tests/testthat/_problems/test_gge-135.R

In gge: Genotype Plus Genotype-by-Environment Biplots

# Extracted from test_gge.R:135

# prequel ----------------------------------------------------------------------
require(gge)
mat1 <- matrix(c(50, 55, 65, 50, 60, 65, 75,
                 67, 71, 76, 80, 82, 89, 95,
                 90, 93, 95, 102, 97, 106, 117,
                 98, 102, 105, 130, 135, 137, 133,
                 120, 129, 134, 138, 151, 153, 155),
               ncol=5, byrow=FALSE)
colnames(mat1) <- c("E1","E2","E3","E4","E5")
rownames(mat1) <- c("G1","G2","G3","G4","G5","G6","G7")
mat2 <- mat1
mat2[1,1] <- NA
bar <- transform(lattice::barley, env=paste0(site,year))

# test -------------------------------------------------------------------------
expect_silent(NULL)
m11 <- gge(mat1)
plot(m11)
m21 <- gge(mat2)
plot(m21)
biplot(m11)
biplot(m11, main="Example biplot", subtitle="GGE biplot")
biplot(m11, main="Example biplot", subtitle="GGE biplot")
biplot(m11, subtitle=NULL)
biplot(m11, xlab=NULL, ylab=NULL)
biplot(m11, xlab="Axis 1", ylab="Axis 2")
biplot(m11, main=NULL, subtitle=NULL)
biplot(m11, cex.gen=0)
biplot(m11, cex.gen=2)
biplot(m11, cex.env=2)
biplot(m11, col.gen="blue")
biplot(m11, col.gen=c("blue","red"))
biplot(m11, pch.gen=20)
biplot(m11, col.env=c("red","blue"))
biplot(m11, comps=2:3)
biplot(m11, lab.env=FALSE)
biplot(m11, flip="")
biplot(m11, flip=FALSE)
biplot(m11, flip=TRUE)
biplot(m11, flip=c(TRUE,FALSE))
biplot(m11, flip=c(FALSE,TRUE))
biplot(m11, flip=c(FALSE,FALSE))
biplot(m11, flip=c(TRUE,TRUE))
biplot(m11, zoom.gen=.8)
biplot(m11, zoom.env=.8)
biplot(m11, zoom.gen=.8, zoom.env=.8)
m31 <- gge(mat1, method="svd")
biplot(m31)
m32 <- gge(mat1, method="nipals")
biplot(m32)
m34 <- gge(mat2)
biplot(m34)
m35 <- gge(mat2, method="svd")
biplot(m35)
m36 <- gge(mat2, method="nipals")
biplot(m36)
m24 <- gge(mat2, env.group=c(1,1,1,2,2))
biplot(m24)
m25 <- gge(mat2, gen.group=c(1,1,1,1,2,2,2))
biplot(m25, col.gen=c('blue','red'), pch.gen=1:2)
require(lattice)
m32 <- gge(bar, yield~variety*env)