Bayesian data analysis for agricultural experiments

Che, X. and Xu, S. 2010. Bayesian data analysis for agricultural experiments. Can. J. Plant Sci. 90: 575-603. Data collected in agricultural experiments can be analyzed in many different ways using different models. The most commonly used models are the linear model and the generalized linear model. The maximum likelihood method is often used for data analysis. However, this method may not be able to handle complicated models, especially multiple level hierarchical models. The Bayesian method partitions complicated models into simple components, each of which may be formulated analytically. Therefore, the Bayesian method is capable of handling very complicated models. The Bayesian method itself may not be more complicated than the maximum likelihood method, but the analysis is time consuming, because numerical integration involved in Bayesian analysis is almost exclusively accomplished based on Monte Carlo simulations, the so called Markov Chain Monte Carlo (MCMC) algorithm. Although the MCMC algorithm is intuitive and straightforward to statisticians, it may not be that simple to agricultural scientists, whose main purpose is to implement the method and interpret the results. In this review, we provide the general concept of Bayesian analysis and the MCMC algorithm in a way that can be understood by non-statisticians. We also demonstrate the implementation of the MCMC algorithm using professional software packages such as the MCMC procedure in SAS. Three datasets from agricultural experiments were analyzed to demonstrate the MCMC algorithm.