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######################################################################
##
### Commentary: Estimate the effect of the rhizoctonia disease on
### yield using full Bayesian analysis.
##
######################################################################
library(geoBayes)
### Load the data
data(rhizoctonia)
rhiz <- na.omit(rhizoctonia)
rhiz$IR <- rhiz$Infected/rhiz$Total # Incidence rate of the
# rhizoctonia disease
### Define the model
corrf <- "spherical"
ssqdf <- 4
ssqsc <- 1
tsqdf <- 4
tsqsc <- 1
betm0 <- 0
betQ0 <- diag(.01, 2, 2)
phiprior <- c(200, 1, 1000, 100) # U(100, 300)
phisc <- .7
omgprior <- c(3, 1, 1000, 0) # U(0, 3)
omgsc <- 1
linkp <- 1
## MCMC parameters
Nout <- 1000
Nbi <- 3000
Nthin <- 10
samplt <- mcstrga(Yield ~ IR, data = rhiz,
atsample = ~ Xcoord + Ycoord, corrf = corrf,
Nout = Nout, Nthin = Nthin,
Nbi = Nbi, betm0 = betm0, betQ0 = betQ0,
ssqdf = ssqdf, ssqsc = ssqsc,
tsqdf = tsqdf, tsqsc = tsqsc,
corrprior = list(phi = phiprior, omg = omgprior),
linkp = linkp,
corrtuning = list(phi = phisc, omg = omgsc, kappa = 0),
test=100)
sample <- update(samplt, test = FALSE)
mcsamp <- mcmcmake(sample)
library(mcmcplots)
ipar <- grep(paste(c("phi", "tsq", "ssq", "beta(_[0-9]+)?", "omg"),
collapse = "|"), dimnames(mcsamp)[[2]])
traplot(mcsamp[, ipar])
denplot(mcsamp[, ipar])
summary(mcsamp[, ipar])
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