A robust I-sample analysis of means type randomization test for variances for unbalanced designs

Two analysis of means type randomization tests for testing the equality of I variances for unbalanced designs are presented. Randomization techniques for testing statistical hypotheses can be used when parametric tests are inappropriate. Suppose that I independent samples have been collected. Randomization tests are based on shuffles or rearrangements of the (combined) sample. Putting each of the I samples ‘in a bowl’ forms the combined sample. Drawing samples ‘from the bowl’ forms a shuffle. Shuffles can be made with replacement (bootstrap shuffling) or without replacement (permutation shuffling). The tests that are presented offer two advantages. They are robust to non-normality and they allow the user to graphically present the results via a decision chart similar to a Shewhart control chart. A Monte Carlo study is used to verify that the permutation version of the tests exhibit excellent power when compared to other robust tests. The Monte Carlo study also identifies circumstances under which the popular Levene's test fails.     

The effects of nonnormality on the analysis of supersaturated designs: a comparison of stepwise,SCAD and permutation test methods

Supersaturated designs (SSDs) are useful in examining many factors with a restricted number of experimental units. Many analysis methods have been proposed to analyse data from SSDs, with some methods performing better than others when data are normally distributed. It is possible that data sets violate assumptions of standard analysis methods used to analyse data from SSDs, and to date the performance of these analysis methods have not been evaluated using nonnormally distributed data sets. We conducted a simulation study with normally and nonnormally distributed data sets to compare the identification rates, power and coverage of the true models using a permutation test, the stepwise procedure and the smoothly clipped absolute deviation (SCAD) method. Results showed that at the level of significance α=0.01, the identification rates of the true models of the three methods were comparable; however at α=0.05, both the permutation test and stepwise procedures had considerably lower identification rates than SCAD. For most cases, the three methods produced high power and coverage. The experimentwise error rates (EER) were close to the nominal level (11.36%) for the stepwise method, while they were somewhat higher for the permutation test. The EER for the SCAD method were extremely high (84–87%) for the normal and t-distributions, as well as for data with outlier.     

The Performance of Randomization Tests that Use Permutations of Independent Variables

ABSTRACT

In this article we evaluate the performance of a randomization test for a subset of regression coefficients in a linear model. This randomization test is based on random permutations of the independent variables. It is shown that the method maintains its level of significance, except for extreme situations, and has power that approximates the power of another randomization test, which is based on the permutation of residuals from the reduced model. We also show, via an example, that the method of permuting independent variables is more valuable than other randomization methods because it can be used in connection with the downweighting of outliers.     

On the theory of modified randomization tests for nonparametric hypotheses

A general randomization test for nonparametric hypotheses which is a modification of permutation tests in proposed. The exact level of the test is derived and under mild gegularity conditions, a general result on the consistency of the power function is obtained. Applications to several testing problems are considered. Asymptotic expansions of the power of this test are derived with respect to contiguous alternatives thus test are derived with respect to contiguous alternatives thus enabling us to make deficiency comparisons with permutation tests. The paper concludes with some Monte Carlo simulations verifying the theoretical results derived.     

A simulation study on the influence of ties on uniform scores test for circular data

Uniform scores test is a rank-based method that tests the homogeneity of k-populations in circular data problems. The influence of ties on the uniform scores test has been emphasized by several authors in several articles and books. Moreover, it is suggested that the uniform scores test should be used with caution if ties are present in the data. This paper investigates the influence of ties on the uniform scores test by computing the power of the test using average, randomization, permutation, minimum, and maximum methods to break ties. Monte Carlo simulation is performed to compute the power of the test under several scenarios such as having 5% or 10% of ties and tie group structures in the data. The simulation study shows no significant difference among the methods under the existence of ties but the test loses its power when there are many ties or complicated group structures. Thus, randomization or average methods are equally powerful to break ties when applying uniform scores test. Also, it can be concluded that k-sample uniform scores test can be used safely without sacrificing the power if there are only less than 5% of ties or at most two groups of a few ties.     

