Package {redlistr}

Title:	Tools for the IUCN Red List of Ecosystems and Species
Version:	2.1.0
Description:	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.
License:	GPL (≥ 3) | file LICENSE
URL:	https://github.com/red-list-ecosystem/redlistr, http://red-list-ecosystem.github.io/redlistr/
BugReports:	https://github.com/red-list-ecosystem/redlistr/issues
Depends:	R (≥ 4.1.0)
Imports:	terra (≥ 1.8-54), sf (≥ 1.0-21), dplyr, methods, ggplot2, rlang, units, stringr, mgcv
Suggests:	devtools, knitr, rmarkdown, testthat, leaflet
VignetteBuilder:	knitr
Encoding:	UTF-8
RoxygenNote:	7.3.3
Config/Needs/website:	rmarkdown
LazyData:	true
NeedsCompilation:	no
Packaged:	2026-07-09 23:38:24 UTC; z3531221
Author:	Calvin Lee [aut] (Original functions and examples), Nicholas Murray [aut] (Original functions and examples), Aniko Toth [cre, aut] (Updated functions, classes and methods), José R. Ferrer-Paris [aut] (Documentation, contributions to classes and methods)
Maintainer:	Aniko Toth <anikobtoth@gmail.com>
Repository:	CRAN
Date/Publication:	2026-07-14 07:30:02 UTC

AOOgrid class

Description

A class to represent an AOO grid object

Slots

name

the name of the assessment unit

grid

an AOO grid as a shapefile

AOO

the number of grid squares in grid

params

a named vector of input parameters (grid size, jitter, n_jitter)

pctrule

logical indicating whether the 1% rule was applied

input

the input ecosystem data used to generate the AOO grid

AOOvals

the list of AOO values

EOO class

Description

A class to represent an EOO convex hull object

Slots

name

the name of the assessment unit

pol

an EOO convex hull polygon

EOO

the area of the EOO polygon as a numeric

unit

the unit in which the area is provided

input

the input ecosystem data used to generate the EOO polygon

Mangrove area combined

Description

Area of mangroves in 2000 and 2017

Usage

a

Format

a

A data frame with 2 rows and 3 columns:

layer

name of the layer

value

raster value from which area was computed

area

area in km2

Source

computed from mangrove.2000 and mangrove.2017 using getArea

Mangrove distribution data

Description

Mangrove distribution from the northern regions of Western Port Bay, Victoria, Australia, in the year 2000.

Usage

a.2000

Format

a.2000

A data frame with 1 row and 3 columns:

layer

name of the layer

value

raster value from which area was computed

area

area in km2

Details

The dataset is stored as a GeoTIFF file in inst/extdata and can be loaded with:

terra::rast(system.file("extdata", "example_distribution_2000.tif", package = "redlistr"))

The dataset is stored as a GeoTIFF file in inst/extdata and can be loaded with:

terra::rast(system.file("extdata", "example_distribution_2017.tif", package = "redlistr"))

Mangrove area

Area of mangroves in 2000

Source

https://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2010.00584.x/abstract Mangrove distribution data

Mangrove distribution from the northern regions of Western Port Bay, Victoria, Australia, in the year 2017.

computed from mangrove.2000 using getArea

Mangrove area

Description

Area of mangroves in 2017

Usage

a.2017

Format

a.2017

A data frame with 1 row and 3 columns:

layer

name of the layer

value

raster value from which area was computed

area

area in km2

Source

computed from mangrove.2017 using getArea

AOOgrid as.list

Description

as.list method for AOOgrid object

Usage

## S3 method for class 'AOOgrid'
as.list(x, ...)

Arguments

EOO as.list

Description

as.list method for EOO object

Usage

## S3 method for class 'EOO'
as.list(x, ...)

Arguments

Compute AOO and EOO, return as table

Description

bundle performs AOO and EOO calculations on an input object and returns the results as a table

Usage

bundle(input_data, names_from = NA, ...)

Arguments

Value

a data.frame containing AOO and EOO information for all input units as rows.

Author(s)

Aniko B. Toth anikobtoth@gmail.com

See Also

Other synthesis functions: list2table()

Create empty Area of Occupancy (AOO) Grid.

Description

createGrid produces empty grid which can be used as the basis to help compute AOO.

Usage

createGrid(input_data, cell_size = 10000)

Arguments

Value

A regular grid raster with extent input_data expanded by two cells in each direction and grid size cell_size. Each grid square has a unique raster value that serves as its identification number.

