Fitting DNA sequences through log-linear modelling with linear constraints

For some discrete state series, such as DNA sequences, it can often be postulated that its probabilistic behaviour is given by a Markov chain. For making the decision on whether or not an uncharacterized piece of DNA is part of the coding region of a gene, under the Markovian assumption, there are two statistical tools that are essential to be considered: the hypothesis testing of the order in a Markov chain and the estimators of transition probabilities. In order to improve the traditional statistical procedures for both of them when stationarity assumption can be considered, a new version for understanding the homogeneity hypothesis is proposed so that log-linear modelling is applied for conditional independence jointly with homogeneity restrictions on the expected means of transition counts in the sequence. In addition we can consider a variety of test-statistics and estimators by using φ-divergence measures. As special case of them the well-known likelihood ratio test-statistics and maximum-likelihood estimators are obtained.     

Improved testing for the binomial distribution using chi-squared components with data-dependent cells

A power study suggests that a good test of fit analysis for the binomial distribution is provided by a data-dependent Chernoff–Lehmann X ² test with class expectations greater than unity, and its components. These data-dependent statistics involve arithmetically simple parameter estimation, convenient approximate distributions and provide a comprehensive assessment of how well the data agree with a binomial distribution. We suggest that a well-performed single test of fit statistic is the Anderson–Darling statistic.     

A likelihood ratio test of quasi-independence for sparse two-way contingency tables

We consider a likelihood ratio test of independence for large two-way contingency tables having both structural (non-random) and sampling (random) zeros in many cells. The solution of this problem is not available using standard likelihood ratio tests. One way to bypass this problem is to remove the structural zeroes from the table and implement a test on the remaining cells which incorporate the randomness in the sampling zeros; the resulting test is a test of quasi-independence of the two categorical variables. This test is based only on the positive counts in the contingency table and is valid when there is at least one sampling (random) zero. The proposed (likelihood ratio) test is an alternative to the commonly used ad hoc procedures of converting the zero cells to positive ones by adding a small constant. One practical advantage of our procedure is that there is no need to know if a zero cell is structural zero or a sampling zero. We model the positive counts using a truncated multinomial distribution. In fact, we have two truncated multinomial distributions; one for the null hypothesis of independence and the other for the unrestricted parameter space. We use Monte Carlo methods to obtain the maximum likelihood estimators of the parameters and also the p-value of our proposed test. To obtain the sampling distribution of the likelihood ratio test statistic, we use bootstrap methods. We discuss many examples, and also empirically compare the power function of the likelihood ratio test relative to those of some well-known test statistics.     

On gart's test for interaction of second order

Gart (1972) ottered a Statistic on testing the hypothesis of no second-order interaction in a 2×s×t contingency table. The statistic was tn be used as an asymptotic chi-square with (s-1) (t-1) degrees of freedom. We show that this statistic suiters from the drawback that unless certain side conditions hold, the statistic would reject the null hypothesis with probability approaching one asymptotically even in the null case. Hence the statistic is not strictly valid for the hypothesis for which it was intended.     

Extreme probabilities for contingency tables under row and column independence with application to fisher's exact test

Theorerms are proved for the maxima and minima of IIR_i!/IIC_j!/T!II_yij ! over r× c contingcncy tables Y=(y_ij) with row sums R₁,…,R_r, column sums C₁,…,C_c, and grand total T. These results are imlplemented into the network algorithm of Mehta and Patel (1983) for computing the P-value of Fisher's exact test for unordered r×c contingency tables. The decrease in the amount of computing time can be substantial when the column sums are very different.     

A modified Kolmogorov-Smirnov test for a rectangular distribution with unknown parameters: Computation of the distribution of the test statistic

A recursive scheme for the calculation of the distribution of the test statistic of a modified Kolmogorov-Smirnov-test for a rectangular distribution with unknown parameters is given.     

A modified chi-square test for Bertholon model with censored data

In this work, we propose the construction of a chi-squared goodness-of-fit test in censored data case, for Bertholon model which can analyse various competing risks of failure or death. This test is based on a modification of the Nikulin-Rao-Robson (NRR) statistic proposed by Bagdonavicius and Nikulin (2011a Bagdonavicius, V., Nikulin, M. (2011a). Chi-squared tests for general composite hypotheses from censored samples. Comptes Rendus Mathématiques: Series I 349(3–4):219–223. [Google Scholar], 2011b Bagdonavicius, V., Nikulin, M. (2011b). Chi-squared goodness-of-fit test for right censored data. International Journal of Applied Mathematics and Statistics 24:30–50. [Google Scholar]) for censored data. We applied this test to numerical examples from simulated samples and real data.     

