subpop.comp: Estimate the number of subpopulations for one or multiple...

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

Estimate the number of subpopulations for one or multiple species

Description

Estimate the number of subpopulations following the method circular buffer method (overlapping buffered circles form a single subpopulation)

Usage

subpop.comp(
  XY,
  resol_sub_pop = NULL,
  proj_type = "cea",
  export_shp = FALSE,
  parallel = FALSE,
  show_progress = TRUE,
  NbeCores = 2
)

Arguments

XY	a data frame containing the geographical coordinates for each taxon (see Details).
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.
proj_type	string or numeric
export_shp	logical. Whether the resulting shapefiles should be exported. FALSE by default.
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.

Details

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

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

1. The first column is contains numeric value i.e. latitude in decimal degrees

2. The second column is contains numeric value i.e. longitude in decimal degrees

3. The third column is contains character value i.e. the names of the species

Value

If export_shp is TRUE,

1. number_subpop a numeric vector of AOO estimates for each taxa

2. poly_subpop a simple feature collection

a ⁠Simple feature collection⁠ with as many MULTIPOLYGON as taxa. If export_shp is FALSE, a vector with estimated number of subpopulation per taxa.

Author(s)

Gilles Dauby & Renato A. Ferreira de Lima

References

Rivers MC, Bachman SP, Meagher TR, Lughadha EN, Brummitt NA (2010) Subpopulations, locations and fragmentation: applying IUCN red list criteria to herbarium specimen data. Biodiversity and Conservation 19: 2071-2085. doi: 10.1007/s10531-010-9826-9

Examples

data(dataset.ex)

subpop.comp(dataset.ex, resol_sub_pop = 5)
rad.df <- data.frame(
    tax = unique(dataset.ex$tax),
    radius = seq(3,13, by=2),
    stringsAsFactors = FALSE
  )
subpop.comp(dataset.ex, resol_sub_pop = rad.df)
subpop.comp(dataset.ex, resol_sub_pop = rad.df, export_shp = TRUE)

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