data("burgueno.alpha")

## Not run: 

  library(agridat)
  data(burgueno.alpha)
  dat <- burgueno.alpha

  libs(desplot)
  desplot(dat, yield~col*row,
          out1=rep, out2=block, # aspect unknown
          text=gen, cex=1,shorten="none",
          main='burgueno.alpha')


  libs(lme4,lucid)
  # Inc block model
  m0 <- lmer(yield ~ gen + (1|rep/block), data=dat)
  vc(m0) # Matches Burgueno p. 26
  ##        grp        var1 var2   vcov sdcor
  ##  block:rep (Intercept) <NA>  86900 294.8
  ##        rep (Intercept) <NA> 200900 448.2
  ##   Residual        <NA> <NA> 133200 365  


  libs(asreml) # asreml4
    
  dat <- transform(dat, xf=factor(col), yf=factor(row))
  dat <- dat[order(dat$xf, dat$yf),]                 
  
  # Sequence of models on page 36
  
  m1 <- asreml(yield ~  gen, data=dat)
  m1$loglik # -232.13
  
  m2 <- asreml(yield ~  gen, data=dat,
               random = ~ rep)
  m2$loglik # -223.48
  
  # Inc Block model
  m3 <- asreml(yield ~  gen, data=dat,
               random = ~ rep/block)
  m3$loglik # -221.42
  m3$coef$fixed # Matches solution on p. 27
  
  # AR1xAR1 model
  m4 <- asreml(yield ~ 1 + gen, data=dat,
               resid = ~ar1(xf):ar1(yf))
  m4$loglik # -221.47
  plot(varioGram(m4), main="burgueno.alpha") # Figure 1
  
  m5 <- asreml(yield ~ 1 + gen, data=dat,
               random= ~ yf, resid = ~ar1(xf):ar1(yf))
  m5$loglik # -220.07
  
  m6 <- asreml(yield ~ 1 + gen + pol(yf,-2), data=dat,
               resid = ~ar1(xf):ar1(yf))
  m6$loglik # -204.64
  
  m7 <- asreml(yield ~ 1 + gen + lin(yf), data=dat,
               random= ~ spl(yf), resid = ~ar1(xf):ar1(yf))
  m7$loglik # -212.51
  
  m8 <- asreml(yield ~ 1 + gen + lin(yf), data=dat,
               random= ~ spl(yf))
  m8$loglik # -213.91
  
  # Polynomial model with predictions
  m9 <- asreml(yield ~ 1 + gen + pol(yf,-2) + pol(xf,-2), data=dat,
               random= ~ spl(yf),
               resid = ~ar1(xf):ar1(yf))
  m9 <- update(m9)
  m9$loglik # -191.44 vs -189.61
  p9 <- predict(m9, classify="gen:xf:yf", levels=list(xf=1,yf=1)) 
  p9
  
  m10 <- asreml(yield ~ 1 + gen + lin(yf)+lin(xf), data=dat,
                resid = ~ar1(xf):ar1(yf))
  m10$loglik # -211.56
  
  m11 <- asreml(yield ~ 1 + gen + lin(yf)+lin(xf), data=dat,
                random= ~ spl(yf),
                resid = ~ar1(xf):ar1(yf))
  m11$loglik # -208.90
  
  m12 <- asreml(yield ~ 1 + gen + lin(yf)+lin(xf), data=dat,
                random= ~ spl(yf)+spl(xf),
                resid = ~ar1(xf):ar1(yf))
  m12$loglik # -206.82
  
  m13 <- asreml(yield ~ 1 + gen + lin(yf)+lin(xf), data=dat,
                random= ~ spl(yf)+spl(xf))
  m13$loglik # -207.52


## End(Not run)