kNCN_average: Construct spatially constrained sample-based rarefaction...

In MoBiodiv/mobr: Measurement of Biodiversity

Construct spatially constrained sample-based rarefaction (sSBR) curve using the k-Nearest-Centroid-neighbor (k-NCN) algorithm

Description

This function accumulates samples according their proximity to all previously included samples (their centroid) as opposed to the proximity to the initial focal sample. This ensures that included samples mutually close to each other and not all over the place.

Usage

kNCN_average(
  x,
  n = NULL,
  coords = NULL,
  repetitions = 1,
  no_pb = TRUE,
  latlong = FALSE,
  cl = NULL
)

Arguments

x	a mob_in object or a community site x species matrix
n	number of sites to include.
coords	spatial coordinates of the samples. If x is a mob_in object, the function uses its 'spat' table as coordinates.
repetitions	Number of times to repeat the procedure. Useful in situations where there are many ties in the distance matrix.
no_pb	binary, if TRUE then a progress bar is not printed, defaults to TRUE
latlong	if longitude latitudes are supplied
cl	A cluster object created by makeCluster, or an integer to indicate number of child-processes (integer values are ignored on Windows) for parallel evaluations (see Details on performance). It can also be "future" to use a future backend (see Details), NULL (default) refers to sequential evaluation.

Details

Internally the function constructs one curve per sample whereby each sample serves as the initial sample repetition times. Finally, the average curve is returned.

Value

a numeric vector of estimated species richness

Examples

data(inv_comm)
data(inv_plot_attr)
inv_mob_in = make_mob_in(inv_comm, inv_plot_attr, coord_names = c('x', 'y'))
kNCN_average(inv_mob_in, n = 5)

# parallel evaluation using the parallel package 
# run in parallel
library(parallel)
cl = makeCluster(2L)
clusterEvalQ(cl, library(mobr))
clusterExport(cl, 'inv_mob_in')
S_kNCN = kNCN_average(inv_mob_in, cl=cl)

stopCluster(cl)

MoBiodiv/mobr documentation built on Oct. 26, 2024, 10:51 a.m.