Specify Gaussian process in occARU models

Specify Gaussian process (GP) random effects in occARU models, with a choice of kernel and whether to estimate species-level length-scales.

Usage

gp(
  kernel = c("exp_quad_cov", "matern32", "matern52"),
  species_length_scales = FALSE,
  periodic = FALSE,
  period = NULL
)

kernel: character. The type of GP kernel to use. Must be one of "exp_quad" (exponentiatated quadratic), "matern32" (Matern 3/2), or "matern52" (Matern 5/2).
species_length_scales: logical. If TRUE, species-specific length scales are estimated for that GP, each drawn independently from the shared length scale priors. Note that enabling this requires additional Cholesky decompositions per species and GP, which can substantially increase sampling time. If FALSE (default), only one length scale is estimated with one Cholesky decomposition performed per GP. Only used when multiple species are included.
periodic: logical. If TRUE, a periodic kernel is added to the kernel for survey effects. Default: FALSE.
period: Positive numeric. Period length in survey units (i.e. number of survey periods per cycle). Only used when periodic = TRUE. Defaults to 365 / survey_length, corresponding to an annual cycle. For example, with survey_length = 7 the default is period = 52.1. Override if your data span a different temporal cycle.

A gp object (a named list with class "gp") for use in the random argument of occARU(). Contains the following elements:

random: Integer. Always 1L, indicating a random effect.
kernel: Integer. Kernel index (1 = exponentiated quadratic, 2 = Matern 3/2, 3 = Matern 5/2).
species_length_scales: Integer. Whether to estimate species-specific length scales (0 or 1).
periodic: Integer. Whether a periodic kernel component is included (0 or 1).
period: Numeric. Period length in survey units, or 0 if not periodic.