criterion_B: Assess IUCN Criterion B

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

Assess IUCN Criterion B

Description

Preliminary assessment of species conservation status following IUCN Criterion B, which is based on species geographic distribution (i.e. extent of occurrence - EOO, and area of occupancy, AOO)

Usage

criterion_B(
  x = NULL,
  AOO = NULL,
  EOO = NULL,
  locations = NULL,
  severe.frag = NULL,
  subpops = NULL,
  decline = NULL,
  EOO.threshold = c(20000, 5000, 100),
  AOO.threshold = c(2000, 500, 10),
  Loc.threshold = c(10, 5, 1),
  comp_subpop = TRUE,
  comp_severe.frag = FALSE,
  resol_sub_pop = 5,
  cell_size_locations = 10,
  method_locations = "fixed_grid",
  method_polygons = "no_more_than_one",
  rel_cell_size = 0.05,
  threat_list = NULL,
  names_threat = NULL,
  threat_weight = NULL,
  id_shape = "id_orig",
  country_map = NULL,
  method.range = "convex.hull",
  alpha = 1,
  buff.alpha = 0.1,
  exclude.area = FALSE,
  cell_size_AOO = 2,
  nbe.rep.rast.AOO = 0,
  threshold_severe = 50,
  parallel = FALSE,
  show_progress = TRUE,
  NbeCores = 2,
  proj_type = "cea",
  mode = "spheroid",
  DrawMap = FALSE,
  add.legend = TRUE
)

Arguments

x	a dataframe or an object of class spgeoIN see https://github.com/azizka/speciesgeocodeR. See Details
AOO	a vector of species AOO, if available
EOO	a vector of species EOO, if available
locations	a vector of species number of locations, if available
severe.frag	a vector indicating if species is severely fragmented, if available
subpops	a vector of the number of subpopulations (sensu IUCN), if available
decline	a vector providing the status of the species continuing decline in EOO, AOO, habitat, locations or subpopulations or population size (i.e. condition 'b') to be passed on to function cat_criterion_b(). If different of 'Decreasing', the condition 'b' of criterion B will not be met.
EOO.threshold	numeric vector indicating the thresholds used to categorize EOO in IUCN categories
AOO.threshold	numeric vector indicating the thresholds used to categorize AOO in IUCN categories
Loc.threshold	numeric vector indicating the thresholds used to categorize the number of locations in IUCN categories
comp_subpop	logical if the number of sub-populations should be computed. By default is TRUE
comp_severe.frag	logical if severe fragmentation should be computed. By default is FALSE
resol_sub_pop	a value defining the radius of the circles around each occurrence (in kilometres) or data frame vector containing a column 'tax' with the taxa names and a column 'radius' with the species-specific radius (in kilometre as well). Typically, this data frame is the output of ConR function subpop.radius.
cell_size_locations	numeric, value indicating the grid size in kilometres used for estimating the number of location. By default, equal to 10
method_locations	string, indicating the method used for estimating the number of locations. See Details "fixed_grid" (by default) "sliding_scale"
method_polygons	string. Used if threat_list is provided. See Details. "no_more_than_one" (the default): each single POLYGON will be considered as a single location "grid": a grid of cell_size_locations size will be used to estimate the number of location within polygons
rel_cell_size	numeric, if method_locations="sliding_scale", cell_size_locations is ignored and the resolution is given by the maximum distance separating two occurrences multiplied by rel_cell_size. By default, it is 0.05
threat_list	list or sfc objects POLYGON or MULTIPOLYGON documenting threats. If provided, this will be taken into account for calculating number of location (see Details and method_polygons). By default, no shapefile is provided
names_threat	character vector, indicating names of threats, optional
threat_weight	numeric vector, indicating weight given to each threat
id_shape	string
country_map	a SpatialPolygonsDataFrame or SpatialPolygons showing for example countries or continent borders. This shapefile will be used for cropping the SpatialPolygonsl if exclude.area is TRUE
method.range	a character string, "convex.hull" or "alpha.hull". By default is "convex.hull"
alpha	a numeric, if method.range is "alpha.hull", value of alpha of the alpha hull, see alphahull::ahull(). By default is 1
buff.alpha	a numeric, if method.range is "alpha.hull", define the buffer in decimal degree added to alpha hull. By default is 0.1
exclude.area	a logical, if TRUE, areas outside of country_map are cropped of SpatialPolygons used for calculating EOO. By default is FALSE
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.
threshold_severe	numeric of one value indicates the threshold to identify severe fragmentation. By default is 50
parallel	logical, whether running in parallel. By default, it is FALSE
show_progress	logical, whether a bar showing progress in computation should be shown. By default, it is TRUE
NbeCores	integer, register the number of cores for parallel execution. By default, it is 2
proj_type	string or numeric
mode	character string either 'spheroid' or 'planar'. By default 'spheroid'
DrawMap	logical, by default is FALSE, if TRUE, a png map is created for each species in a directory of the working environment
add.legend	logical, whether legend should be added to map

Value

A data frame containing, for each of taxon, (EOO, AOO, n.locs, n.subpops?), the IUCN categories associated with the sub-criteria and the consensus category for criterion B.

Author(s)

Gilles Dauby & Renato A. Ferreira de Lima

References

IUCN 2019. Guidelines for Using the IUCN Red List Categories and Criteria. Version 14. Standards and Petitions Committee. Downloadable from: http://www.iucnredlist.org/documents/RedListGuidelines.pdf.

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