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com, Aniko B. Toth anikobtoth@gmail.com

References

Bland, L.M., Keith, D.A., Miller, R.M., Murray, N.J. and Rodriguez, J.P. (eds.) 2016. Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 1.0. Gland, Switzerland: IUCN. ix + 94pp. Available at the following web site: https://iucnrle.org/

See Also

Other AOO functions: getAOO(), jplot(), makeAOOGrid(), top_pct()

Decline forecasts

Description

declineForecast calculates rates of change from two inputs and extrapolates the rate of change to a desired future time interval.

Usage

declineForecast(
  x,
  y,
  names_from_x = NA,
  names_from_y = NA,
  t1,
  year_diff,
  forecast_year = t1 + 50
)

Arguments

Value

returns a list of two elements: a table of areas and change in areas and a table of forecasts including decline rate, forecast area, and forecast percent decline.

Author(s)

Aniko B. Toth anikobtoth@gmail.com

See Also

Other Change functions: getArea(), getAreaChange(), getAreaTrend(), getDeclineStats()

Extrapolate Estimate

Description

extrapolateEstimate uses rates of decline from getDeclineStats to extrapolate estimates to a given time

Usage

extrapolateEstimate(A.t1, year.t1, nYears, ARD = NA, PRD = NA, ARC = NA)

Arguments

Value

A dataframe with the forecast year, and a combination of:

• Values as extrapolated with absolute rate of decline (ARD)

• Values as extrapolated with proportional rate of decline (PRD)

• Values as extrapolated with annual rate of change (ARC)

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com

References

IUCN 2024. Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 2.0. Keith, D.A., Ferrer-Paris, J.R., Ghoraba, S.M.M., Henriksen, S., Monyeki, M., Murray, N.J., Nicholson, E., Rowland, J., Skowno, A., Slingsby, J.A., Storeng, A.B., Valderrábano, M. & Zager, I. (Eds.) Gland, Switzerland: IUCN. ix + 94pp.

See Also

Other change_functions: futureAreaEstimate(), sequentialExtrapolate()

Examples

a.r1 <- 23.55
a.r2 <- 15.79
decline.stats <- getDeclineStats(a.r1, a.r2, year.t1 = 1990, year.t2 = 2012,
                                 methods = 'PRD')
a.2040.PRD <- extrapolateEstimate(a.r1, a.r2, year.t1 = 1990, nYears = 50,
                                  PRD = decline.stats$PRD)

Future Area Estimate

Description

futureAreaEstimate is now deprecated, please use extrapolateEstimate instead

Usage

futureAreaEstimate(A.t1, year.t1, nYears, ARD = NA, PRD = NA, ARC = NA)

Arguments

Value

A dataframe with the forecast year, and a combination of:

• Future area as estimated with absolute rate of decline (ARD)

• Future area as estimated with proportional rate of decline (PRD)

• Future area as estimated with annual rate of change (ARC)

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com

References

IUCN 2024. Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 2.0. Keith, D.A., Ferrer-Paris, J.R., Ghoraba, S.M.M., Henriksen, S., Monyeki, M., Murray, N.J., Nicholson, E., Rowland, J., Skowno, A., Slingsby, J.A., Storeng, A.B., Valderrábano, M. & Zager, I. (Eds.) Gland, Switzerland: IUCN. ix + 94pp.

See Also

Other change_functions: extrapolateEstimate(), sequentialExtrapolate()

Compute Area of Occupancy (AOO)

Description

getAOO determines the number of area of occupancy (AOO) grid cells occupied by a species or ecosystem. It includes capability for specifying whether at least one percent of the grid cell needs to be occupied before it is counted in the AOO. This functionality is important for assessing the IUCN Red List of Ecosystems Criteria B.

Usage

getAOO(
  input_data,
  cell_size = 10000,
  names_from = NA,
  bottom_1pct_rule = TRUE,
  percent = 1,
  jitter = 150,
  n_jitter = 35
)

Arguments

Value

an object of class AOOgrid or a list of AOOgrid objects. Ecosystems that received an AOO of 60 cells or fewer on a first pass are run with a jittered grid with n specified by n_jitter

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com, Aniko B. Toth anikobtoth@gmail.com

References

Bland, L.M., Keith, D.A., Miller, R.M., Murray, N.J. and Rodriguez, J.P. (eds.) 2016. Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 1.0. Gland, Switzerland: IUCN. ix + 94pp. Available at the following web site: https://iucnrle.org/

See Also

Other AOO functions: createGrid(), jplot(), makeAOOGrid(), top_pct()

Calculates the Area of ecosystems in spatial data

Description

getArea reports the area of ecosystem units provided as spatial data

Usage

getArea(x, names_from = NA, ...)

