Nonparametric rank-based test procedures for non-additive models in the two-way layout I. no replications

One of the major unresolved problems in the area of nonparametric statistics is the need for satisfactory rank-based test procedures for non-additive models in the two-way layout, especially when there is only one observation on each combination of the levels of the experimental factors. In this paper we consider an arbitrary non-additive model for the two-way layout with n levels of each factor. We utilize both alignment and ranking of the data together with basic properties of Latin squares to develop rank tests for interaction (non-additivity). Our technique involves first aligning within one of the main effects, ranking within the other main effects (columns and rows) and then adding the resulting ranks within “interaction bands” corresponding to orthogonal partitions of the interaction for the model, as denoted by the letters of an n × n Latin square. A Friedman-type statistic is then computed on the resulting sums. This is repeated for each of (n?1) mutually orthogonal Latin squares (thus accounting for all the interaction degrees of freedom). The resulting (n?1) Friedman-type statistics are finally combined to obtain an overall test statistic. The necessary null distribution tables for applying the proposed test for non-additivity are presented and we discuss the results of a Monte Carlo simulation study of the relative powers of this new procedure and other (parametric and nonparametric) procedures designed to detect interaction in a two-way layout with one observation per cell.     

TWO-WAY CHANGE-POINT MODEL AND ITS APPLICATION

Exact null and alternative distributions of the two-way maximally selected x² for interaction between the ordered rows and columns are derived for each of the normal and Poisson models, respectively. The method is one of the multiple comparison procedures for ordered parameters and is useful for defining a block interaction or a two-way change-point model as a simple alternative to the two-way additive model. The construction of a confidence region for the two-way change-point is then described. An important application is found in a dose-response clinical trial with ordered categorical responses, where detecting the dose level which gives significantly higher responses than the lower doses can be formulated as a problem of detecting a change in the interaction effects.     

ON TESTS FOR INTERACTION IN A NONREPLICATED TWO-WAY LAYOUT

The paper proposes tests for interaction in a two-way table with one observation per cell. The power of these tests is independent of the additive main effects in the linear model. This is an advantage compared to a test suggested earlier, which has low power if main effects are very variable.     

Rank-based test procedures for interaction in the two-way layout with one observation per cell

New aligned-rank test procedures for the composite null hypothesis of no interaction effects (without placing restrictions on the two main effects) against appropriate composite general alternatives are developed for the standard two-way layout with a single observation per cell. Relative power performances of the two new aligned-rank procedures and existing tests due to Tukey (1949) and to de Kroon & van der Laan (1981) are examined via Monte Carlo simulation. Extensive power studies conducted on the 5 × 6 and 5 × 9 two-way layouts with one observation per cell show superior performance of the new procedures for a variety of interaction effects. Simulated critical values for the new procedures are provided in settings where the number of levels for each of the factors is between 3 and 9, inclusive.     

Testing additivity in two-way classifications with no replications:the locally best invariant test

Row x column interaction is frequently assumed to be negligible in two-way classifications having one observation per cell. Absence of interaction allows the researcher to estimate experimental error and to proceed with making inferences about row and column effects. If additivity is suspect, it is conventional to test it against a structured alternative. If the structured alternative missspecifies the existing nonadditivity, then the power of the test is low, even if the magnitude of the existing nonadditivity is large. The locally best invariant (LBI) test of additivity is less subject to model misspecification because a particular structural alternative need not be hypothesized. This paper illustrates the LBI test of additivity and compares its power to that of the Johnson-Graybill likelihood ratio (LR) test. The LBI test performs as well as the LR test under a Johnson-Graybill alternative and performs better than the LR test under more general alternatives.     

Bayesian clustering for row effects models

We deal with two-way contingency tables having ordered column categories. We use a row effects model wherein each interaction term is assumed to have a multiplicative form involving a row effect parameter and a fixed column score. We propose a methodology to cluster row effects in order to simplify the interaction structure and to enhance the interpretation of the model. Our method uses a product partition model with a suitable specification of the cohesion function, so that we can carry out our analysis on a collection of models of varying dimensions using a straightforward MCMC sampler. The methodology is illustrated with reference to simulated and real data sets.     

Modification of Tukey's additivity test

In this paper we discuss testing for an interaction in the two-way ANOVA with just one observation per cell. The known results are reviewed and a simulation study is performed to evaluate type I and type II risks of the tests. It is shown that the Tukey and Mandel additivity tests have very low power in case of more general interaction scheme. A modification of Tukey's test is developed to resolve this issue. All tests mentioned in the paper have been implemented in R package Additivity Tests.     

