severe_frag: Assessment of fragmentation subpopulations

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

Assessment of fragmentation subpopulations

Description

Assess whether species populations are severely fragmented

Usage

severe_frag(
  XY = NULL,
  cell_size = 2,
  nbe_rep = 0,
  AOO_poly = NULL,
  resol_sub_pop = NULL,
  habitat_poly = NULL,
  dist_isolated = NULL,
  proj_type = "cea",
  export_shp = FALSE,
  parallel = FALSE,
  show_progress = TRUE,
  NbeCores = 2,
  threshold_severe = 50
)

Arguments

XY	data frame
cell_size	numeric
nbe_rep	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.
AOO_poly	numeric. AOO of the species in squared kilometres.
resol_sub_pop	numeric. Defines in kilometres the radius of the circles around each occurrence
habitat_poly	Simple feature collection documenting habitat of species, see Details
dist_isolated	numeric vector providing a value for each species. Distance in kilometres for identifying subpopulations considered to be isolated. See details
proj_type	string or numeric
export_shp	logical
parallel	a logical. Whether running should be performed in parallel. FALSE by default.
show_progress	logical. Whether progress informations should displayed. TRUE by default
NbeCores	an integer. Register the number of cores for parallel execution. Two by default.
threshold_severe	numeric of one value indicates the threshold to identify severe fragmentation. By default is 50

Details

This function evaluates the proportion of the total area of occupancy in habitat patches separated from others by a large distance. Based on IUCN guidelines page 48: "A taxon can be considered to be severely fragmented if most (>50%) of its total area of occupancy is in habitat patches that are (...) separated from other habitat patches by a large distance."

This function interpret subpopulations as obtained using subpop.estimation function as habitat patches. First, subpopulations that are isolated i.e. distant to all others subpopulations by at least dist_isolated kilometres, are identified. Then, the percentage of the AOO concerned by those "isolated" subpopulations is calculated.

Examples

mydf <- data.frame(ddlat = c(-44.6,-46.2,-45.4,-42.2,-43.7,-45.0,-48.0),
                   ddlon = c(-42.2,-42.6,-45.3,-42.5,-42.3,-39.0,-37.2),
                   tax = rep("a", 7),
                   stringsAsFactors = FALSE)

severe_frag(XY = mydf, dist_isolated = 200, resol_sub_pop = 10)

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