sim_ays_covar_spde function

Simulate age-year-space covariance using SPDE approach

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

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

Returns

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")

}