Paired permutation testing in 2<Superscript><Emphasis Type="Italic">k</Emphasis></Superscript> unreplicated factorials

Exact permutation testing of effects in unreplicated two-level multifactorial designs is developed based on the notion of realigning observations and on paired permutations. This approach preserves the exchangeability of error components for testing up tok effects. Advantages and limitations of exact permutation procedures for unreplicated factorials are discussed and a simulation study on paired permutation testing is presented.     

A comparative study of tests for paired lifetime data

In this paper, we investigate different procedures for testing the equality of two mean survival times in paired lifetime studies. We consider Owen’s M-test and Q-test, a likelihood ratio test, the paired t-test, the Wilcoxon signed rank test and a permutation test based on log-transformed survival times in the comparative study. We also consider the paired t-test, the Wilcoxon signed rank test and a permutation test based on original survival times for the sake of comparison. The size and power characteristics of these tests are studied by means of Monte Carlo simulations under a frailty Weibull model. For less skewed marginal distributions, the Wilcoxon signed rank test based on original survival times is found to be desirable. Otherwise, the M-test and the likelihood ratio test are the best choices in terms of power. In general, one can choose a test procedure based on information about the correlation between the two survival times and the skewness of the marginal survival distributions.     

Robust I-sample analysis of means type randomization tests for variances

Four Analysis of Means (ANOM) type randomization tests for testing the equality of I variances are presented. Randomization techniques for testing statistical hypotheses can be used when parametric tests are inappropriate. Suppose that I independent samples have been collected. Randomization tests are based on shuffles or rearrangements of the (combined) sample. Putting each of the I samples "in a bowl" forms the combined sample. Drawing samples "from the bowl" forms a shuffle. Shuffles can be made with replacement (bootstrap shuffling) or without replacement (permutation shuffling). The tests that are presented offer two advantages. They are robust to non-normality and they allow the user to graphically present the results via a decision chart similar to a Shewhart control chart. The decision chart facilitates easy assessment of both statistical and practical significance. A Monte Carlo study is used to identify robust randomization tests that exhibit excellent power when compared to other robust tests.     

Permutation Methods for Comparing the Accuracy of Nested Prediction Models in Survival Analysis

When making patient-specific prediction, it is important to compare prediction models to evaluate the gain in prediction accuracy for including additional covariates. We propose two statistical testing methods, the complete data permutation (CDP) and the permutation cross-validation (PCV) for comparing prediction models. We simulate clinical trial settings extensively and show that both methods are robust and achieve almost correct test sizes; the methods have comparable power in moderate to large sample situations, while the CDP is more efficient in computation. The methods are also applied to ovarian cancer clinical trial data.     

The weighted log-rank class under truncated binomial design: saddlepoint p-values and confidence intervals

The randomization design used to collect the data provides basis for the exact distributions of the permutation tests. The truncated binomial design is one of the commonly used designs for forcing balance in clinical trials to eliminate experimental bias. In this article, we consider the exact distribution of the weighted log-rank class of tests for censored data under the truncated binomial design. A double saddlepoint approximation for p-values of this class is derived under the truncated binomial design. The speed and accuracy of the saddlepoint approximation over the normal asymptotic facilitate the inversion of the weighted log-rank tests to determine nominal 95% confidence intervals for treatment effect with right censored data.     

A Bayesian sequential design with adaptive randomization for 2‐sided hypothesis test

Bayesian sequential and adaptive randomization designs are gaining popularity in clinical trials thanks to their potentials to reduce the number of required participants and save resources. We propose a Bayesian sequential design with adaptive randomization rates so as to more efficiently attribute newly recruited patients to different treatment arms. In this paper, we consider 2‐arm clinical trials. Patients are allocated to the 2 arms with a randomization rate to achieve minimum variance for the test statistic. Algorithms are presented to calculate the optimal randomization rate, critical values, and power for the proposed design. Sensitivity analysis is implemented to check the influence on design by changing the prior distributions. Simulation studies are applied to compare the proposed method and traditional methods in terms of power and actual sample sizes. Simulations show that, when total sample size is fixed, the proposed design can obtain greater power and/or cost smaller actual sample size than the traditional Bayesian sequential design. Finally, we apply the proposed method to a real data set and compare the results with the Bayesian sequential design without adaptive randomization in terms of sample sizes. The proposed method can further reduce required sample size.     

