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

Usage

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

if (FALSE) { # \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")

  if(require("mumm", quietly=TRUE)){
    libs(mumm) # The mumm package can reproduce Piepho's results

    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 
    # 17.70287377  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 
  }
  
} # }