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

In bamm: Species Distribution Models as a Function of Biotic, Abiotic and Movement Factors (BAM)

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

Description

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

Usage

bam_sim(
  sp1,
  sp2,
  set_M,
  initial_points,
  periods_toxic,
  periods_suitable,
  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
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). The model is cellular automata where the occupied area of a species at time t+1 is estimated by the multiplication of three binary matrices: one matrix represents movements (M), another abiotic -niche- tolerances (A), and a third, biotic interactions (B) (Soberon and Osorio-Olvera, 2022).

\mathbf{G}_j(t+1) =\mathbf{B}_j(t)\mathbf{A}_j(t)\mathbf{M}_j \mathbf{G}_j(t)

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.

Author(s)

Luis Osorio-Olvera & Jorge Soberón

References

\insertRef

SoberonOsoriobamm.

Examples

# Compute dispersal dynamics of Urania boisduvalii as a function of
# palatable Omphalea
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_sim <- bamm::bam_sim(sp1=ura, sp2=omp, set_M=set_M,
                         initial_points=initial_points,
                         periods_toxic=5,
                         periods_suitable=1,
                         nsteps=40)
ura_omp <- bamm::sim2Raster(ura_sim)
raster::plot(ura_omp[[c(1,5,10,15,20,30,35,40)]])

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

bamm documentation built on Sept. 11, 2024, 6:19 p.m.