Estimation of Generalized Linear Gaussian Process Models
glgpm.Rd
Fits generalized linear Gaussian process models to spatial data, incorporating spatial Gaussian processes with a Matern correlation function. Supports Gaussian, binomial, and Poisson response families.
Usage
glgpm(
formula,
data,
family,
distr_offset = NULL,
cov_offset = NULL,
crs = NULL,
convert_to_crs = NULL,
scale_to_km = TRUE,
control_mcmc = set_control_sim(),
par0 = NULL,
S_samples = NULL,
return_samples = TRUE,
messages = TRUE,
fix_var_me = NULL,
start_pars = list(beta = NULL, sigma2 = NULL, tau2 = NULL, phi = NULL, sigma2_me =
NULL, sigma2_re = NULL)
)
Arguments
- formula
A formula object specifying the model to be fitted. The formula should include fixed effects, random effects (specified using
re()
), and spatial effects (specified usinggp()
).- data
A data frame or sf object containing the variables in the model.
- family
A character string specifying the distribution of the response variable. Must be one of "gaussian", "binomial", or "poisson".
- distr_offset
Optional offset for binomial or Poisson distributions. If not provided, defaults to 1 for binomial.
- cov_offset
Optional numeric vector for covariate offset.
- crs
Optional integer specifying the Coordinate Reference System (CRS) if data is not an sf object. Defaults to 4326 (long/lat).
- convert_to_crs
Optional integer specifying a CRS to convert the spatial coordinates.
- scale_to_km
Logical indicating whether to scale coordinates to kilometers. Defaults to TRUE.
- control_mcmc
Control parameters for MCMC sampling. Must be an object of class "mcmc.RiskMap" as returned by
set_control_sim
.- par0
Optional list of initial parameter values for the MCMC algorithm.
- S_samples
Optional matrix of pre-specified sample paths for the spatial random effect.
- return_samples
Logical indicating whether to return MCMC samples when fitting a Binomial or Poisson model. Defaults to FALSE.
- messages
Logical indicating whether to print progress messages. Defaults to TRUE.
- fix_var_me
Optional fixed value for the measurement error variance.
- start_pars
Optional list of starting values for model parameters: beta (regression coefficients), sigma2 (spatial process variance), tau2 (nugget effect variance), phi (spatial correlation scale), sigma2_me (measurement error variance), and sigma2_re (random effects variances).
Value
An object of class "RiskMap" containing the fitted model and relevant information:
- y
Response variable.
- D
Covariate matrix.
- coords
Unique spatial coordinates.
- ID_coords
Index of coordinates.
- re
Random effects.
- ID_re
Index of random effects.
- fix_tau2
Fixed nugget effect variance.
- fix_var_me
Fixed measurement error variance.
- formula
Model formula.
- family
Response family.
- crs
Coordinate Reference System.
- scale_to_km
Indicator if coordinates are scaled to kilometers.
- data_sf
Original data as an sf object.
- kappa
Spatial correlation parameter.
- units_m
Distribution offset for binomial/Poisson.
- cov_offset
Covariate offset.
- call
Matched call.
Details
Generalized linear Gaussian process models extend generalized linear models (GLMs) by incorporating spatial Gaussian processes to account for spatial correlation in the data. This function fits GLGPMs using maximum likelihood methods, allowing for Gaussian, binomial, and Poisson response families. In the case of the Binomial and Poisson families, a Monte Carlo maximum likelihood algorithm is used.
The spatial Gaussian process is modeled with a Matern correlation function, which is flexible and commonly used in geostatistical modeling. The function supports both spatial covariates and unstructured random effects, providing a comprehensive framework to analyze spatially correlated data across different response distributions.
Additionally, the function allows for the inclusion of unstructured random effects, specified through the re()
term in the model formula. These random effects can capture unexplained variability at specific locations beyond the fixed and spatial covariate effects, enhancing the model's flexibility in capturing complex spatial patterns.
The convert_to_crs
argument can be used to reproject the spatial coordinates to a different CRS. The scale_to_km
argument scales the coordinates to kilometers if set to TRUE.
The control_mcmc
argument specifies the control parameters for MCMC sampling. This argument must be an object returned by set_control_sim
.
The start_pars
argument allows for specifying starting values for the model parameters. If not provided, default starting values are used.