This function generates holes (regions of low probability) in a spatial simulation object based on user-defined parameters. The function uses a kernel density estimate to simulate holes, and returns a modified version of the input object with the holes added. The function also has options to compute a density heatmap and to assign points within the holes to be dropped or kept based on a scaled probability value.
Usage
GenerateHoles(
sim_object,
xmin = NA,
xmax = NA,
ymin = NA,
ymax = NA,
sdmin = 1/2,
sdmax = 2,
hole_prob = c(0.2, 0.35),
force = FALSE,
density_heatmap = FALSE,
step_size = 1,
cores = 1,
overwrite = FALSE,
use_window = FALSE
)Arguments
- sim_object
A spatial simulation object of class
SpatSimObj- xmin
Minimum x-coordinate for the holes (default: NA)
- xmax
Maximum x-coordinate for the holes (default: NA)
- ymin
Minimum y-coordinate for the holes (default: NA)
- ymax
Maximum y-coordinate for the holes (default: NA)
- sdmin
Minimum standard deviation for the kernels (default: 1/2)
- sdmax
Maximum standard deviation for the kernels (default: 2)
- hole_prob
A vector of length 2 with the minimum and maximum probabilities of a point being within a hole (default: c(0.2, 0.35))
- force
Logical; if TRUE, forces the function to simulate outside the window boundaries (default: FALSE)
- density_heatmap
Logical; if TRUE, computes a density heatmap (default: FALSE)
- step_size
The step size for the grid (default: 1)
- cores
The number of cores to use for parallel processing (default: 1)
- overwrite
boolean to replace holes if they have been simulated previously
- use_window
boolean whether to use the simulation window to set x and y limits
Details
The function first checks that the input object is of the correct class, and that no parameters are NULL. If any parameters are NULL, the function stops with an error message. If the x- and y-ranges for the holes extend beyond the boundaries of the simulation window, the function also stops with an error message, unless the force parameter is set to TRUE. The function then produces kernel parameter lists for each simulated pattern, and generates a grid based on the user-defined step size. If density_heatmap is set to TRUE, the function computes a density heatmap using the CalculateGrid function. Finally, the function computes hole probabilities for each simulated pattern, assigns each point to be dropped or kept based on a scaled probability value, and returns the modified simulation object.
Examples
sim_object <- CreateSimulationObject()
#> No `window` specified - defaulting to x (0, 10); y (0, 10)
#simulate points
sim_object <- GenerateSpatialPattern(sim_object, lambda = 20)
# Generate tissue with default parameters
sim_object <- GenerateTissue(sim_object)
#> Computing tissue probability
#>
| | 0%, ETA NA
|==================== | 33%, ETA 00:02
|======================================= | 67%, ETA 00:01
|=======================================================| 100%, Elapsed 00:02
# Generate holes in the simulation object
sim_object <- GenerateHoles(sim_object, hole_prob = c(0.1, 0.3), force = TRUE)
#> Computing hole probability
#>
| | 0%, ETA NA
|==================== | 33%, ETA 00:01
|======================================= | 67%, ETA 00:00
|=======================================================| 100%, Elapsed 00:01