Arguments

Value

A data frame containing ecosystem identifiers and the total area of the ecosystem units in x as a units vector (km^2). For raster bricks it also contains the layer number.

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com, Aniko B. Toth anikobtoth@gmail.com

See Also

Other Change functions: declineForecast(), getAreaChange(), getAreaTrend(), getDeclineStats()

Area change between two inputs in km2

Description

getAreaChange reports the difference in area between two inputs. Inputs can be SpatRaster, SpatVector, sf or a data frame of areas and may contain data for multiple ecosystem types. Ensure x and y are the same data type. If using data frame as input, ensure areas are measured in km2

Usage

getAreaChange(x, y, names_from_x = NA, names_from_y = NA)

Arguments

Value

Returns a table containing ecosystem labels, areas, and the difference in area of the two inputs in km2

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com, Aniko B. Toth anikobtoth@gmail.com

See Also

Other Change functions: declineForecast(), getArea(), getAreaTrend(), getDeclineStats()

Examples

if (requireNamespace("terra", quietly = TRUE)) {
  ok <- try({
    m1 <- matrix(sample(1:4, 500, replace = TRUE, prob = c(4,1,1,6)), 25, 20)
    r1 <- terra::rast(m1)
    terra::crs(r1) <- "+proj=utm +zone=55 +south +datum=WGS84 +units=m +no_defs"

    m2 <- matrix(sample(1:4, 500, replace = TRUE, prob = c(4,1,1,6)), 25, 20)
    r2 <- terra::rast(m2)
    terra::crs(r2) <- "+proj=utm +zone=55 +south +datum=WGS84 +units=m +no_defs"

    getAreaChange(r1, r2)
  }, silent = TRUE)
}

Extracts the area from an EOO polygon

Description

getEOOarea wrapper that extracts the area slot of the EOO input

Usage

getAreaEOO(EOO)

Arguments

Value

an integer

See Also

Other EOO functions: getEOO(), makeEOO()

Calculate area trends of ecosystems

Description

getAreaTrend is used to calculate changes in area over time. Output is a list can be used to easily visualise trends for one ecosystem at a time.

Usage

getAreaTrend(x, names_from = NA)

Arguments

Value

returns a list

Author(s)

Aniko B. Toth anikobtoth@gmail.com

See Also

Other Change functions: declineForecast(), getArea(), getAreaChange(), getDeclineStats()

Change statistics.

Description

getDeclineStats calculates the Proportional Rate of Decline (PRD), Absolute Rate of Decline (ARD) and Annual Rate of Change (ARC), given two areas at two points in time. Also provides the total area difference. Inputs are usually the results from getArea.

Usage

getDeclineStats(A.t1, A.t2, year.t1, year.t2, methods)

Arguments

Value

A dataframe with absolute differences between the two inputs, and a selection of:

• Proportional Rate of Decline (PRD)

• Absolute Rate of Decline (ARD)

• Annual Rate of Change (ARC)

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com

References

IUCN 2024. Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 2.0. Keith, D.A., Ferrer-Paris, J.R., Ghoraba, S.M.M., Henriksen, S., Monyeki, M., Murray, N.J., Nicholson, E., Rowland, J., Skowno, A., Slingsby, J.A., Storeng, A.B., Valderrábano, M. & Zager, I. (Eds.) Gland, Switzerland: IUCN. ix + 94pp. Puyravaud, J.-P. 2003. Standardizing the calculation of the annual rate of deforestation. Forest Ecology and Management, 177, 593-596.

See Also

Other Change functions: declineForecast(), getArea(), getAreaChange(), getAreaTrend()

Examples

a.r1 <- 23.55
a.r2 <- 15.79
decline.stats <- getDeclineStats(a.r1, a.r2, year.t1 = 1990, year.t2 = 2012,
                                 methods = c('ARD', 'ARC'))

Calculates area of the created EOO polygon and returns a summary object with useful info.

Description

getEOO calculates the area of the EOO polygon generated from makeEOO the provided data and returns an EOO class object or a list of these with defined summary and plot functions available.

