![[Experimental]](figures/lifecycle-experimental.svg)
Estimate areas of occupancy (AOO) decline for multiple taxa in square kilometres and percentage
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.mapto be considered as suitable- hab.map.type
logical, vector of same length of
hab.map,TRUEmeans the habitat ofhab.mapis suitableFALSEmeans the habitat ofhab.mapis unsuitable
- all_individual_layers
logical
TRUEcompute AOO decline for each individualhab.mapFALSE(the default) compute AOO decline for all layers together
Value
AOOs a
dataframeof AOO estimates for each taxa and for each layer/spatial polygons ifall_individual_layersis TRUEAOO_decline a
dataframeof AOO.decline in percentagescategories based on the sub-criteria of IUCN criterion A
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.
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
)
#> hab.map.type not provided, all hab.map provided are considered as suitable
#> Total Area of occupancy
#>
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
#> Area of occupancy minus threatened areas for each layers individually
#> [1] "hab.map.1"
#>
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
#>
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
#> Warning: The following subcriteria were not used in the assessment: A1, A3, A4
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
)
#> Total Area of occupancy
#>
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
#> Area of occupancy minus threatened areas for each layers individually
#> [1] "hab.map.1"
#>
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
#>
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
#> Warning: The following subcriteria were not used in the assessment: A1, A3, A4