ramps.control: Auxiliary for Controlling georamps Model Fitting

Description

Auxiliary function that provides a user interface to control the georamps model fitting algorithm.

Usage

ramps.control(iter = 1000, beta, sigma2.e, phi, sigma2.z, sigma2.re,
                 z.monitor = TRUE, file)

Arguments

iter

numerical value indicating monitoring of all sample iterations up to that point, or a vector containing specific iterations to monitor.

beta

'param' object of initial values and hyperparameters for the main effects coefficients. Flat priors are currently supported for these parameters. Argument is optional if no main effects appear in the model.

sigma2.e

'param' object of initial values and hyperparameters for the measurement error variances. Inverse-gamma priors are currently supported. Argument is optional if no measurement error variances appear in the model.

phi

'param' object of initial values and hyperparameters for the spatial correlation parameters. Uniform priors are currently supported. Argument is optional if no correlation parameters appear in the model.

sigma2.z

'param' object of initial values and hyperparameters for the spatial variances. Inverse-gamma priors are currently supported. Argument is optional if no spatial variances appear in the model.

sigma2.re

'param' object of initial values and hyperparameters for the random effects variances. Inverse-gamma priors are currently supported. Argument is optional if no random effects appear in the model.

z.monitor

logical value indicating whether to monitor the latent spatial parameters, or data frame containing a subset of the coordinates at which to monitor the parameters.

file

vector or list of character strings specifying external files to which to save monitored parameters. Elements of the object named params and z will be taken to be the output files for model parameters and latent paramete

Value

A list containing the following components:
itersorted numerical vector of unique MCMC iterations to be monitored.
beta'param' object of initial values for the main effects coefficients.
sigma2.e'param' object of initial values for the measurement error variances.
phi'param' object of initial values for the spatial correlation parameters.
sigma2.z'param' object of initial values for the spatial variances.
sigma2.re'param' object of initial values for the random effects variances.
zlist with element: monitor containing a logical monitoring indicator for the latent spatial parameters or a data frame of coordinates at which to monitor the parameters.
filelist with elements: params and z character strings specifying external files to which to save monitored model and spatial parameters.
expandnon-negative integer value indicating the starting point of the MCMC sampler, initialized to zero.

Details

Tuning parameters may be set for the sigma2 and phi arguments via the param function. These are used in the MCMC algorithm as factors by which the widths of the slice sampling windows are multiplied. Separate tuning parameters may be set for each of the arguments. However, only the minimum of user-specified sigma2 tuning parameters is used in the sampling of those model parameters.

Examples

Run this code

ctrl <- ramps.control(
   iter = seq(1, 100, by = 2),
   beta = param(rep(0, 2), "flat"),
   sigma2.e = param(rep(1, 2), "invgamma", shape = 2.0, scale = 0.1),
   phi = param(10, "uniform", min = 0, max = 100, tuning = 0.5),
   sigma2.z = param(1, "invgamma", shape = 2.0, scale = 0.1),
   file = c("params.txt", "z.txt")
)