sim2Animation {bamm}

sim2Animation: Animate BAM simulation object.

Description

Animates BAM simulation object.

Usage

sim2Animation(
  sdm_simul,
  which_steps,
  fmt = "GIF",
  filename,
  png_keyword = "sdm_sim",
  extra_legend = NULL,
  bg_color = "#F6F2E5",
  suit_color = "#0076BE",
  occupied_color = "#03C33F",
  gif_vel = 0.8,
  ani.width = 1200,
  ani.height = 1200,
  ani.res = 300
)

Arguments

sdm_simul

A bam object. See sdm_sim

which_steps

A numeric vector indicating the simulation steps that are going to be converted into raster layers.

fmt

Animation format. Possible values are GIF and HTML

filename

File name.

png_keyword

A keyword name for the png images generated by the function

extra_legend

A legend to add to the animation.

bg_color

Color for unsuitable pixels. Default "#F6F2E5".

suit_color

Color for suitable pixels. Default "#0076BE".

occupied_color

Color for occupied pixels. Default "#03C33F".

gif_vel

A value that regulates the velocity of frame transitions. The bigger it is the transition will be slower default 0.8

ani.width

Animation width unit in px

ani.height

Animation height unit in px

ani.res

Animation resolution unit in px

Details

The animation can be saved in a GIF or HTML format. Note that the generation of the GIF can be time consuming for large simulation (simulations with more than 60 time steps).

Value

A RasterStack of species' distribution at each simulation step

Author(s)

Luis Osorio-Olvera & Jorge Soberón

Examples

model_path <- system.file("extdata/Lepus_californicus_cont.tif",
                          package = "bamm")
model <- raster::raster(model_path)
sparse_mod <- bamm::model2sparse(model,0.1)
adj_mod <- bamm::adj_mat(sparse_mod,ngbs=2)
occs_lep_cal <- data.frame(longitude = c(-115.10417,
                                         -104.90417),
                           latitude = c(29.61846,
                                        29.81846))
occs_sparse <- bamm::occs2sparse(modelsparse = sparse_mod,
                                occs = occs_lep_cal)
sdm_lep_cal <- bamm::sdm_sim(set_A = sparse_mod,
                            set_M = adj_mod,
                            initial_points = occs_sparse,
                            nsteps = 50)

if(requireNamespace("animation")){
ani_name <- tempfile(pattern = "simulation_",fileext = ".html")
#sdm_lep_cal_st <- bamm::sim2Animation(sdm_simul = sdm_lep_cal,
#                                      which_steps = seq(1,50,by=1),
#                                      fmt = "HTML",ani.width = 1200,
#                                      ani.height = 1200,
#                                      filename = ani_name)
}