Screening for prostate cancer using multivariate mixed-effects models

Using several variables known to be related to prostate cancer, a multivariate classification method is developed to predict the onset of clinical prostate cancer. A multivariate mixed-effects model is used to describe longitudinal changes in prostate specific antigen (PSA), a free testosterone index (FTI), and body mass index (BMI) before any clinical evidence of prostate cancer. The patterns of change in these three variables are allowed to vary depending on whether the subject develops prostate cancer or not and the severity of the prostate cancer at diagnosis. An application of Bayes' theorem provides posterior probabilities that we use to predict whether an individual will develop prostate cancer and, if so, whether it is a high-risk or a low-risk cancer. The classification rule is applied sequentially one multivariate observation at a time until the subject is classified as a cancer case or until the last observation has been used. We perform the analyses using each of the three variables individually, combined together in pairs, and all three variables together in one analysis. We compare the classification results among the various analyses and a simulation study demonstrates how the sensitivity of prediction changes with respect to the number and type of variables used in the prediction process.     

Graphical Comparison of Covariance Matrices

Procedures for comparing within-group covariance matrices are developed, based on separate analyses of the variances and of the correlations. The variances and the correlations are represented as two two-way tables, with the columns representing groups. Graphical procedures based on comparisons of linear regressions are presented, by considering a multiplicative columns-regression model for the interaction of groups x variances and of groups x correlations. A multivariate comparison leads to the use of a generalized eigenanalysis to display any differences in covariance structure.     

Visualizing main effects and interaction in multiple non-symmetric correspondence analysis

Non-symmetric correspondence analysis (NSCA) is a useful technique for analysing a two-way contingency table. Frequently, the predictor variables are more than one; in this paper, we consider two categorical variables as predictor variables and one response variable. Interaction represents the joint effects of predictor variables on the response variable. When interaction is present, the interpretation of the main effects is incomplete or misleading. To separate the main effects and the interaction term, we introduce a method that, starting from the coordinates of multiple NSCA and using a two-way analysis of variance without interaction, allows a better interpretation of the impact of the predictor variable on the response variable. The proposed method has been applied on a well-known three-way contingency table proposed by Bockenholt and Bockenholt in which they cross-classify subjects by person's attitude towards abortion, number of years of education and religion. We analyse the case where the variables education and religion influence a person's attitude towards abortion.     

A method for testing interaction in unreplicated two-way tables: using all pairwise interaction contrasts

Several methods exist for testing interaction in unreplicated two-way layouts. Some are based on specifying a functional form for the interaction term and perform well provided that the functional form is appropriate. Other methods do not require such a functional form to be specified but only test for the presence of non-additivity and do not provide a suitable estimate of error variance for a non-additive model. This paper presents a method for testing for interaction in unreplicated two-way tables that is based on testing all pairwise interaction contrasts. This method (i) is easy to implement, (ii) does not assume a functional form for the interaction term, (iii) can find a sub-table of data which may be free from interaction and to base the estimate of unknown error variance, and (iv) can be used for incomplete two-way layouts. The proposed method is illustrated using examples and its power is investigated via simulation studies. Simulation results show that the proposed method is competitive with existing methods for testing for interaction in unreplicated two-way layouts.     

A New Method for Testing Interaction in Unreplicated Two-Way Analysis of Variance

For a two-way ANOVA table, with a single observation per cell, the standard approach is to assume that interaction between the two factors is negligible, and to base inferences about the main factors on the model without interaction. But there is no totally satisfactory method for testing if interaction can be ignored. The classical approach is to specify a functional form for the interaction terms, involving a small number of parameters, and then use an appropriate test. But, such tests have low power if the functional form is inappropriate. This has led researchers to propose tests which do not assume a specific form for the interactions. In this article, we present a new approach for testing interaction which also does not assume a specific form for the interaction. This approach is fairly simple and flexible, and its usefulness is illustrated with several examples. We also present a general result which shows that there is no test of interaction with good power properties against all types of interaction.     

Use of the experimentwise error rate in simultaneous tests of main effects in two-way disproportionate ANOVA without interaction

It is argued that the probability of committing at least one type I error should be reported when testing the main effects simultaneously in a two-way disproportionate ANOVA without interaction. The circumstances where the two F-statistics depart appreciably from statistical independence are characterized, and it is pointed out that procedures now exist for evaluating the bivariate F-probabilities when required. The augmented analysis is illustrated with a numerical example and an extension is offered for assymmetric BIBD's with random block effects.     

Decomposition of the main effects and interaction term by using orthogonal polynomials in multiple non symmetrical correspondence analysis

The multiple non symmetric correspondence analysis (MNSCA) is a useful technique for analyzing a two-way contingency table. In more complex cases, the predictor variables are more than one. In this paper, the MNSCA, along with the decomposition of the Gray–Williams Tau index, in main effects and interaction term, is used to analyze a contingency table with two predictor categorical variables and an ordinal response variable. The Multiple-Tau index is a measure of association that contains both main effects and interaction term. The main effects represent the change in the response variables due to the change in the level/categories of the predictor variables, considering the effects of their addition, while the interaction effect represents the combined effect of predictor categorical variables on the ordinal response variable. Moreover, for ordinal scale variables, we propose a further decomposition in order to check the existence of power components by using Emerson's orthogonal polynomials.     