Usage

getEOO(input_data, names_from = NA)

Arguments

Value

An object of type EOO or a list of EOO objects that store the EOO polygon, its area, and its input_data

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com

See Also

Other EOO functions: getAreaEOO(), makeEOO()

Examples

if (requireNamespace("terra", quietly = TRUE)) {
  ok <- try({
    m <- matrix(sample(1:4, 500, replace = TRUE, prob = c(4,1,1,6)), nrow=25, ncol=20)
     r1 <- terra::rast(m, crs = "+proj=utm +zone=55 +south +datum=WGS84 +units=m +no_defs")
    EOO <- getEOO(r1)
  }, silent = TRUE)
}

AOOgrid hist

Description

hist method for AOOgrid objects

Usage

## S4 method for signature 'AOOgrid'
hist(x, ...)

Arguments

Union of spatial classes

Description

Allows either sf, spatVector, or SpatRaster objects in the spatial slot.

Make elbow plot to check jitter iterations

Description

jplot creates an elbow plot of the min AOO against the number of grid replicates run. Jplots that fall to the minimum value well before the highest n are robust.

Usage

jplot(x)

Arguments

Value

NULL; plots min AOO against number of reps

Author(s)

Aniko B. Toth anikobtoth@gmail.com

See Also

Other AOO functions: createGrid(), getAOO(), makeAOOGrid(), top_pct()

Summarises a list of EOO or AOOgrid objects in a table

Description

list2table wrapper that summarises a list of EOO or AOOgrid objects as a table.

Usage

list2table(l)

Arguments

Value

a data.frame

See Also

Other synthesis functions: bundle()

Create Area of Occupancy (AOO) grid for an ecosystem or species distribution

Description

makeAOOGrid is a generic function that creates grids representing the area of occupancy for distributions based on the input spatial data. It includes capability for specifying whether the least occupied cells collectively containing less than 1% of the ecosystem are counted in the AOO. This functionality is important for assessing the IUCN Red List of Ecosystems Criteria B.

Usage

makeAOOGrid(
  input_data,
  cell_size = 10000,
  names_from = NA,
  bottom_1pct_rule = TRUE,
  percent = 1,
  jitter = 150,
  n_jitter = 35
)

Arguments

Value

A shapefile of grid cells occupied by an ecosystem or species, or a list of these if multiple ecosystems were input.

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com, Aniko B. Toth anikobtoth@gmail.com

References

Bland, L.M., Keith, D.A., Miller, R.M., Murray, N.J. and Rodriguez, J.P. (eds.) 2016. Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 1.0. Gland, Switzerland: IUCN. ix + 94pp. Available at the following web site: https://iucnrle.org/

See Also

Other AOO functions: createGrid(), getAOO(), jplot(), top_pct()

Examples

if (requireNamespace("terra", quietly = TRUE)) {
  ok <- try({
      m <- matrix(sample(1:4, 500, replace = TRUE, prob = c(4,1,1,6)), nrow=25, ncol=20)
      r1 <- terra::rast(m, crs = "+proj=utm +zone=55 +south +datum=WGS84 +units=m +no_defs")
      AOO_grid <- makeAOOGrid(r1, cell_size = 3)
  }, silent = TRUE)
}

Creates Extent of occurrence (EOO) Polygon

Description

makeEOO is a generic function that creates a minimum convex polygon enclosing all occurrences of the ecosystems provided in the input data. If the input provided is a raster layer, the points are taken from a buffer that has the radius of half of the shorter edge of the pixel around the centroid.

Usage

makeEOO(input_data, names_from)

Arguments

Value

An object of class sf representing the EOO of input_data, or a list of sf objects if multiple ecosystems were input. Also inherits its CRS from input_data.

Author(s)

Nicholas Murray murr.nick@gmail.com, Calvin Lee calvinkflee@gmail.com

References

IUCN 2024. Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 2.0. Keith, D.A., Ferrer-Paris, J.R., Ghoraba, S.M.M., Henriksen, S., Monyeki, M., Murray, N.J., Nicholson, E., Rowland, J., Skowno, A., Slingsby, J.A., Storeng, A.B., Valderrábano, M. & Zager, I. (Eds.) Gland, Switzerland: IUCN. ix + 94pp.

