agridat (version 1.23)

tesfaye.millet: Multi-environment trial of millet

Description

Multi-environment trial of millet

Usage

data("tesfaye.millet")

Format

A data frame with 415 observations on the following 9 variables.

year

year

site

site (location)

rep

replicate

col

column ordinate

row

row ordinate

plot

plot number

gen

genotype

entry_number

entry

yield

yield, kg/ha

Details

Experiments conducted at Bako and Assosa research centers in Ethiopia. The data has: 4 years, 2 sites = 7 environments, 2-3 reps per trial, 47 genotypes.

Tesfaye et al used asreml to fit a GxE model with Factor Analytic covariance structure for the GxE part and AR1xAR1 for spatial residuals at each site.

Data in PloS ONE was published under Creative Commons Attribution License.

References

None

Examples

if (FALSE) {

  library(agridat)
  data(tesfaye.millet)
  dat <- tesfaye.millet

  dat <- transform(dat, year=factor(year), site=factor(site))
  libs(dplyr,asreml,lucid)
  dat <- mutate(dat,
                env=factor(paste0(site,year)),
                gen=factor(gen),
                rep=factor(rep),
                xfac=factor(col), yfac=factor(row))
  libs(desplot)
  desplot(dat, yield~col*row|env, main="tesfaye.millet")
  dat <- arrange(dat, env, xfac, yfac)

  # Fixed environment
  # Random row/col within environment, Factor Analytic GxE
  # AR1xAR1 spatial residuals within each environment
  if(require("asreml", quietly=TRUE)){
    libs(asreml)
    m1 <- asreml(yield ~ 1 + env,
                 data=dat,
                 random = ~  at(env):xfac + at(env):yfac + gen:fa(env),
                 residual = ~ dsum( ~ ar1(xfac):ar1(yfac)|env) )
    m1 <- update(m1)
    lucid::vc(m1)
  }

}