Multi-environment trial of sorghum at 3 locations across 5 years
Multi-environment trial of sorghum at 3 locations across 5 years
A data frame with 289 observations on the following 6 variables.
gengenotype, 28 levels
trialtrial, 2 levels
envenvironment, 13 levels
yieldyield kg/ha
yearyear, 2001-2005
loclocation, 3 levels
Sorghum yields at 3 locations across 5 years. The trials were carried out at three locations in dry, hot lowlands of Ethiopia:
Melkassa (39 deg 21 min E, 8 deg 24 min N)
Mieso (39 deg 22 min E, 8 deg 41 min N)
Kobo (39 deg 37 min E, 12 deg 09 min N)
Trial 1 was 14 hybrids and one open-pollinated variety.
Trial 2 was 12 experimental lines.
Used with permission of Asfaw Adugna.
Asfaw Adugna (2008). Assessment of yield stability in sorghum using univariate and multivariate statistical approaches. Hereditas, 145, 28–37. https://doi.org/10.1111/j.0018-0661.2008.2023.x
## Not run:
library(agridat)
data(adugna.sorghum)
dat <- adugna.sorghum
libs(lattice)
redblue <- colorRampPalette(c("firebrick", "lightgray", "#375997"))
levelplot(yield ~ env*gen, data=dat, main="adugna.sorghum gxe heatmap",
col.regions=redblue)
# Genotype means match Adugna
tapply(dat$yield, dat$gen, mean)
# CV for each genotype. G1..G15 match, except for G2.
# The table in Adugna scrambles the means for G16..G28
libs(reshape2)
mat <- acast(dat, gen~env, value.var='yield')
round(sqrt(apply(mat, 1, var, na.rm=TRUE)) / apply(mat, 1, mean, na.rm=TRUE) * 100,2)
# Shukla stability. G1..G15 match Adugna. Can't match G16..G28.
dat1 <- droplevels(subset(dat, trial=="T1"))
mat1 <- acast(dat1, gen~env, value.var='yield')
w <- mat1; k=15; n=8 # k=p gen, n=q env
w <- sweep(w, 1, rowMeans(mat1, na.rm=TRUE))
w <- sweep(w, 2, colMeans(mat1, na.rm=TRUE))
w <- w + mean(mat1, na.rm=TRUE)
w <- rowSums(w^2, na.rm=TRUE)
sig2 <- k*w/((k-2)*(n-1)) - sum(w)/((k-1)*(k-2)*(n-1))
round(sig2/10000,1) # Genotypes in T1 are divided by 10000
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