See Also

Other EOO functions: getAreaEOO(), getEOO()

Examples

if (requireNamespace("terra", quietly = TRUE)) {
  ok <- try({
     m <- matrix(sample(1:4, 500, replace = TRUE, prob = c(4,1,1,6)), nrow=25, ncol=20)
     r1 <- terra::rast(m, crs = "+proj=utm +zone=55 +south +datum=WGS84 +units=m +no_defs")
     EOO.polygon <- makeEOO(r1)
  }, silent = TRUE)
}

AOOgrid plot

Description

plot method for AOOgrid object

Usage

## S4 method for signature 'AOOgrid,ANY'
plot(x, title = x@name)

Arguments

EOO plot

Description

plot method for EOO object

Usage

## S4 method for signature 'EOO,ANY'
plot(x, title = x@name)

Arguments

trend plot

Description

plot method for trend object

Usage

## S4 method for signature 'trend,ANY'
plot(x, y, ...)

Arguments

Safely project SpatRaster object CRS

Description

Safely project SpatRaster object CRS

Usage

safe_project(x, crs)

Safely transform sf object CRS

Description

Safely transform sf object CRS

Usage

safe_transform(x, crs)

Sequential extrapolation estimate

Description

sequentialExtrapolate uses rates of decline from getDeclineStats and generates a sequence of estimates at regular time-steps. Useful for generating a sequence for plotting graphs.

Usage

sequentialExtrapolate(A.t1, year.t1, nYears, ARD = NA, PRD = NA, ARC = NA)

Arguments

Value

A dataframe with the forecast year, and a combination of:

• Sequence of values as extrapolated with absolute rate of decline (ARD)

• Sequence of values as extrapolated with proportional rate of decline (PRD)

• Sequence of values as extrapolated with annual rate of change (ARC)

Author(s)

Calvin Lee calvinkflee@gmail.com

References

IUCN 2024. Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 2.0. Keith, D.A., Ferrer-Paris, J.R., Ghoraba, S.M.M., Henriksen, S., Monyeki, M., Murray, N.J., Nicholson, E., Rowland, J., Skowno, A., Slingsby, J.A., Storeng, A.B., Valderrábano, M. & Zager, I. (Eds.) Gland, Switzerland: IUCN. ix + 94pp.

See Also

Other change_functions: extrapolateEstimate(), futureAreaEstimate()

Examples

a.r1 <- 23.55
a.r2 <- 15.79
decline.stats <- getDeclineStats(a.r1, a.r2, year.t1 = 1990, year.t2 = 2012,
                                 methods = 'PRD')
a.2040.PRD.seq <- sequentialExtrapolate(a.r1, a.r2, year.t1 = 1990, nYears = 50,
                                        PRD = decline.stats$PRD)

AOOgrid show

Description

show method for AOOgrid object

Usage

## S4 method for signature 'AOOgrid'
show(object)

Arguments

EOO show

Description

show method for EOO object

Usage

## S4 method for signature 'EOO'
show(object)

Arguments

AOOgrid summary

Description

summary method for AOOgrid object

Usage

## S4 method for signature 'AOOgrid'
summary(object)

Arguments

EOO summary

Description

summary method for EOO object

Usage

## S4 method for signature 'EOO'
summary(object)

Arguments

trend summary

Description

summary method for trend object

Usage

## S4 method for signature 'trend'
summary(object)

Arguments

Identify positions of the bottom 1% of ecosystem area in AOO grid

Description

top_pct returns the vector positions of the largest elements collectively comprising a given percentage more of the vector sum. This function helps perform the bottom_1pct_rule when selecting the AOO grid by identifying grid positions to keep.

Usage

top_pct(v, pct = 99)

Arguments

Value

a numeric vector indicating the indices of the elements to keep.

Author(s)

Aniko B. Toth anikobtoth@gmail.com

References

IUCN (2024). Guidelines for the application of IUCN Red List of Ecosystems Categories and Criteria, Version 2.0. Keith, D.A., Ferrer-Paris, J.R., Ghoraba, S.M.M., Henriksen, S., Monyeki, M., Murray, N.J., Nicholson, E., Rowland, J., Skowno, A., Slingsby, J.A., Storeng, A.B., Valderrábano, M. & Zager, I. (Eds.). Gland, Switzerland: IUCN. ix + 94pp. Available at the following web site: https://iucnrle.org/

See Also

Other AOO functions: createGrid(), getAOO(), jplot(), makeAOOGrid()

trend class

Description

A class to represent change in area over time for an ecosystem.

Slots

input

binary raster or list of sf POLYGON objects representing the input ecosystem extent

areas

the area of the ecosystem in each layer or list element

model

a fitted model object typically of the class lm containing the model used to calculate the trend

netdiff

difference between the area in the first layer or list element and the last.

diff

raster stack showing change over layers or list elements of the ecosystem extent.

Fit linear model with log-link.

Description

fit_lm_ll produces a simple model to estimate trends in short time series.

Usage

fit_lm_ll(df)

fit_glm_ll(df)

fit_spline(df)

Arguments

Value

an lm object

Author(s)

Aniko B. Toth anikobtoth@gmail.com