We consider Markov chain Monte Carlo methods for calculating conditional p values of statistical models for count data arising in Box-Behnken designs. The statistical model we consider is a discrete version of the first-order model in the response su
rface methodology. For our models, the Markov basis, a key notion to construct a connected Markov chain on a given sample space, is characterized as generators of the toric ideals for the centrally symmetric configurations of root system D_n. We show the structure of the Groebner bases for these cases. A numerical example for an imaginary data set is given.
We consider conditional exact tests of factor effects in designed experiments for discrete response variables. Similarly to the analysis of contingency tables, Markov chain Monte Carlo methods can be used for performing exact tests, especially when l
arge-sample approximations of the null distributions are poor and the enumeration of the conditional sample space is infeasible. To construct a connected Markov chain over the appropriate sample space, a common approach is to compute a Markov basis. Theoretically, a Markov basis can be characterized as a generator of a well-specified toric ideal in a polynomial ring and is computed by computational algebraic softwares. However, the computation of a Markov basis sometimes becomes infeasible even for problems of moderate sizes. In this paper, we obtain the closed form expression of minimal Markov bases for the main effect models of $2^{p-1}$ fractional factorial designs of resolution $p$.
We give an expository review of applications of computational algebraic statistics to design and analysis of fractional factorial experiments based on our recent works. For the purpose of design, the techniques of Grobner bases and indicator function
s allow us to treat fractional factorial designs without distinction between regular designs and non-regular designs. For the purpose of analysis of data from fractional factorial designs, the techniques of Markov bases allow us to handle discrete observations. Thus the approach of computational algebraic statistics greatly enlarges the scope of fractional factorial designs.
We present some optimal criteria to evaluate model-robustness of non-regular two-level fractional factorial designs. Our method is based on minimizing the sum of squares of all the off-diagonal elements in the information matrix, and considering expe
ctation under appropriate distribution functions for unknown contamination of the interaction effects. By considering uniform distributions on symmetric support, our criteria can be expressed as linear combinations of $B_s(d)$ characteristic, which is used to characterize the generalized minimum aberration. We give some empirical studies for 12-run non-regular designs to evaluate our method.
A new class of two-level non-regular fractional factorial designs is defined. We call this class an {it affinely full-dimensional factorial design}, meaning that design points in the design of this class are not contained in any affine hyperplane in
the vector space over $mathbb{F}_2$. The property of the indicator function for this class is also clarified. A fractional factorial design in this class has a desirable property that parameters of the main effect model are simultaneously identifiable. We investigate the property of this class from the viewpoint of $D$-optimality. In particular, for the saturated designs, the $D$-optimal design is chosen from this class for the run sizes $r equiv 5,6,7$ (mod 8).
We consider testing independence in group-wise selections with some restrictions on combinations of choices. We present models for frequency data of selections for which it is easy to perform conditional tests by Markov chain Monte Carlo (MCMC) metho
ds. When the restrictions on the combinations can be described in terms of a Segre-Veronese configuration, an explicit form of a Grobner basis consisting of moves of degree two is readily available for performing a Markov chain. We illustrate our setting with the National Center Test for university entrance examinations in Japan. We also apply our method to testing independence hypotheses involving genotypes at more than one locus or haplotypes of alleles on the same chromosome.
We consider Markov basis arising from fractional factorial designs with three-level factors. Once we have a Markov basis, $p$ values for various conditional tests are estimated by the Markov chain Monte Carlo procedure. For designed experiments with
a single count observation for each run, we formulate a generalized linear model and consider a sample space with the same sufficient statistics to the observed data. Each model is characterized by a covariate matrix, which is constructed from the main and the interaction effects we intend to measure. We investigate fractional factorial designs with $3^{p-q}$ runs noting correspondences to the models for $3^{p-q}$ contingency tables.
Suppose several two-valued input-output systems are designed by setting the levels of several controllable factors. For this situation, Taguchi method has proposed to assign the controllable factors to the orthogonal array and use ANOVA model for the
standardized SN ratio, which is a natural measure for evaluating the performance of each input-output system. Though this procedure is simple and useful in application indeed, the result can be unreliable when the estimated standard errors of the standardized SN ratios are unbalanced. In this paper, we treat the data arising from the full factorial or fractional factorial designs of several controllable factors as the frequencies of high-dimensional contingency tables, and propose a general testing procedure for the main effects or the interaction effects of the controllable factors.
