australia.soybean {agridat}R Documentation

Multi-environment trial of soybean in Australia

Description

Yield and other traits of 58 varieties of soybeans, grown in four locations across two years in Australia. This is four-way data of Year x Loc x Gen x Trait.

Format

A data frame with 464 observations on the following 10 variables.

env

environment, 8 levels, first character of location and last two characters of year

loc

location

year

year

gen

genotype of soybeans, 1-58

yield

yield, metric tons / hectare

height

height (meters)

lodging

lodging

size

seed size, (millimeters)

protein

protein (percentage)

oil

oil (percentage)

Details

Measurement are available from four locations in Queensland, Australia in two consecutive years 1970, 1971.

The 58 different genotypes of soybeans consisted of 43 lines (40 local Australian selections from a cross, their two parents, and one other which was used a parent in earlier trials) and 15 other lines of which 12 were from the US.

Lines 1-40 were local Australian selections from Mamloxi (CPI 172) and Avoyelles (CPI 15939).

No. Line
1-40 Local selections
41 Avoyelles (CPI 15939) Tanzania
42 Hernon 49 (CPI 15948) Tanzania
43 Mamloxi (CPI 172) Nigeria
44 Dorman USA
45 Hampton USA
46 Hill USA
47 Jackson USA
48 Leslie USA
49 Semstar Australia
50 Wills USA
51 C26673 Morocco
52 C26671 Morocco
53 Bragg USA
54 Delmar USA
55 Lee USA
56 Hood USA
57 Ogden USA
58 Wayne USA

Note on the data in Basford and Tukey book. The values for line 58 for Nambour 1970 and Redland Bay 1971 are incorrectly listed on page 477 as 20.490 and 15.070. They should be 17.350 and 13.000, respectively. In the data set made available here, these values have been corrected.

Used with permission of Kaye Basford, Pieter Kroonenberg.

Source

Basford, K. E., and Tukey, J. W. (1999). Graphical analysis of multiresponse data illustrated with a plant breeding trial. Chapman and Hall/CRC.

Retrieved from: https://three-mode.leidenuniv.nl/data/soybeaninf.htm

References

K E Basford (1982). The Use of Multidimensional Scaling in Analysing Multi-Attribute Genotype Response Across Environments, Aust J Agric Res, 33, 473–480.

Kroonenberg, P. M., & Basford, K. E. B. (1989). An investigation of multi-attribute genotype response across environments using three-mode principal component analysis. Euphytica, 44, 109–123.

Marcin Kozak (2010). Use of parallel coordinate plots in multi-response selection of interesting genotypes. Communications in Biometry and Crop Science, 5, 83-95.

Examples

## Not run: 

library(agridat)

data(australia.soybean)
dat <- australia.soybean

libs(reshape2)
dm <- melt(dat, id.var=c('env', 'year','loc','gen'))

# Joint plot of genotypes & traits. Similar to Figure 1 of Kroonenberg 1989
dmat <- acast(dm, gen~variable, fun=mean)
dmat <- scale(dmat)
biplot(princomp(dmat), main="australia.soybean trait x gen biplot", cex=.75)


# Figure 1 of Kozak 2010, lines 44-58
  libs(reshape2, lattice, latticeExtra)
  data(australia.soybean)
  dat <- australia.soybean
  dat <- melt(dat, id.var=c('env', 'year','loc','gen'))
  dat <- acast(dat, gen~variable, fun=mean)
  dat <- scale(dat)
  dat <- as.data.frame(dat)[,c(2:6,1)]
  dat$gen <- rownames(dat)
  # data for the graphic by Kozak
  dat2 <- dat[44:58,]
  dat3 <- subset(dat2, is.element(gen, c("G48","G49","G50","G51")))
  
  parallelplot( ~ dat3[,1:6]|dat3$gen, main="australia.soybean",
               as.table=TRUE, horiz=FALSE) +
    parallelplot( ~ dat2[,1:6], horiz=FALSE, col="gray80") +
    parallelplot( ~ dat3[,1:6]|dat3$gen,
                 as.table=TRUE, horiz=FALSE, lwd=2)


## End(Not run)

[Package agridat version 1.18 Index]