diversity_range_analysis: range_diversity_analysis: diversity analysis

In luismurao/bam: Species Distribution Models in the light of the BAM theory

range_diversity_analysis: diversity analysis

Description

diversity_range_analysis biodiversity indices related to diversity-range plots

Usage

diversity_range_analysis(
  pam,
  xy_mat = NULL,
  lower_interval = 0.05,
  upper_interval = 0.95,
  raster_templete = NULL,
  niter = 100,
  return_null_dfield = FALSE,
  parallel = TRUE,
  n_cores = 2
)

Arguments

pam	A Presence-Absence-Matrix of matrix class or sparse matrix.
xy_mat	A two dimensional matrix with longitude and latitude data.
lower_interval	Lower interval.
upper_interval	Upper interval.
raster_templete	Araster templete.
niter	Number of iterations to obtain the distribution.
return_null_dfield	If TRUE the null distribution of dispersal field will be returned.
parallel	If TRUE the computations will be performed in parallel.
n_cores	Number of cores for the parallel computation.

Examples

## Not run: 
set.seed(111)
pam <- matrix(rbinom(10000,1,0.5),nrow = 100,ncol = 1000)
rdivan <- diversity_range_analysis(pam=pam,parallel = FALSE,
                                   return_null_dfield=TRUE)
bam::plot(rdivan,plot_type="diversity_range")
# Lagomorphos
lagos_path <- system.file("extdata/conejos",
                          package = "bam")
enm_path <- list.files(lagos_path,
                       pattern = ".tif",
                       full.names = TRUE)
en_models <- raster::stack(enm_path) >0.01
nonas <- which(!is.na(en_models[[1]][]))
xy_mat <- sp::coordinates(en_models[[1]])[ nonas,]
pam <- bam::models2pam(en_models,sparse=FALSE)
rdivan <- diversity_range_analysis(pam=pam,parallel = FALSE,
                                   xy_mat=xy_mat,
                                   raster_templete = en_models[[1]],
                                   return_null_dfield=TRUE)
bam::plot(rdivan,plot_type="diversity_range")
bam::plot(rdivan,plot_type="diversity_range_map")
bam::plot(rdivan,plot_type="diversity_range_interactive")


## End(Not run)

luismurao/bam documentation built on Nov. 28, 2022, 3:02 p.m.