agridat (version 1.23)

besag.bayesian: RCB experiment of spring barley in United Kingdom

Description

RCB experiment of spring barley in United Kingdom

Format

A data frame with 225 observations on the following 4 variables.

col

column (also blocking factor)

row

row

yield

yield

gen

variety/genotype

Details

RCB design, each column is one rep.

Used with permission of David Higdon.

References

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

Examples

if (FALSE) {
  
  library(agridat)
  data(besag.bayesian)
  dat <- besag.bayesian

  # Yield values were scaled to unit variance
  # var(dat$yield, na.rm=TRUE)
  # .999

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

  if(require("asreml", quietly=TRUE)) {
    libs(asreml, lucid)

    # Use asreml to fit a model with AR1 gradient in rows  
    dat <- transform(dat, cf=factor(col), rf=factor(rrow))
    m1 <- asreml(yield ~ -1 + gen, data=dat, random= ~ rf)
    m1 <- update(m1, random= ~ ar1v(rf))
    m1 <- update(m1)
    m1 <- update(m1)
    m1 <- update(m1)
    lucid::vc(m1)
  
    # Visualize trends, similar to Besag figure 2.
    # Need 'as.vector' because asreml uses a named vector
    dat$res <- unname(m1$resid)
    dat$geneff <- coef(m1)$fixed[as.numeric(dat$gen)]
    dat <- transform(dat, fert=yield-geneff-res)
    libs(lattice)
    xyplot(geneff ~ rrow|col, dat, layout=c(1,3), type='s',
           main="besag.bayesian - Variety effects", ylim=c(5,15 ))
    xyplot(fert ~ rrow|col, dat, layout=c(1,3), type='s',
           main="besag.bayesian - Fertility", ylim=c(-2,2))
    xyplot(res ~ rrow|col, dat, layout=c(1,3), type='s',
           main="besag.bayesian - Residuals", ylim=c(-4,4))
  }
}