Atlas of Living Australia (ALA) Data and Resources in R

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://ala.org.au/>. ALA4R provides a subset of the tools to be directly used within R. It enables the R community to directly access data and resources hosted by the ALA.


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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 http://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.

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.

News

ALA4R 1.6.2

  • updates to handle ALA API field changes
  • update vignette to be more robust to server outage

ALA4R 1.6.0

ALA4R 1.5.10

  • bugfixes

ALA4R 1.5.6

  • added biocache_version parameter to server configuration, to support use of ALA4R with other server instances (e.g. other national installations using the ALA server infrastructure)
  • minor bugfixes

ALA4R 1.5

  • updated code,examples and vignette for new ALA taxonomic backbone
  • "offline" method added to occurrences(), allowing download of larger datasets with more fields
  • fieldguide() function added
  • fields="all" option added to taxinfo_download()
  • ala_list() and ala_lists() functions added

ALA4R 1.24

  • better handling of text encoding (https://github.com/AtlasOfLivingAustralia/ALA4R/issues/15)

ALA4R 1.23

  • added image_number parameter to image_info()

ALA4R 1.21

  • added image_info() and occurrence_details() functions

  • added extra="all" and qa="all" options to occurrences()

ALA4R 1.20

  • fixed as_is behaviour in ala_fields().

  • usage of stringr functions now compatible with stringr v1.0.

  • parameter occurrence_count added to search_names().

  • tests added to tests/testthat.

ALA4R 1.191

  • improved parsing of field names in internal function check_fq() (https://github.com/AtlasOfLivingAustralia/ALA4R/issues/13).

ALA4R 1.19

  • internal function check_fq() throws a warning not an error if it thinks there is a problem with the fq string (https://github.com/AtlasOfLivingAustralia/ALA4R/issues/13).

ALA4R 1.18

  • for improperly classified taxa, the result$classification object returned by species_info() is now a data.frame (https://github.com/AtlasOfLivingAustralia/ALA4R/issues/11).

ALA4R 1.18

  • bugfix in species_info() (https://github.com/AtlasOfLivingAustralia/ALA4R/issues/11).

Reference manual

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install.packages("ALA4R")

1.7.0 by Peggy Newman, 2 months ago


https://github.com/AtlasOfLivingAustralia/ALA4R


Report a bug at https://github.com/AtlasOfLivingAustralia/ALA4R/issues


Browse source code at https://github.com/cran/ALA4R


Authors: Peggy Newman [aut, cre] , Ben Raymond [aut] , Jeremy VanDerWal [aut] , Lee Belbin [aut] , Michael Sumner [ctb] , Tom August [ctb] , John Baumgartner [ctb]


Documentation:   PDF Manual  


MPL-2.0 license


Imports assertthat, data.table, digest, httr, jsonlite, sp, stringr, wellknown

Suggests ape, covr, dplyr, ggplot2, jpeg, knitr, mapdata, maps, maptools, phytools, rmarkdown, testthat, tidyr, vegan


See at CRAN