agridat (version 1.5)

vargas.wheat1: Durum wheat yields in 7 years with genetic and environment covariates

Description

Yield of Durum wheat, 7 genotypes, 6 years, with 16 genotypic variates and 16 environment variates.

Usage

data(vargas.wheat1)

source

Mateo Vargas and Jose Crossa and Ken Sayre and Matthew Renolds and Martha E Ramirez and Mike Talbot, 1998. Interpreting Genotype x Environment Interaction in Wheat by Partial Least Squares Regression, Crop Science, 38, 679--689. Data kindly provided by Jose Crossa.

Details

Conducted in Ciudad Obregon, Mexico.

Examples

gvals <- vargas.wheat1$genvals
evals <- vargas.wheat1$envvals

require("pls")

# Yield as a function of gen variates
require("reshape2")
gv <- melt(gvals, id.var=c('gen','rep','year'))
Y0 <- subset(gv, variable=="yield")
Y0 <- acast(Y0, gen~year, mean)
Y0 <- sweep(Y0, 1, rowMeans(Y0))
Y0 <- sweep(Y0, 2, colMeans(Y0)) # GxE residuals
Y1 <- scale(Y0) # scaled columns
X1 <- subset(gv, variable!="yield")
X1 <- acast(X1, gen~variable, mean)
X1 <- scale(X1) # scaled columns
m1 <- plsr(Y1~X1)
loadings(m1)[,1,drop=FALSE] # X loadings in Table 1 of Vargas

# Yield as a function of env variates
Y2 <- t(Y0)
X2 <- vargas.wheat1$envvals
rownames(X2) <- X2$year
X2 <- as.matrix(X2[,-1])
Y2 <- scale(Y2)
X2 <- scale(X2)

m2 <- plsr(Y2~X2)
loadings(m2)[,1,drop=FALSE] # X loadings in Table 2 of Vargas