func.cl.ord: Composite Likelihood Calculation for Spatial Ordinal Data
In clespr: Composite Likelihood Estimation for Spatial Data

Description Usage Arguments Value References Examples

func.cl.ord calculates the composite log-likelihood for spatial ordered probit models.

1	func.cl.ord(vec.yobs, mat.X, mat.lattice, radius, n.cat, vec.par)

`vec.yobs`	a vector of observed responses for all N sites.
`mat.X`	regression (design) matrix, including intercepts.
`mat.lattice`	a data matrix containing geographical information of sites. The i th row constitutes a set of geographical coordinates.
`radius`	weight radius.
`n.cat`	number of categories, at least 2.
`vec.par`	a vector of parameters consecutively as follows: a series of cutoffs (excluding -Inf, 0 and Inf) for latent responses, a vector of covariate parameters, a parameter 'sigmasq' modeling covariance matrix, 0<=sigmasq<=1, and a parameter 'rho' reflecting spatial correlation, abs(rho)<=1.

func.cl.ord returns a list: number of categories, sum of weights, composite log-likelihood, a vector of scores, and a matrix of first-order partial derivatives for vec.par.

Feng, Xiaoping, Zhu, Jun, Lin, Pei-Sheng, and Steen-Adams, Michelle M. (2014) Composite likelihood Estimation for Models of Spatial Ordinal Data and Spatial Proportional Data with Zero/One values. Environmetrics 25(8): 571–583.

# True parameter
vec.cutoff <- 2; vec.beta <- c(1, 2, 1, 0, -1); sigmasq <- 0.8; rho <- 0.6; radius <- 5
vec.par <- c(vec.cutoff, vec.beta, sigmasq, rho)

# Coordinate matrix
n.cat <- 3; n.lati <- 30; n.long <- 30
n.site <- n.lati * n.long
mat.lattice <- cbind(rep(1:n.lati, n.long), rep(1:n.long, each=n.lati))
mat.dist <- as.matrix(dist(mat.lattice, upper=TRUE, diag=TRUE))
mat.cov <- sigmasq * rho^mat.dist

set.seed(1228)
# Generate regression (design) matrix with intercept
mat.X <- cbind(rep(1, n.site),scale(matrix(rnorm(n.site*(length(vec.beta)-1)),nrow=n.site)))
vec.Z <- t(chol(mat.cov)) %*% rnorm(n.site) + mat.X %*% vec.beta
vec.epsilon <- diag(sqrt(1-sigmasq), n.site) %*% rnorm(n.site)
vec.ylat <- as.numeric(vec.Z + vec.epsilon)

# Convert to the vector of observation
vec.yobs <- func.obs.ord(vec.ylat, vec.alpha=c(-Inf,0,vec.cutoff,Inf))

# Using func.cl.ord()
ls <- func.cl.ord(vec.yobs, mat.X, mat.lattice, radius, n.cat, vec.par)
ls$log.lkd