AOO.decline: Area of occupancy decline

In gdauby/ConR: Computation of Parameters Used in Preliminary Assessment of Species Conservation Status

Area of occupancy decline

Description

Estimate areas of occupancy (AOO) decline for multiple taxa in square kilometres and percentage

Usage

AOO.decline(
  XY,
  hab.map,
  cell_size_AOO = 2,
  nbe.rep.rast.AOO = 0,
  parallel = FALSE,
  NbeCores = 2,
  show_progress = TRUE,
  proj_type = "cea",
  hab.class = NULL,
  hab.map.type = NULL,
  all_individual_layers = FALSE
)

Arguments

XY	data.frame see Details.
hab.map	SpatRaster or sf polygons containing the habitat spatial information
cell_size_AOO	numeric, by default is 2. Value indicating the grid size in kilometres used for estimating Area of Occupancy.
nbe.rep.rast.AOO	numeric, by default is 0. Indicate the number of raster with random starting position used for estimating the AOO. If 0 but some translation of the raster are still done.
parallel	a logical. Whether running should be performed in parallel. FALSE by default.
NbeCores	an integer. Register the number of cores for parallel execution. Two by default.
show_progress	logical. Whether progress informations should displayed. TRUE by default
proj_type	string or numeric
hab.class	classes of values in hab.map to be considered as suitable
hab.map.type	logical, vector of same length of hab.map, TRUE means the habitat of hab.map is suitable FALSE means the habitat of hab.map is unsuitable
all_individual_layers	logical TRUE compute AOO decline for each individual hab.map FALSE (the default) compute AOO decline for all layers together

Details

Input as a data.frame should have the following structure:

It is mandatory to respect field positions, but field names do not matter

latitude	longitude	species
numeric	numeric	character

The argument nbe.rep.rast.AOO should ideally be higher than 20 for increasing the chance to get the minimal number of occupied cell. Increasing nbe.rep.rast.AOO however also increase the computing time. So this is a trade-off that depends on the importance to get the minimal AOO and the size of the dataset.

Value

1. AOOs a dataframe of AOO estimates for each taxa and for each layer/spatial polygons if all_individual_layers is TRUE

2. AOO_decline a dataframe of AOO.decline in percentages

3. categories based on the sub-criteria of IUCN criterion A

Author(s)

Gilles Dauby, [e-mail]

Examples

m <- matrix(1:25, nrow=5, ncol=5)
rm <- terra::rast(m)
terra::values(rm) <- sample(c("forest", "cities", "roads"), 25, replace = TRUE)
cls <- data.frame(id=1:3, cover=c("forest", "cities", "roads"))
levels(rm) <- cls
terra::crs(rm) <- "epsg:4326"


test_data <- dummy_dist(n = 5, xmin = 0, xmax = 5, ymin = 0, ymax = 5)


res <- AOO.decline(
XY = test_data,
hab.map = rm,
hab.class = c("forest"),
all_individual_layers = TRUE
)


res <- AOO.decline(
XY = test_data,
hab.map = rm,
hab.class = c("cities", "roads"),
all_individual_layers = TRUE, 
hab.map.type = FALSE ### this means the provided hab.map is unsuitable
)

gdauby/ConR documentation built on Jan. 30, 2024, 11:10 p.m.