bam_ssim: bam_ssim: Simulate dispersal dynamics using the set B of the...

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

bam_ssim: Simulate dispersal dynamics using the set B of the BAM framework.

Description

bam_ssim: Simulate dispersal dynamics using the set B of the BAM framework.

Usage

bam_ssim(
  sp1,
  sp2,
  set_M,
  initial_points,
  periods_toxic,
  periods_suitable,
  dispersal_prob = 0.2,
  palatable_matrices = FALSE,
  nsteps,
  progress_bar = TRUE
)

Arguments

sp1	Niche model of the focal species (the one that disperses).
sp2	Niche model of the species with whom sp1 interacts (currently no dispersal dynamics for this species).
set_M	A setM object cointaining the adjacency matrix for sp1. See adj_mat
initial_points	A sparse vector returned by the function occs2sparse
periods_toxic	Time periods that sps2 takes to develop defense mechanisms (i.e. toxic).
periods_suitable	This is the time that sp2 takes to become non-toxic
dispersal_prob	A numeric value indicating the probability to disperse to neighboring cells. This probability is assumed to be binomially distributed
palatable_matrices	Logical. If TRUE palatable matices for each time will be returned.
nsteps	Number of steps to run the simulation
progress_bar	Show progress bar

Examples

## Not run: 
ura <- raster::raster(system.file("extdata/urania_omph/urania_guanahacabibes.tif",
                                  package = "bam"))
omp <- raster::raster(system.file("extdata/urania_omph/omphalea_guanahacabibes.tif",
                                  package = "bam"))
msparse <- bam::model2sparse(ura)
init_coordsdf <- data.frame(x=-84.38751, y= 22.02932)
initial_points <- bam::occs2sparse(modelsparse = msparse,init_coordsdf)
set_M <- bam::adj_mat(modelsparse = msparse,ngbs = 1)
ura_sim <- bam::bam_sim(sp1=ura, sp2=omp, set_M=set_M,
                        initial_points=initial_points,
                        periods_toxic=3,
                        periods_suitable=3,
                        nsteps=40)
# Animation example
anp <-"C:/Users/l916o895/Dropbox/TeoriadeBAM/articulo_bam/ura_omp_sim.gif"
new_sim <- bam::sim2Animation(sdm_simul = ura_sim,
                              which_steps = 1:ura_sim@sim_steps,
                              fmt = "GIF",
                              filename = anp)

## End(Not run)

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