Inference for Multi‐dimensional High‐frequency Data with an Application to Conditional Independence Testing

We find the asymptotic distribution of the multi‐dimensional multi‐scale and kernel estimators for high‐frequency financial data with microstructure. Sampling times are allowed to be asynchronous and endogenous. In the process, we show that the classes of multi‐scale and kernel estimators for smoothing noise perturbation are asymptotically equivalent in the sense of having the same asymptotic distribution for corresponding kernel and weight functions. The theory leads to multi‐dimensional stable central limit theorems and feasible versions. Hence, they allow to draw statistical inference for a broad class of multivariate models, which paves the way to tests and confidence intervals in risk measurement for arbitrary portfolios composed of high‐frequently observed assets. As an application, we enhance the approach to construct a test for investigating hypotheses that correlated assets are independent conditional on a common factor.     

The exact unconditional z-pooled test for equality of two binomial probabilities: optimal choice of the Berger and Boos confidence coefficient

Exact unconditional tests for comparing two binomial probabilities are generally more powerful than conditional tests like Fisher's exact test. Their power can be further increased by the Berger and Boos confidence interval method, where a p-value is found by restricting the common binomial probability under H ₀ to a 1?γ confidence interval. We studied the average test power for the exact unconditional z-pooled test for a wide range of cases with balanced and unbalanced sample sizes, and significance levels 0.05 and 0.01. The detailed results are available online on the web. Among the values 10^?3, 10^?4, …, 10^?10, the value γ=10^?4 gave the highest power, or close to the highest power, in all the cases we looked at, and can be given as a general recommendation as an optimal γ.     

A density-based empirical likelihood ratio goodness-of-fit test for the Rayleigh distribution and power comparison

The Rayleigh distribution has been used to model right skewed data. Rayleigh [On the resultant of a large number of vibrations of the some pitch and of arbitrary phase. Philos Mag. 1880;10:73–78] derived it from the amplitude of sound resulting from many important sources. In this paper, a new goodness-of-fit test for the Rayleigh distribution is proposed. This test is based on the empirical likelihood ratio methodology proposed by Vexler and Gurevich [Empirical likelihood ratios applied to goodness-of-fit tests based on sample entropy. Comput Stat Data Anal. 2010;54:531–545]. Consistency of the proposed test is derived. It is shown that the distribution of the proposed test does not depend on scale parameter. Critical values of the test statistic are computed, through a simulation study. A Monte Carlo study for the power of the proposed test is carried out under various alternatives. The performance of the test is compared with some well-known competing tests. Finally, an illustrative example is presented and analysed.     

Shift in re‐randomization distribution with conditional randomization test

Proschan, Brittain, and Kammerman made a very interesting observation that for some examples of the unequal allocation minimization, the mean of the unconditional randomization distribution is shifted away from 0. Kuznetsova and Tymofyeyev linked this phenomenon to the variations in the allocation ratio from allocation to allocation in the examples considered in the paper by Proschan et al. and advocated the use of unequal allocation procedures that preserve the allocation ratio at every step. In this paper, we show that the shift phenomenon extends to very common settings: using conditional randomization test in a study with equal allocation. This phenomenon has the same cause: variations in the allocation ratio among the allocation sequences in the conditional reference set, not previously noted. We consider two kinds of conditional randomization tests. The first kind is the often used randomization test that conditions on the treatment group totals; we describe the variations in the conditional allocation ratio with this test on examples of permuted block randomization and biased coin randomization. The second kind is the randomization test proposed by Zheng and Zelen for a multicenter trial with permuted block central allocation that conditions on the within‐center treatment totals. On the basis of the sequence of conditional allocation ratios, we derive the value of the shift in the conditional randomization distribution for specific vector of responses and the expected value of the shift when responses are independent identically distributed random variables. We discuss the asymptotic behavior of the shift for the two types of tests. Copyright © 2013 John Wiley & Sons, Ltd.     

Some Theoretical and Simulation Results on the Frequency Domain Causality Test

Breitung and Candelon (2006 Breitung , J. , Candelon , B. ( 2006 ). Testing for short- and long-run causality: A frequency-domain approach . Journal of Econometrics 132 : 363 – 378 .[Crossref], [Web of Science ®] , [Google Scholar]) in Journal of Econometrics proposed a simple statistical testing procedure for the noncausality hypothesis at a given frequency. In their paper, however, they reported some theoretical results indicating that their test severely suffers from quite low power when the noncausality hypothesis is tested at a frequency close to 0 or pi. This paper examines whether or not these results indicate their procedure is useless at such frequencies.     

