Model Selection and Validation for Yield Trials with Interaction

Abstract

SUMMARY The additive main effects and multiplicative interaction (AMMI) model first applies the additive analysis of variance (ANOVA) model to two-way data, and then applies the multiplicative principal components analysis (PCA) model to the residual from the additive model, that is, to the interaction. AMMI analysis of yield trial data is a useful extension of the more familiar ANOVA, PCA, and linear regression procedures, particularly given a large genotype-by-environment interaction. Model selection and validation are considered from both predictive and postdictive perspectives, using data splitting and F-tests, respectively. A New York soybean yield trial serves as an example. Yield trials generate observations of yield, ordinarily replicated, for a number of genotypes grown in a number of environments (site-year combinations). Often the data are rather noisy, with a standard deviation for plot yields in excess of 25 % of the mean. An additional challenging feature of these data is the frequent presence of important and complex genotype-by-environment (GE) interactions. Plant breeders use yield trials to identify promising genotypes, and agronomists use them to make recommendations for farmers. The level of success in meeting these goals depends critically on two factors: (i) the accuracy of yield estimates, and (ii) the magnitudes of genotype-by-site, genotype-by-year, and genotype-by-site-by-year interactions (Talbot, 1984). In essence, these two factors reflect within-trial accuracy and between-trial predictability. This paper addresses only the first concern. Nothing is said regarding between-trial predictability, or agrotechnology transfer, other than to observe that success with withintrial accuracy is a necessary prelude to success with between-trial predictability. The within-trial accuracy of a statistical model may be assessed by two fundamentally different criteria: Postdictive success concerns a model's fit to its own data, whereas predictive success concerns the fit between a model constructed using part of the data and validation data not used in modelling. In either case, the statistical setting is that of an incompletely specified model, where empirical considerations enter into the decision to include a given' potential source in the model, or alternatively to relegate it to the model's residual (Bancroft, 1964). Whenever the data are noisy, postdiction and prediction are different tasks, and in general the model chosen by predictive criteria will be different and simpler than the model chosen by postdictive criteria. Because the several replicates of a yield trial constitute a noisy sample, a model chosen by predictive criteria may be expected to provide yield estimates that are closer to the true means (and to validation observations) than will a model chosen by postdictive criteria. This claim is readily subjected to experimental test. In what follows, the relative performances of statistical models chosen