agridat (version 1.12)

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.

Format

A list of two data frames, genvals and envvals.

The genvals data frame contains 126 observations of genetic variables for each year*rep*gen:

year	Year, 1990-1995
rep	Replicate factor, 3 levels
gen	Genotype factor, 7 levels
yield	Yield, kg/ha
ANT	Anthesis, days after emergence
MAT	Maturity, days after emergence
GFI	Grainfill, MAT-ANT
PLH	Plant height, cm
BIO	Biomass above ground, kg/ha
HID	Harvest index
STW	Straw yield, kg/ha
NSM	Spikes / m^2
NGM	Grains / m^2
NGS	Grains per spike
TKW	Thousand kernel weight, g
WTI	Weight per tiller, g
SGW	Spike grain weight, g
VGR	Vegetative growth rate, kg/ha/day, STW/ANT
KGR	Kernel growth rate, mg/kernel/day

The envals data frame has 17 variables for each of 6 years:

year	Year, 1990-1995
MTD	Mean daily max temperature December, deg C
MTJ	January
MTF	February
MTM	March
mTD	Mean daily minimum temperature December, deg C
mTJ	January
mTF	February
mTM	March
PRD	Monthly precipitation in December, mm
PRJ	January
PRF	February
PRM	March
SHD	Sun hours per day December
SHJ	Sun hours per day January
SHF	Sun hours per day February
SHM	Sun hours per day March

Details

Conducted in Ciudad Obregon, Mexico.

Examples

# NOT RUN {
data(vargas.wheat1)

# }
# NOT RUN {
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

biplot(m1, cex=.5, which="x", var.axes=TRUE,
       main="vargas.wheat1 - gen ~ trait") # Vargas figure 2a

# 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
# }