omer.sorghum.Rd
Multi-environment trial of sorghum, 6 environments
data("omer.sorghum")
A data frame with 432 observations on the following 4 variables.
env
environment
rep
replication
gen
genotype factor
yield
yield, kg/ha
Trials were conducted in Sudan, 3 years at 2 locations, 4 reps in RCBD at each location. The year and location have been combined to form 6 environments. Only environments are given in the data, not the individual year and location.
Siraj Osman Omer, Abdel Wahab Hassan Abdalla, Mohammed Hamza Mohammed, Murari Singh (2015). Bayesian estimation of genotype-by-environment interaction in sorghum variety trials Communications in Biometry and Crop Science, 10 (2), 82-95.
Electronic data provided by Siraj Osman Omer.
None.
library(agridat) data(omer.sorghum) dat <- omer.sorghum # REML approach libs(lme4) libs(lucid) # 1 loc, 2 years. Match Omer table 1. m1 <- lmer(yield ~ 1 + env + (1|env:rep) + (1|gen) + (1|gen:env), data=subset(dat, is.element(env, c('E2','E4')))) vc(m1)#> grp var1 var2 vcov sdcor #> gen:env (Intercept) <NA> 17050 130.6 #> gen (Intercept) <NA> 2760 52.54 #> env:rep (Intercept) <NA> 959.2 30.97 #> Residual <NA> <NA> 43090 207.6## grp var1 var2 vcov sdcor ## gen:env (Intercept) <NA> 17050 130.6 ## gen (Intercept) <NA> 2760 52.54 ## env:rep (Intercept) <NA> 959.1 30.97 ## Residual <NA> <NA> 43090 207.6 # 1 loc, 3 years. Match Omer table 1. m2 <- lmer(yield ~ 1 + env + (1|env:rep) + (1|gen) + (1|gen:env), data=subset(dat, is.element(env, c('E2','E4','E6')))) vc(m2)#> grp var1 var2 vcov sdcor #> gen:env (Intercept) <NA> 22210 149 #> gen (Intercept) <NA> 9287 96.37 #> env:rep (Intercept) <NA> 1332 36.5 #> Residual <NA> <NA> 40270 200.7## grp var1 var2 vcov sdcor ## gen:env (Intercept) <NA> 22210 149 ## gen (Intercept) <NA> 9288 96.37 ## env:rep (Intercept) <NA> 1332 36.5 ## Residual <NA> <NA> 40270 200.7 # all 6 locs. Match Omer table 3, frequentist approach m3 <- lmer(yield ~ 1 + env + (1|env:rep) + (1|gen) + (1|gen:env), data=dat) vc(m3)#> grp var1 var2 vcov sdcor #> gen:env (Intercept) <NA> 21340 146.1 #> env:rep (Intercept) <NA> 1152 33.95 #> gen (Intercept) <NA> 1169 34.19 #> Residual <NA> <NA> 24660 157## grp var1 var2 vcov sdcor ## gen:env (Intercept) <NA> 21340 146.1 ## env:rep (Intercept) <NA> 1152 33.95 ## gen (Intercept) <NA> 1169 34.2 ## Residual <NA> <NA> 24660 157