A note on a parametric extension of rank tests to the analysis of multifactor experiments within blocks

A general rank test procedure based on an underlying multinomial distribution is suggested for randomized block experiments with multifactor treatment combinations within each block. The Wald statistic for the multinomial is used to test hypotheses about the within–block rankings. This statistic is shown to be related to the one–sample Hotellingt's T² statistic, suggesting a method for computing the test statistic using the standard statistical computer packages.     

Transform methods for the hypergeometric distribution

Two new methods for computing with hypergeometric distributions on lattice points are presented. One uses Fourier analysis, and the other uses Gröbner bases in the Weyl algebra. Both are very general and apply to log-linear models that are graphical or non-graphical.     

Computation of the percentage points and the power for the two-sided Kolmogorov-Smirnov one sample test

Two recursive schemes are presented for the calculation of the probabilityP(g(x)≤S _n (x)≤h(x) for allx∈®), whereS _n is the empirical distribution function of a sample from a continuous distribution andh, g are continuous and isotone functions. The results are specialized for the calculation of the distribution and the corresponding percentage points of the test statistic of the two-sided Kolmogorov-Smirnov one sample test. The schemes allow the calculation of the power of the test too. Finally an extensive tabulation of percentage points for the Kolmogorov-Smirnov test is given.     

Conditional estimation of average on the basis of weighting data

LetF(x,y) be a distribution function of a two dimensional random variable (X,Y). We assume that a distribution functionF _x(x) of the random variableX is known. The variableX will be called an auxiliary variable. Our purpose is estimation of the expected valuem=E(Y) on the basis of two-dimensional simple sample denoted by:U=[(X ₁, Y₁)…(X_n, Y_n)]=[X Y]. LetX=[X ₁…X _n]andY=[Y ₁…Y _n].This sample is drawn from a distribution determined by the functionF(x,y). LetX _(k)be the k-th (k=1, …,n) order statistic determined on the basis of the sampleX. The sampleU is truncated by means of this order statistic into two sub-samples: % MathType!End!2!1! and % MathType!End!2!1!.Let % MathType!End!2!1! and % MathType!End!2!1! be the sample means from the sub-samplesU _k,1 andU _k,2, respectively. The linear combination % MathType!End!2!1! of these means is the conditional estimator of the expected valuem. The coefficients of this linear combination depend on the distribution function of auxiliary variable in the pointx _(k).We can show that this statistic is conditionally as well as unconditionally unbiased estimator of the averagem. The variance of this estimator is derived. The variance of the statistic % MathType!End!2!1! is compared with the variance of the order sample mean. The generalization of the conditional estimation of the mean is considered, too.     

The information matrix test in the linear regression with ARMA errors

Summary The paper shows that the informaton matrix test presented by White (1982) decomposes into the sum of quadratic forms in the case of a linear model with ARMA errors. By extending previous results, which analysed the information matrix test in the presence of serial correlation, the test allows detection of additional sources of misspecification.     

A comparison of test statistics for the recovery of rapid growth‐based enumeration tests

This paper considers five test statistics for comparing the recovery of a rapid growth‐based enumeration test with respect to the compendial microbiological method using a specific nonserial dilution experiment. The finite sample distributions of these test statistics are unknown, because they are functions of correlated count data. A simulation study is conducted to investigate the type I and type II error rates. For a balanced experimental design, the likelihood ratio test and the main effects analysis of variance (ANOVA) test for microbiological methods demonstrated nominal values for the type I error rate and provided the highest power compared with a test on weighted averages and two other ANOVA tests. The likelihood ratio test is preferred because it can also be used for unbalanced designs. It is demonstrated that an increase in power can only be achieved by an increase in the spiked number of organisms used in the experiment. The power is surprisingly not affected by the number of dilutions or the number of test samples. A real case study is provided to illustrate the theory. Copyright © 2013 John Wiley & Sons, Ltd.     

A Remark on the Zhang Omnibus Test for Normality

Zhang (1999) proposed a novel test statistic Q for testing normality based on the ratio of two unbiased standard deviation estimators, q₁ and q₂, for the true population standard deviation σ. Mingoti & Neves (2003) discussed some properties of q₁ and q₂ and showed that the variance of q₁ increases as the true population variance increases. In this paper, we show that the distribution of q₁ is not normal. As a result, normality percentage points for Q are not appropriate. In this paper, percentage points of Q are obtained using simulations. Monte Carlo simulations are provided to evaluate the performance of the new method and Zhang's method.