A comparison of recent nonparametric methods for testing effects in two-by-two factorial designs

The two-way two-levels crossed factorial design is a commonly used design by practitioners at the exploratory phase of industrial experiments. The F-test in the usual linear model for analysis of variance (ANOVA) is a key instrument to assess the impact of each factor and of their interactions on the response variable. However, if assumptions such as normal distribution and homoscedasticity of errors are violated, the conventional wisdom is to resort to nonparametric tests. Nonparametric methods, rank-based as well as permutation, have been a subject of recent investigations to make them effective in testing the hypotheses of interest and to improve their performance in small sample situations. In this study, we assess the performances of some nonparametric methods and, more importantly, we compare their powers. Specifically, we examine three permutation methods (Constrained Synchronized Permutations, Unconstrained Synchronized Permutations and Wald-Type Permutation Test), a rank-based method (Aligned Rank Transform) and a parametric method (ANOVA-Type Test). In the simulations, we generate datasets with different configurations of distribution of errors, variance, factor's effect and number of replicates. The objective is to elicit practical advice and guides to practitioners regarding the sensitivity of the tests in the various configurations, the conditions under which some tests cannot be used, the tradeoff between power and type I error, and the bias of the power on one main factor analysis due to the presence of effect of the other factor. A dataset from an industrial engineering experiment for thermoformed packaging production is used to illustrate the application of the various methods of analysis, taking into account the power of the test suggested by the objective of the experiment.     

Goodness-of-fit testing of a weak memoryless property of life distributions

A life distribution is said to have a weak memoryless property if its conditional probability of survival beyond a fixed time point is equal to its (unconditional) survival probability at that point. Goodness‐of‐fit testing of this notion is proposed in the current investigation, both when the fixed time point is known and when it is unknown but estimable from the data. The limiting behaviour of the proposed test statistic is obtained and the null variance is explicitly given. The empirical power of the test is evaluated for a commonly known alternative using Monte Carlo methods, showing that the test performs well. The case when the fixed time point t₀ equals a quantile of the distribution F gives a distribution‐free test procedure. The procedure works even if t₀ is unknown but is estimable.     

A review of optimal designs in survey sampling

Results in five areas of survey sampling dealing with the choice of the sampling design are reviewed. In Section 2, the results and discussions surrounding the purposive selection methods suggested by linear regression superpopulation models are reviewed. In Section 3, similar models to those in the previous section are considered; however, random sampling designs are considered and attention is focused on the optimal choice of π_j. Then in Section 4, systematic sampling methods obtained under autocorrelated superpopulation models are reviewed. The next section examines minimax sampling designs. The work in the final section is based solely on the randomization. In Section 6 methods of sample selection which yield inclusion probabilities π_j = n/N and π_ij = n(n - 1)/N(N - 1), but for which there are fewer than _NC_n possible samples, are mentioned briefly.     

Design and inference for 3‐stage bioequivalence testing with serial sampling data

A bioequivalence test is to compare bioavailability parameters, such as the maximum observed concentration (C_max) or the area under the concentration‐time curve, for a test drug and a reference drug. During the planning of a bioequivalence test, it requires an assumption about the variance of C_max or area under the concentration‐time curve for the estimation of sample size. Since the variance is unknown, current 2‐stage designs use variance estimated from stage 1 data to determine the sample size for stage 2. However, the estimation of variance with the stage 1 data is unstable and may result in too large or too small sample size for stage 2. This problem is magnified in bioequivalence tests with a serial sampling schedule, by which only one sample is collected from each individual and thus the correct assumption of variance becomes even more difficult. To solve this problem, we propose 3‐stage designs. Our designs increase sample sizes over stages gradually, so that extremely large sample sizes will not happen. With one more stage of data, the power is increased. Moreover, the variance estimated using data from both stages 1 and 2 is more stable than that using data from stage 1 only in a 2‐stage design. These features of the proposed designs are demonstrated by simulations. Testing significance levels are adjusted to control the overall type I errors at the same level for all the multistage designs.     

