Multi-environment trial of cucumbers in a latin square design
Cucumber yields in latin square design at two locs.
A data frame with 32 observations on the following 5 variables.
loc
location
gen
genotype/cultivar
row
row
col
column
yield
weight of marketable fruit per plot
Conducted at Clemson University in 1985. four cucumber cultivars were grown in a latin square design at Clemson, SC, and Tifton, GA.
Separate variances are modeled each location.
Plot dimensions are not given.
Bridges (1989) used this data to illustrate fitting a heterogeneous mixed model.
Used with permission of William Bridges.
William Bridges (1989). Analysis of a plant breeding experiment with heterogeneous variances using mixed model equations. Applications of mixed models in agriculture and related disciplines, S. Coop. Ser. Bull, 45–51.
## Not run: library(agridat) data(bridges.cucumber) dat <- bridges.cucumber dat <- transform(dat, rowf=factor(row), colf=factor(col)) libs(desplot) desplot(dat, yield~col*row|loc, # aspect unknown text=gen, cex=1, main="bridges.cucumber") # Graphical inference test for heterogenous variances libs(nullabor) # Create a lineup of datasets fun <- null_permute("loc") dat20 <- lineup(fun, dat, n=20, pos=9) # Now plot libs(lattice) bwplot(yield ~ loc|factor(.sample), dat20, main="bridges.cucumber - graphical inference") libs(asreml) # asreml4 ## Random row/col/resid. Same as Bridges 1989, p. 147 m1 <- asreml(yield ~ 1 + gen + loc + loc:gen, random = ~ rowf:loc + colf:loc, data=dat) libs(lucid) lucid::vc(m1) ## effect component std.error z.ratio bound ## rowf:loc 31.62 23.02 1.4 P 0 ## colf:loc 18.08 15.32 1.2 P 0 ## units(R) 31.48 12.85 2.4 P 0 ## Random row/col/resid at each loc. Matches p. 147 m2 <- asreml(yield ~ 1 + gen + loc + loc:gen, random = ~ at(loc):rowf + at(loc):colf, data=dat, resid = ~ dsum( ~ units|loc)) lucid::vc(m2) ## effect component std.error z.ratio bound ## at(loc, Clemson):rowf 32.32 36.58 0.88 P 0 ## at(loc, Tifton):rowf 30.92 28.63 1.1 P 0 ## at(loc, Clemson):colf 22.55 28.78 0.78 P 0 ## at(loc, Tifton):colf 13.62 14.59 0.93 P 0 ## loc_Clemson(R) 46.85 27.05 1.7 P 0 ## loc_Tifton(R) 16.11 9.299 1.7 P 0 predict(m2, data=dat, classify='loc:gen')$pvals ## loc gen predicted.value std.error status ## 1 Clemson Dasher 45.6 5.04 Estimable ## 2 Clemson Guardian 31.6 5.04 Estimable ## 3 Clemson Poinsett 21.4 5.04 Estimable ## 4 Clemson Sprint 26 5.04 Estimable ## 5 Tifton Dasher 50.5 3.89 Estimable ## 6 Tifton Guardian 38.7 3.89 Estimable ## 7 Tifton Poinsett 33 3.89 Estimable ## 8 Tifton Sprint 39.2 3.89 Estimable # Is a heterogeneous model justified? Maybe not. # m1$loglik ## -67.35585 # m2$loglik ## -66.35621 ## End(Not run)
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