agridat (version 1.16)

besag.beans: Competition experiment in beans with height measurements

Description

Competition experiment in beans with height measurements

Usage

data("besag.beans")

Format

A data frame with 152 observations on the following 6 variables.

gen

genotype / variety

height

plot height, cm

yield

plot yield, g

row

row / block

rep

replicate factor

col

column

Details

Field beans of regular height were grown beside shorter varieties. In each block, each variety occurred once as a left-side neighbor and once as a right-side neighbor of every variety (including itself). Border plots were placed at the ends of each block. Each block with 38 adjacent plots. Each plot was one row, 3 meters long with 50 cm spacing between rows. No gaps between plots. Spacing between plants was 6.7 cm. Four blocks (rows) were used, each with six replicates.

Plot yield and height was recorded.

Kempton and Lockwood used models that adjusted yield according to the difference in height of neighboring plots.

Field length: 4 plots * 3m = 12m

Field width: 38 plots * 0.5 m = 19m

References

Kempton, RA and Lockwood, G. (1984). Inter-plot competition in variety trials of field beans (Vicia faba L.). The Journal of Agricultural Science, 103, 293--302.

Examples

# NOT RUN {
data(besag.beans)
dat = besag.beans

if(require(desplot)){
  desplot(yield ~ col*row, data=dat,
          aspect=12/19, out1=row, out2=rep, num=gen, cex=1, # true aspect
          main="besag.beans")
}

if(require(reshape2)){
  # Add a covariate = excess height of neighbors
  mat <- acast(dat, row~col, value.var='height')
  mat2 <- matrix(NA, nrow=4, ncol=38)
  mat2[,2:37] <- (mat[,1:36] + mat[,3:38] - 2*mat[,2:37])
  dat2 <- melt(mat2)
  colnames(dat2) <- c('row','col','cov')
  dat <- merge(dat, dat2)
  
  # Drop border plots
  dat <- subset(dat, rep != 'R0')
  
  require(lattice)
  # Plot yield vs neighbors height advantage
  xyplot(yield~cov, data=dat, group=gen,
         main="besag.beans",
         xlab="Mean excess heights of neighbor plots",
         auto.key=list(columns=3))
  
  # Trial mean.
  mean(dat$yield) # 391 matches Kempton table 3
  
  # Mean excess height of neighbors for each genotype
  tapply(dat$cov, dat$gen, mean)/2 # Matches Kempton table 4

  # Variety means, matches Kempton table 4 mean yield
  m1 <- lm(yield ~ -1 + gen, dat)
  coef(m1)

  # Full model used by Kempton, eqn 5.  Not perfectly clear.
  # Appears to include rep term, perhaps within block
  dat$blk <- factor(dat$row)
  dat$blkrep <- factor(paste(dat$blk, dat$rep))
  m2 <- lm(yield ~ -1 + gen + blkrep + cov, data=dat)
  coef(m2) # slope 'cov' = -.72, while Kempton says -.79
}


# }