Joint analysis of longitudinal data and competing terminal events in the presence of dependent observation times with application to chronic kidney disease

In many prospective clinical and biomedical studies, longitudinal biomarkers are repeatedly measured as health indicators to evaluate disease progression when patients are followed up over a period of time. Patient visiting times can be referred to as informative observation times if they are assumed to carry information in addition to that of the longitudinal biomarker measures alone. Irregular visiting times may reflect compliance with physician instruction, disease progression and symptom severity. When the follow-up time may be stopped by competing terminal events, it is possible that patient observation times may correlate with the competing terminal events themselves, thus making the observation times difficult to assess. To explicitly account for the impact of competing terminal events and dependent observation times on the longitudinal data analysis in the context of such complex data, we propose a joint model using latent random effects to describe the association among them. A likelihood-based approach is derived for statistical inference. Extensive simulation studies reveal that the proposed approach performs well for practical situations, and an analysis of patients with chronic kidney disease in a cohort study is presented to illustrate the proposed method.     

Optimality in the presence of two factor interactions among the nuisance factors

Here we consider an m way heterogeneity settingin the presence of two factor interactions among the heterogeneity directions . The set of experimental units considered do not exhaust all possible level combinations of the heterogeneity directions ; but the set is such that all heterogeneity effects assumed i n the model are orthogonally estmable.In such a setting , calleda doubly balanced m-way setting , the C-matrix of the reduced normal equations for the treatment effects is derived . Universally optimal designs are obtained in the cases where the settingis (i) Completely regular or (ii) partly regular of a special type . An interesting observation is that there are situations where the universally optimal designsin the present setting are totally different from the designs known t o be universally optimal when there is no interaction effect among the heterogeneity directions. This indicates that the usual optimality criteria are sensitive to validity or otherwise of the usual assumptions of lack of interactions among heterogeneity directions.     

A bayesian approach to prediction in analysis of variance settings

This paper takes the results of Lindley and smith ( 1972 ) one step further, by finding the predictive distribution of an observation y^* whose distribution is normal, and centred at A^* ₁θ₁ We then apply this distribution to the case of prediction based on data obtained in one and two wau ANOVA situations. For Example, it turns out that for two way ANOVA with interaction, the predictive mean, (which we would use as the predictor) is a weighted combination of sample main effects and interaction effects     

Some empirical results on the two-way analysis of variance by ranks

Iman (1974) and Conover and Iman (1976) have shown by means of simulation studies that a rank transform, whereby the ordinary F-tests are applied to the ranks of the original observations in two-way experimental designs, presents a remarkably powerful method of analysis. In the present study it is shown that this rank transform is closely related to the procedure proposed by Lemmer and Stoker (1967) for the two-way analysis of variance. The main conclusions are that the Iman tests are generally slightly more powerful than those of Lemmer and Stoker, but that in the presence of interaction the latter tests for main effects are safer to use than the former because interaction tends to make the Iman tests for main effects significant even if no main effects exist.     

Clustering for contingency tables: boxes and partitions

The correspondence analysis (CA) method appears to be an effective tool for analysis of interrelations between rows and columns in two-way contingency data. A discrete version of the method, box clustering, is developed in the paper using an approximation version of the CA model extended to the case when CA factor values are required to be Boolean. Several properties of the proposed SEFIT-BOX algorithm are proved to facilitate interpretation of its output. It is also shown that two known partitioning algorithms (applied within row or column sets only) could be considered as locally optimal algorithms for fitting the model, and extensions of these algorithms to a simultaneous row and column partitioning problem are proposed.     

Nonparametric estimation of current status data with dependent censoring

This paper discusses nonparametric estimation of a survival function when one observes only current status data (McKeown and Jewell, Lifetime Data Anal 16:215-230, 2010; Sun, The statistical analysis of interval-censored failure time data, 2006; Sun and Sun, Can J Stat 33:85-96, 2005). In this case, each subject is observed only once and the failure time of interest is observed to be either smaller or larger than the observation or censoring time. If the failure time and the observation time can be assumed to be independent, several methods have been developed for the problem. Here we will focus on the situation where the independent assumption does not hold and propose two simple estimation procedures under the copula model framework. The proposed estimates allow one to perform sensitivity analysis or identify the shape of a survival function among other uses. A simulation study performed indicates that the two methods work well and they are applied to a motivating example from a tumorigenicity study.