sim_ays_covar_spde: Simulate age-year-space covariance using SPDE approach

In SimSurvey: Test Surveys by Simulating Spatially-Correlated Populations

Simulate age-year-space covariance using SPDE approach

Description

Returns a function to use inside sim_distribution to generate the error term.

Usage

sim_ays_covar_spde(
  sd = 2.8,
  range = 300,
  model = "spde",
  phi_age = 0.5,
  phi_year = 0.9,
  group_ages = 5:20,
  group_years = NULL,
  mesh,
  barrier.triangles
)

Arguments

sd	Variance (can be age specific)
range	Decorrelation range
model	String indicating "barrier" or "spde" to generate Q with
phi_age	Defines autocorrelation through ages. Can be one value or a vector of the same length as ages.
phi_year	Defines autocorrelation through years. Can be one value or a vector of the same length as years.
group_ages	Make space-age-year variance equal across these ages
group_years	Make space-age-year variance equal across these years
mesh	The mesh used to generate the precision matrix
barrier.triangles	the set of triangles in the barrier of the mesh for the barrier model

Value

Returns a function for use in sim_distribution.

Examples

if (requireNamespace("INLA")) {

  ## Make a grid
  my_grid <- make_grid(res = c(10,10))

  ## Make a mesh based off it

  my_mesh <- make_mesh(my_grid)
  sim <- sim_abundance(ages = 1:10, years = 1:10) %>%
          sim_distribution(grid = my_grid,
                           ays_covar = sim_ays_covar_spde(phi_age = 0.8,
                                                          phi_year = 0.1,
                                                          model = "spde",
                                                          mesh = my_mesh),
                           depth_par = sim_parabola(mu = 200,
                                                    sigma = 50))
  plot_distribution(sim, ages = 1:5, years = 1:5, type = "heatmap")

}

SimSurvey documentation built on Sept. 19, 2023, 5:07 p.m.