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AMMI biplots

Source: R/ammi_biplot.R
ammi_biplot.Rd

ammi_biplot() draws the two AMMI biplots of a multi-environment trial: the AMMI2 biplot (scores of the first two interaction axes of genotypes and environments) and the AMMI1 biplot (means against the first axis).

Usage

ammi_biplot(.data, .y, .rep, .gen, .env)

# Default S3 method
ammi_biplot(.data, .y, .rep, .gen, .env)

Arguments

.data

a data frame (or data.table) with one row per plot.

.y

response: a column of .data given by name (.y = Yield or .y = "Yield") or a numeric vector of length nrow(.data).

.rep

replicate: as for .y; optional (the scores do not depend on it).

.gen

genotype: a column of .data or a vector, as for .y.

.env

environment: a column of .data or a vector, as for .y.

Value

An object of class c("stab_ammi_biplot", "stab_result", "list") with the components of earlier versions:

ammi_biplot

ggplot: the AMMI2 biplot.

MeanPC1Plot

ggplot: the AMMI1 biplot.

and a new one:

scores

data.table: label, type ("Genotype" or "Environment"), Mean, PC1, PC2.

Methods: print() (draws both), plot() (which = c("ammi2", "ammi1")), stab_interpret().

Details

The scores are those of ammi: \(\gamma_{in}\sqrt{\lambda_n}\) for genotypes and \(\delta_{jn}\sqrt{\lambda_n}\) for environments, so the inner product of a genotype point and an environment point approximates their interaction. In the AMMI1 biplot genotypes to the right of the grand mean yield above average; genotypes close to PC1 = 0 interact little (are stable); genotypes and environments with PC1 scores of the same sign interact positively.

Changes from the earlier version. The genotype means of the AMMI1 plot were paired with the scores of other genotypes unless the data were sorted by genotype; the plot now shows environments too, with the mean on the horizontal axis as is usual. Genotypes and environments are scaled symmetrically.

References

Gauch, H. G. (1992). Statistical Analysis of Regional Yield Trials: AMMI Analysis of Factorial Designs. Elsevier, Amsterdam.

Zobel, R. W., Wright, M. J. and Gauch, H. G. (1988). Statistical analysis of a yield trial. Agronomy Journal, 80(3), 388–393. doi:10.2134/agronj1988.00021962008000030002x

See also

ammi, gge_biplot, stab_interpret

Other stability analyses: add_anova(), ammi(), er_anova(), ge_effects(), ge_means(), gge_biplot(), indiv_anova(), stab_asv(), stab_dist(), stab_eskridge(), stab_fox(), stab_huehn(), stab_kang(), stab_masv(), stab_measures(), stab_par(), stab_reg(), stab_reliability(), stab_superiority()

Author

Muhammad Yaseen (myaseen208@gmail.com), Kent M. Eskridge (keskridge1@unl.edu)

Examples

data(ge_data)
fit <-
  ammi_biplot(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
    )
plot(x = fit, which = c("ammi2", "ammi1")[1])