Multi-environment trial of cock's foot, heading dates for 25 varieties in 7 years

Multi-environment trial of cock's foot, heading dates for 25 varieties in 7 yearsyears

data("piepho.cocksfoot")

Format

A data frame with 111 observations on the following 3 variables.

gen

genotype factor, 25 levels

year

year, numeric

date

heading date (days from April 1)

Details

These data are heading dates (days from April 1 to heading) of 25 cock's foot Dactylis glomerata varieties in trials at Hannover, Germany, repeated over seven years. Values are means over replications.

Piepho fits a model similar to Finlay-Wilkinson regression, but with genotype and environment swapped.

Source

Hans-Pieter Piepho. (1999). Fitting a Regression Model for Genotype-by-Environment Data on Heading Dates in Grasses by Methods for Nonlinear Mixed Models. Biometrics, 55, 1120-1128. https://doi.org/10.1111/j.0006-341X.1999.01120.x

Examples

# \dontrun{
  
  library(agridat)
  data(piepho.cocksfoot)
  dat <- piepho.cocksfoot
  dat$year <- factor(dat$year)
  
  libs(lattice)
  # Gaussian, not gamma distn
  densityplot(~date|year, data=dat, main="piepho.cocksfoot - heading date")
  
  libs(mumm) # The mumm package can reproduce Piepho's results
#> 
#> Attaching package: 'mumm'
#> The following object is masked from 'package:asreml':
#> 
#>     lrt

  levelplot(date ~ year*gen, dat)
  # note mp(random,fixed)
  mod3 <- mumm(date ~ -1 + gen + (1|year) + mp(year, gen), dat)
  
  # Compare to Piepho table 3, "full maximum likelihood"
  mod3$sigmas^2 # variances for year:gen, residual match
#>        year mp year:gen    Residual 
#> 17.70292945  0.02944156  0.49024751 
  #        year mp year:gen    Residual 
  # 17.70287377  0.02944158  0.49024737
  
  # mod3$par_fix # fixed genotypes match
  
  # mod3$sdreport # estim/stderr
  #               Estimate Std. Error
  # nu          49.0393183 1.55038652
  # nu          42.0889493 1.67597832
  # nu          45.3411252 1.59818620
  # etc
  
  # mod3$par_rand # random year:gen match
  # $`mp year:gen`
  #        1990        1991        1992        1993        1994        1995 
  #  0.10595661 -0.05298523  0.08228274 -0.09629696 -0.11045540  0.29637268 
  
# }