agridat (version 1.8.1)

besag.bayesian: Spring barley in United Kingdom

Description

An experiment with 75 varieties of barley, planted in 3 reps.

source

Besag, J. E., Green, P. J., Higdon, D. and Mengersen, K. (1995). Bayesian computation and stochastic systems. Statistical Science, 10, 3-66.

Details

RCB design, each column is one rep.

References

Davison, A. C. (2003). Statistical Models. Cambridge University Press. Pages 534-535.

Examples

dat <- besag.bayesian

# Yield values were scaled to unit variance
var(dat$yield, na.rm=TRUE)

# Besag Fig 2. Reverse row numbers to match Besag, Davison
dat$rrow <- 76 - dat$row
library("lattice")
xyplot(yield ~ rrow|col, dat, layout=c(1,3), type='s')

# Use asreml to fit a model with AR1 gradient in rows
require(asreml)
dat <- transform(dat, cf=factor(col), rf=factor(rrow))
m1 <- asreml(yield ~ -1 + gen, data=dat, random=~ar1v(rf))

# Visualize trends, similar to Besag figure 2.
dat$res <- resid(m1)
dat$geneff <- coef(m1)$fixed[as.numeric(dat$gen)]
dat <- transform(dat, fert=yield-geneff-res)
xyplot(geneff ~ rrow|col, dat, layout=c(1,3), type='s',
       main="Variety effects", ylim=c(5,15 ))
xyplot(fert ~ rrow|col, dat, layout=c(1,3), type='s',
       main="Fertility", ylim=c(-2,2))
xyplot(res ~ rrow|col, dat, layout=c(1,3), type='s',
       main="Residuals", ylim=c(-4,4))