GitHub page.

The Atlas of Living Australia (ALA) provides tools to enable users of biodiversity information to find, access, combine and visualise data on Australian plants and animals; these have been made available from https://www.ala.org.au/. Here we provide a subset of the tools to be directly used within R.

ALA4R enables the R community to directly access data and resources hosted by the ALA.

The use-examples presented at the 2014 ALA Science Symposium are available in the package vignette, via (in R): vignette("ALA4R"), or browse it online.

Citing ALA4R

To generate a citation for ALA4R run:

citation(package = "ALA4R")

Installing

Stable version from CRAN:

install.packages("ALA4R")

Or the development version from GitHub:

install.packages("devtools")
devtools::install_github("AtlasOfLivingAustralia/ALA4R")

On Linux you will first need to ensure that libcurl and v8 (version <= 3.15) are installed on your system — e.g. on Ubuntu/Debian, open a terminal and do:

sudo apt-get install libcurl4-openssl-dev libv8-3.14-dev

or install via the Software Centre.

Usage

See the online documentation at https://atlasoflivingaustralia.github.io/ALA4R/ including the package vignette.

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Version

Install

install.packages('ALA4R')

Monthly Downloads

96

Version

1.9.1

License

MPL-2.0

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Last Published

July 12th, 2021

Functions in ALA4R (1.9.1)

check_assertions

Check assertions in occurrences object
fieldguide

Generate a PDF field guide using the ALA's field guide generator
ala_fields

Retrieves a list of all field names that can be used with data retrieval functions
ALA4R

ALA4R ALA4R
ala_config

Get or set configuration options that control ALA4R behaviour
images

Retrieve image information using image ids, with an option to download
ala_cache_filename

Returns the name of the cache file associated with the given URL. Note that this file may not actually exist, this function just provides the mapping from URL to filename
aus

Basic Australia raster for visualization A basic raster dataset in SpatialGridDataFrame (package sp) representing Australia at 0.05 degree (~5km) resolution.
ala_list

Species lists
ala_lists

Find ALA species lists
search_fulltext

Full text search
search_guids

Lookup of species identifiers
occurrence_images

Find images using occurrence ids
occurrences

Get occurrence data
intersect_points

Intersect environmental or contextual layers at a given a set of points (coordinates)
occurrence_details

Retrieve the full details of occurrence records
search_layers

Search for environmental and contextual data layers
search_names

Lookup of taxonomic names
sites_by_species

Sites by species
search_partial_name

Partial-name search
occurrences_s3

Summarize, filter and subset occurrence data
occurrences_plot

Quick geographic plot of occurrence data
taxinfo_download

Download taxonomic data
specieslist

Get list of taxa and their occurrence counts
species_info

Fetch a taxon profile given a scientific name or LSID (GUID)