kempton.rowcol: Row-column experiment of wheat

In kwstat/agridat: Agricultural Datasets

Row-column experiment of wheat

Description

Row-column experiment of wheat, 35 genotypes, 2 reps.

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

## Not run: 

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

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


# Model with rep, row, col as random.  Kempton, page 62.
# Use "-1" so that the vcov matrix doesn't include intercept
libs(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)

kwstat/agridat documentation built on Nov. 2, 2024, 6:19 a.m.