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

In agridat: Agricultural Datasets

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.

Source

Besag, J. E., Green, P. J., Higdon, D. and Mengersen, K. (1995). Bayesian computation and stochastic systems. Statistical Science, 10, 3-66. https://www.jstor.org/stable/2246224

References

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

Examples

## Not run: 
  
  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))
  }

## End(Not run) 

agridat documentation built on Oct. 27, 2024, 5:07 p.m.