perry.springwheat {agridat} | R Documentation

## Multi-environment trial of wheat cultivars introduced 1860-1982.

### Description

Yields of wheat cultivars introduced 1860-1982. Grown in 20 environments.

### Usage

    data("perry.springwheat")

### Format

A data frame with 560 observations on the following 6 variables.

`yield`

  yield, kg/ha

`gen`

  genotype/cultivar factor, 28 levels

`env`

  environment factor, 20 levels

`site`

  site factor

`year`

  year, 1979-1982

`yor`

  year of release, 1860-1982

### Details

Twenty-eight of the most significant wheat cultivars of the past century in Western Australia, were grown in 20 field trials over 4 years in the Central and Eastern wheat-belt of Australia.

At the Wongan Hills site there were separate early and late sown trials in 1979 and 1980. Later sowing dates generally have lower yields.

Note: Although not indicated by the original paper, it may be that the Merredin site in 1979 also had early/late sowing dates.

### Source

MW Perry and MF D'Antuono. (1989). Yield improvement and associated characteristics of some Australian spring wheat cultivars introduced between 1860 and 1982. Australian Journal of Agricultural Research, 40(3), 457–472. http://www.publish.csiro.au/nid/43/issue/1237.htm

Used with permission of Mario D'Antuono and CSIRO Publishing.

### Examples

    data(perry.springwheat)
    dat <- perry.springwheat

    library(lattice)
    xyplot(yield~yor|env, dat, type=c('p','r'), xlab="year of release",
           main="perry.springwheat")

    # Show a table of sites*year
    # library(latticeExtra)
    # useOuterStrips(xyplot(yield~yor|site*factor(year), dat,
    #                       type=c('p','r')))

    # Perry reports a rate of gain of 5.8 kg/ha/year.  No model is given.
    # We fit a model with separate intercept/slope for each env
    m1 <- lm(yield ~ env + yor + env:yor, data=dat)
    # Average slope across environments
    mean(c(coef(m1)[21], coef(m1)[21]+coef(m1)[22:40]))
    ## [1] 5.496781

    # ----------------------------------------------------------------------------

    ## Not run:
      # Now a mixed-effects model.  Fixed overall int/slope.  Random env int/slope.

      # First, re-scale response so we don't have huge variances
      dat$y <- dat$yield / 100

      require(lme4)
      # Use || for uncorrelated int/slope.  Bad model.  See below.
      # m2 <- lmer(y ~ 1 + yor + (1+yor||env), data=dat)
      ## Warning messages:
      ## 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
      ##   Model failed to converge with max|grad| = 0.55842 (tol = 0.002, component 1)
      ## 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
      ##   Model is nearly unidentifiable: very large eigenvalue
      ##  - Rescale variables?;Model is nearly unidentifiable: large eigenvalue ratio
      ##  - Rescale variables?

      # Looks like lme4 is having trouble with variance of intercepts
      # There is nothing special about 1800 years, so change the
      # intercept -- 'correct' yor by subtracting 1800 and try again.
      dat$yorc <- dat$yor - 1800
      m3 <- lmer(y ~ 1 + yorc + (1+yorc||env), data=dat)

      # Now lme4 succeeds.  Rate of gain is 100*0.0549 = 5.49
      fixef(m3)
      ## (Intercept)        yorc
      ##  5.87492444  0.05494464

      # asreml3
      require(asreml)
      m3a <- asreml(y ~ 1 + yorc, data=dat, random = ~ env + env:yorc)

      require(lucid)
      vc(m3)
      ##      grp        var1 var2     vcov   sdcor
      ##      env (Intercept) <NA> 11.61    3.407
      ##    env.1        yorc <NA>  0.00063 0.02511
      ## Residual        <NA> <NA>  3.551   1.884

      vc(m3a)
      ##           effect component std.error z.ratio      con
      ##      env!env.var  11.61     4.385        2.6 Positive
      ## env:yorc!env.var   0.00063  0.000236     2.7 Positive
      ##       R!variance   3.551    0.2231      16   Positive

    ## End(Not run)

    # ----------------------------------------------------------------------------

[Package agridat version 1.16 Index]