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Gaussian process spatial structure (NNGP)

Source: R/spatial_gp.R
spatial_gp.Rd

Specify a Gaussian-process spatial random effect, approximated with a nearest-neighbour GP (NNGP) for scalability. Captures smooth spatial variation from point-referenced coordinates.

Usage

spatial_gp(
  coords,
  approx = c("nngp", "hsgp"),
  cov = c("exponential", "matern"),
  nu = 1.5,
  nn = 15,
  m = 6,
  c = 1.5,
  sigma_prior_U = 1,
  sigma_prior_alpha = 0.01,
  shared = NULL,
  scale_coords = TRUE,
  parameterization = c("noncentered", "centered", "collapsed")
)

Arguments

coords

A formula (~ lon + lat) or character vector naming the coordinate variables in the data. With approx = "nngp" the coordinate DIMENSION is however many are named: two for a map, one for a transect or a depth profile, three for a depth-resolved domain. The neighbour graph and the neighbour covariance both read every column. approx = "hsgp" takes exactly two, and so does any sampler mode, because both store coordinates at a fixed 2-D stride.

approx

GP approximation: "nngp" (default, a nearest-neighbour GP with the cov / nu / nn arguments) or "hsgp" (a Hilbert-space basis GP with m functions per dimension and boundary factor c).

cov

Covariance function (NNGP only). One of "exponential" or "matern".

nu

Matern smoothness parameter, one of 1.5 or 2.5. Used only when cov = "matern" (nu = 0.5 is cov = "exponential").

nn

Number of nearest neighbours used in the NNGP approximation.

m

Number of HSGP basis functions per dimension (approx = "hsgp").

c

HSGP boundary factor, >= 1 (approx = "hsgp").

sigma_prior_U, sigma_prior_alpha

Penalized-complexity prior on the field's marginal standard deviation (approx = "hsgp"), calibrated so that P(sigma > sigma_prior_U) = sigma_prior_alpha. Defaults to P(sigma > 1) = 0.01. sigma_prior_U must be positive and sigma_prior_alpha must lie in (0, 1).

shared

Whether the spatial effect is shared across processes in a multi-process model. NULL (default) shares the effect; FALSE fits process-specific effects and emits a warning.

scale_coords

Logical. Standardize coordinates before fitting (default TRUE).

parameterization

Latent parameterization for the exact-NUTS field. One of "noncentered" (default; samples z ~ N(0, I) and reconstructs the field as w = f(z, sigma2, phi), avoiding the field/hyperparameter funnel), "centered" (places the NNGP density on the field directly), or "collapsed" (deprecated).

Value

A tulpa_gp object (also of class tulpa_spatial).

See also

spatial_car(), spatial_bym2() for areal spatial effects.

Examples

# GP spatial specification from coordinate columns
spatial_gp(~ lon + lat)
spatial_gp(~ lon + lat, cov = "matern", nu = 1.5)