Tools for the IUCN Red List of Ecosystems and Species

A toolbox created by members of the International Union for Conservation of Nature (IUCN) Red List of Ecosystems Committee for Scientific Standards. Primarily, it is a set of tools suitable for calculating the metrics required for making assessments of species and ecosystems against the IUCN Red List of Threatened Species and the IUCN Red List of Ecosystems categories and criteria. See the IUCN website for detailed guidelines, the criteria, publications and other information.


redlistr

Build Status

Overview

The redlistr package was developed to assist users conduct assessments for the IUCN Red List of Ecosystems in R. It is also useful for users interested in conducting assessments for the Red List of Threatened Species. Assessments of ecosystems under the IUCN Red List of Ecosystems criteria require calculation of standardised metrics that were developed to objectively assess risk to ecosystem (Keith et al. 2013). This package was designed to assist in the calculation of these metrics, including two methods of calculating the rate of distirbutional decline: Absolute Rate of Decline (ARD) and Proportional Rate of Decline (PRC). An additional metric: the Annual Rate of Change (ARC), which uses a compound interest law to determine the instantaenous rate of change (Puyravaud 2003) is also included.

Also included are the two standard measures of the size of an ecosystems' geographic distribution specified in the red list of ecosystems guidelines (Bland et al. 2016). These are the Extent of Occurrence (EOO) and Area of Occupancy (AOO). As many of these measures are also useful for assessing species under the IUCN Red List of Threatened Species criteria, we expect this package will also be useful for assessors conducting species assessments.

In conducting an assessment with this package, we assume that you are familiar with IUCN red listing protocols. In particular, you should consult the IUCN guidelines for both of the red lists, which are the definitive sources of all information required to ensure consistent application of IUCN criteria (Bland et al. 2016). In addition, the papers by Keith et al. (2013) and Rodriguez et al. (2015) are particularly useful for navigating the IUCN Red List of Ecosystems criteria. A range of important resources, including software tools and guiding material is available on the IUCN Red List of Ecosystems website. There is also plenty of handy material for assessing species available on the IUCN Red List of Threatened Species website.

We also assume that you are reasonably familiar with the R programming language, and have some experience in conducting analyses of vector and raster data within the R environment. Of particular use will be familiarity with the raster, sp and rgeos packages. This is certainly not a prerequisite, but this package is built upon many of the functions available in these three packages.

For a more detailed tutorial explaining how to use this package, please refer to the 'Calculating spatial metrics for IUCN red list assessments' vignette available with the package.

Lastly, this is a work in progress and we aim to continually add new functions to newer versions of package. Suggestions are welcomed, as would offers for collaborative development.

Installation

redlistr is now on CRAN! You can also install the development version from GitHub.

install.packages("redlistr")
 
# For the development version from GitHub:
# install.packages("devtools")
devtools::install_github("red-list-ecosystem/redlistr")

News

redlistr 1.0.2

  • Submission of update to CRAN with improvements from reviewers.

redlistr 1.0.1.9002

  • Fixed ARC calculation in extrapolateEstimate.
  • Added tests to ensure extrapolateEstimate calculations are correct.
  • Renamed ARC to Annual Rate of Change
  • Fixed getArea when raster cells are not squares

redlistr 1.0.1.9001

  • Added sequentialExtrapolate to return sequence of estimates calculated by the selected algorithms.
  • Updated extrapolateEstimate output wording.

redlistr 1.0.1.9000

  • Added extrapolateEstimate which will replace futureAreaEstimate.

redlistr 1.0.1

  • Fixed getArea to output a single value and included test
  • Submission of update to CRAN

redlistr 1.0.0.9004

  • Added test for SpatialPolygons for getArea
  • Updated vignette to have single date

redlistr 1.0.0.9003

  • Fixed an error in getArea where a raster with a single class wouldn't be calculated properly
  • Updated tests to reflect changes to getDeclineStats

redlistr 1.0.0.9002

  • Changed getDeclineStats so ARC now returns a percentage
  • Updated futureAreaEstimate to accept ARC as a percentage

redlistr 1.0.0.9001

  • Updated all functions to accept SpatialPoints and SpatialPointsDataFrame as input.

redlistr 1.0.0.9000

  • Cleaned up code in getEOOPolygon.
  • gridUncertainty functions now have default min.percent.rule set to FALSE.
  • gridUncertainty now uses while, eliminating need for max.rounds parameter.
  • gridUncertaintyBase now includes two new parameters: restriction and min.grids.shift.
  • Added gridUncertaintyRestricted.

redlistr 1.0.0

  • redlistr is now on CRAN!

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("redlistr")

1.0.2 by Calvin Lee, 5 months ago


https://github.com/red-list-ecosystem/redlistr


Report a bug at https://github.com/red-list-ecosystem/redlistr/issues


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


Authors: Calvin Lee [cre, aut] , Nicholas Murray [aut]


Documentation:   PDF Manual  


GPL (>= 3) | file LICENSE license


Imports grDevices, methods, plyr, rgeos

Depends on raster, sp

Suggests devtools, knitr, rgdal, rmarkdown, testthat


See at CRAN