rSPDE model index vector generation — rspde.make.index • rSPDE

Generates a list of named index vectors for an rSPDE model.

Usage

rspde.make.index(
  name,
  n.spde = NULL,
  n.group = 1,
  n.repl = 1,
  mesh = NULL,
  rspde.order = 1,
  nu = NULL,
  dim = NULL
)

Arguments

name: A character string with the base name of the effect.
n.spde: The number of basis functions in the mesh model.
n.group: The size of the group model.
n.repl: The total number of replicates.
mesh: An inla.mesh, an inla.mesh.1d object or a metric_graph object.
rspde.order: The order of the rational approximation
nu: If NULL, then the model will assume that nu will be estimated. If nu is fixed, you should provide the value of nu.
dim: the dimension of the domain. Should only be provided if mesh is not provided.

Value

A list of named index vectors.

name: Indices into the vector of latent variables
name.group: 'group' indices
name.repl: Indices for replicates

Examples

# \donttest{
if (rspde_safe_inla()) {
  library(INLA)

  set.seed(123)

  m <- 100
  loc_2d_mesh <- matrix(runif(m * 2), m, 2)
  mesh_2d <- inla.mesh.2d(
    loc = loc_2d_mesh,
    cutoff = 0.05,
    max.edge = c(0.1, 0.5)
  )
  sigma <- 1
  range <- 0.2
  nu <- 0.8
  kappa <- sqrt(8 * nu) / range
  op <- matern.operators(
    mesh = mesh_2d, nu = nu,
    range = range, sigma = sigma, m = 2,
    parameterization = "matern"
  )
  u <- simulate(op)
  A <- inla.spde.make.A(
    mesh = mesh_2d,
    loc = loc_2d_mesh
  )
  sigma.e <- 0.1
  y <- A %*% u + rnorm(m) * sigma.e
  Abar <- rspde.make.A(mesh = mesh_2d, loc = loc_2d_mesh)
  mesh.index <- rspde.make.index(name = "field", mesh = mesh_2d)
  st.dat <- inla.stack(
    data = list(y = as.vector(y)),
    A = Abar,
    effects = mesh.index
  )
}
# }