bam_ssim {bamm}

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 = 0.85,
  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 containing 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 matrices for each time will be returned.

nsteps

Number of steps to run the simulation

progress_bar

Show progress bar

Details

The returned object inherits from setA, setM classes. Details about the dynamic model can be found in Soberon and Osorio-Olvera (2022).

Value

An object of class bam. The object contains 12 slots of information (see details) from which simulation results are stored in sdm_sim object, a list of sparse matrices with results of each simulation step. Palatable matrices are returned as a list of sparse matrices with information about palatable pixels for each step of the simulation.

Author(s)

Luis Osorio-Olvera & Jorge Soberón

References

Soberón J, Osorio-Olvera L (2023). “A dynamic theory of the area of distribution.” Journal of Biogeography6, 50, 1037-1048. doi:10.1111/jbi.14587, https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.14587..

Examples

urap <- system.file("extdata/urania_omph/urania_guanahacabibes.tif",
                                  package = "bamm")
ura <- raster::raster(urap)
ompp <- system.file("extdata/urania_omph/omphalea_guanahacabibes.tif",
                                  package = "bamm")
omp <- raster::raster(ompp)
msparse <- bamm::model2sparse(ura)
init_coordsdf <- data.frame(x=-84.38751, y= 22.02932)
initial_points <- bamm::occs2sparse(modelsparse = msparse,init_coordsdf)
set_M <- bamm::adj_mat(modelsparse = msparse,ngbs = 1)
ura_ssim <- bamm::bam_ssim(sp1=ura, sp2=omp, set_M=set_M,
                           dispersal_prob = 0.75,
                           initial_points=initial_points,
                           periods_toxic=5,
                           periods_suitable=1,
                           nsteps=40)
ura_omp <- bamm::sim2Raster(ura_ssim)
raster::plot(ura_omp[[c(1,2,5,10,15,20,30,35,40)]])

if(requireNamespace("animation")){
# Animation example
anp <-tempfile(pattern = "simulation_results_",fileext = ".gif")
#new_sim <- bamm::sim2Animation(sdm_simul = ura_ssim,
#                               which_steps = seq_len(ura_ssim@sim_steps),
#                               fmt = "GIF",
#                               filename = anp)
}