connolly.potato {agridat} | R Documentation

## Potato yields in single-drill plots

### Description

Potato yields in single-drill plots

### Usage

    data("connolly.potato")

### Format

A data frame with 80 observations on the following 6 variables.

`rep`

  block

`gen`

  variety

`row`

  row

`col`

  column

`yield`

  yield, kg/ha

`matur`

  maturity group

### Details

Connolly et el use this data to illustrate how yield can be affected by competition from neighboring plots.

This data uses M1, M2, M3 for maturity, while Connolly et al use FE (first early), SE (second early) and M (maincrop).

The trial was 20 sections, each of which was an independent row of 20 drills. The data here are four reps of single-drill plots from sections 1, 6, 11, and 16.

The neighbor covariate for a plot is defined as the average of the plots to the left and right. For drills at the edge of the trial, the covariate was the average of the one neighboring plot yield and the section (i.e. rep) mean.

It would be interesting to fit a model that uses differences in maturity between a plot and its neighbor as the actual covariate. Anyone...?

### Source

Connolly, T and Currie, ID and Bradshaw, JE and McNicol, JW. (1993). Inter-plot competition in yield trials of potatoes Solanum tuberosum L. with single-drill plots. Annals of Applied Biology, 123, 367-377.

http://doi.org/10.1111/j.1744-7348.1993.tb04099.x

Used with permission of Iain Currie.

### Examples

    data(connolly.potato)
    dat <- connolly.potato

    # Field plan
    if(require(desplot)){
      desplot(yield~col*row, data=dat,
              out1=rep, # aspect unknown
              main="connolly.potato yields (reps not contiguous)")
    }

    # Later maturities are higher yielding
    require(lattice)
    bwplot(yield~matur, dat, main="connolly.potato yield by maturity")

    # Observed raw means. Matches Connolly table 2.
    mn <- aggregate(yield~gen, data=dat, FUN=mean)
    mn[rev(order(mn$yield)),]

    # Create a covariate which is the average of neighboring plot yields
    if(require(reshape2)){
    mat <- acast(dat, row~col, value.var='yield')
    mat2 <- matrix(NA, nrow=4, ncol=20)
    mat2[,2:19] <- (mat[ , 1:18] + mat[ , 3:20])/2
    mat2[ , 1] <- (mat[ , 1] + apply(mat, 1, mean))/2
    mat2[ , 20] <- (mat[ , 20] + apply(mat, 1, mean))/2
    dat2 <- melt(mat2)
    colnames(dat2) <- c('row','col','cov')
    dat <- merge(dat, dat2)
    # xyplot(yield ~ cov, data=dat, type=c('p','r'))

    # Connolly et al fit a model with avg neighbor yield as a covariate
    m1 <- lm(yield ~ 0 + gen + rep + cov, data=dat)
    coef(m1)['cov'] # = -.303  (Connolly obtained -.31)

    # Block names and effects
    bnm <- c("R1","R2","R3","R4")
    beff <- c(0, coef(m1)[c('repR2','repR3','repR4')])
    # Variety names and effects
    vnm <- paste0("V", formatC(1:20, width=2, flag='0'))
    veff <- coef(m1)[1:20]

    # Adjust yield for variety and block effects
    dat <- transform(dat, yadj = yield - beff[match(rep,bnm)]
                    - veff[match(gen,vnm)])

    # Similar to Connolly Fig 1.  Point pattern doesn't quite match
    xyplot(yadj~cov, data=dat, type=c('p','r'),
           main="connolly.potato",
           xlab="Avg yield of nearest neighbors",
           ylab="Yield, adjusted for variety and block effects")
    }

[Package agridat version 1.16 Index]