Estimating standard error of intra-class correlation coefficients up to three level unbalanced nested clinical trials

ABSTRACT

Very often researchers plan a balanced design for cluster randomization clinical trials in conducting medical research, but unavoidable circumstances lead to unbalanced data. By adopting three or more levels of nested designs, they usually ignore the higher level of nesting and consider only two levels, this situation leads to underestimation of variance at higher levels. While calculating the sample size for three-level nested designs, in order to achieve desired power, intra-class correlation coefficients (ICCs) at individual level as well as higher levels need to be considered and must be provided along with respective standard errors. In the present paper, the standard errors of analysis of variance (ANOVA) estimates of ICCs for three-level unbalanced nested design are derived. To conquer the strong appeal of distributional assumptions, balanced design, equality of variances between clusters and large sample, general expressions for standard errors of ICCs which can be deployed in unbalanced cluster randomization trials are postulated. The expressions are evaluated on real data as well as highly unbalanced simulated data.     

Permutation Tests for Comparing Inequality Measures

ABSTRACT

Asymptotic and bootstrap tests for inequality measures are known to perform poorly in finite samples when the underlying distribution is heavy-tailed. We propose Monte Carlo permutation and bootstrap methods for the problem of testing the equality of inequality measures between two samples. Results cover the Generalized Entropy class, which includes Theil’s index, the Atkinson class of indices, and the Gini index. We analyze finite-sample and asymptotic conditions for the validity of the proposed methods, and we introduce a convenient rescaling to improve finite-sample performance. Simulation results show that size correct inference can be obtained with our proposed methods despite heavy tails if the underlying distributions are sufficiently close in the upper tails. Substantial reduction in size distortion is achieved more generally. Studentized rescaled Monte Carlo permutation tests outperform the competing methods we consider in terms of power.     

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 Discussion of Permutation Tests Conditional to Observed Responses in Unreplicated 2 M Full Factorial Designs

ABSTRACT

In this article we present a new solution to test for effects in unreplicated two-level factorial designs. The proposed test statistic, in case the error components are normally distributed, follows an F random variable, though our attention is on its nonparametric permutation version. The proposed procedure does not require any transformation of data such as residualization and it is exact for each effect and distribution-free. Our main aim is to discuss a permutation solution conditional to the original vector of responses. We give two versions of the same nonparametric testing procedure in order to control both the individual error rate and the experiment-wise error rate. A power comparison with Loughin and Noble's test is provided in the case of a unreplicated 2⁴ full factorial design.     

Comparison of permutation methods for the partial correlation and partial mantel tests

This study compares empirical type I error and power of different permutation techniques that can be used for partial correlation analysis involving three data vectors and for partial Mantel tests. The partial Mantel test is a form of first-order partial correlation analysis involving three distance matrices which is widely used in such fields as population genetics, ecology, anthropology, psychometry and sociology. The methods compared are the following: (1) permute the objects in one of the vectors (or matrices); (2) permute the residuals of a null model; (3) correlate residualized vector 1 (or matrix A) to residualized vector 2 (or matrix B); permute one of the residualized vectors (or matrices); (4) permute the residuals of a full model. In the partial correlation study, the results were compared to those of the parametric t-test which provides a reference under normality. Simulations were carried out to measure the type I error and power of these permutatio methods, using normal and non-normal data, without and with an outlier. There were 10 000 simulations for each situation (100 000 when n = 5); 999 permutations were produced per test where permutations were used. The recommended testing procedures are the following:(a) In partial correlation analysis, most methods can be used most of the time. The parametric t-test should not be used with highly skewed data. Permutation of the raw data should be avoided only when highly skewed data are combined with outliers in the covariable. Methods implying permutation of residuals, which are known to only have asymptotically exact significance levels, should not be used when highly skewed data are combined with small sample size. (b) In partial Mantel tests, method 2 can always be used, except when highly skewed data are combined with small sample size. (c) With small sample sizes, one should carefully examine the data before partial correlation or partial Mantel analysis. For highly skewed data, permutation of the raw data has correct type I error in the absence of outliers. When highly skewed data are combined with outliers in the covariable vector or matrix, it is still recommended to use the permutation of raw data. (d) Method 3 should never be used.