kempton.rowcol {agridat} | R Documentation

## Wheat row-column experiment

### Description

Wheat yields of 35 genotypes, 2 reps, planted in a row-column design. Two plots are missing.

### Format

A data frame with 68 observations on the following 5 variables.

`rep`

  replicate factor, 2 levels

`row`

  row

`col`

  column

`gen`

  genotype factor, 35 levels

`yield`

  yield

### Details

Included to illustrate REML analysis of a row-column design.

### Source

R A Kempton and P N Fox, Statistical Methods for Plant Variety Evaluation, Chapman and Hall, 1997.

### Examples

    data(kempton.rowcol)
    dat <- kempton.rowcol
    dat <- transform(dat, rowf=factor(row), colf=factor(col))

    if(require(desplot)){
      desplot(yield~col*row|rep, dat,
              num=gen, out1=rep, # unknown aspect
              main="kempton.rowcol")
    }

    ## Not run:
      # Model with rep, row, col as random.  Kempton, page 62.
      # Use "-1" so that the vcov matrix doesn't include intercept
      require(lme4)
      m1 <- lmer(yield ~ -1 + gen + rep + (1|rep:rowf) + (1|rep:colf), data=dat)

      # Variance components match Kempton.
      print(m1, corr=FALSE)

      # Standard error of difference for genotypes.  Kempton page 62, bottom.
      covs <- as.matrix(vcov(m1)[1:35, 1:35])
      vars <- diag(covs)
      vdiff <- outer(vars, vars, "+") - 2 * covs
      sed <- sqrt(vdiff[upper.tri(vdiff)])
      min(sed) # Minimum SED
      mean(sed) # Average SED
      max(sed) # Maximum SED

    ## End(Not run)

[Package agridat version 1.16 Index]