PrepareINLAFunc: Prepare for running INLA functio

In PointProcess/SealPupProduction-JRSSC-code:

Description

Gathers and stacks the input to the INLA function

Usage

PrepareINLAFunc(
  mesh,
  covMesh,
  obsLoc,
  y.pp,
  e.pp,
  covGrid,
  spatial = TRUE,
  covariate.fitting = "quadratic",
  additional.iid.term = FALSE,
  Matern.alpha = 2,
  covariates.type = "band1",
  INLA.theta.startval = NULL,
  INLA.constr = TRUE
)

Arguments

mesh	Mesh object, being the output from inla.mesh.2d
covMesh	Mesh object representing the mesh for the covariate when applicable, being the output from inla.mesh.1d
obsLoc	Matrix with at least two columns specifying, respectively, the x- and y-coordinates of the observations
y.pp	Numeric vector, indicating number of counts at each of the locations
e.pp	Numeric vector, indicating the weight to be assigned to each location
covGrid,	im object representing the covariate values on a dense grid where the counts live.
spatial	Logical indicating whether a spatial spde model should be used
covariate.fitting	String, indicating how to model covariates. "no", "linear", "quadratic" (default), "linAndLog" or "nonlinear"
additional.iid.term	Logical, indicating whether to include an additional iid (Gaussian) term in the latent field specification. FALSE is default
Matern.alpha	Numeric, corresponding to the alpha parameter in the Matern covariance function (2 is the default)
covariates.type	String equal to "band1" or "band2" indicating which of the bands from the satellite data should be used.
INLA.theta.startval	List containing the start values for the theta parameter in the INLA run. (NULL indicates that automatic start values should be used, and is the default)

Value

List with all variables necessary to run the INLA function, in addition to the spde object

PointProcess/SealPupProduction-JRSSC-code documentation built on Jan. 27, 2020, 10:06 p.m.