Critical value functions for likelihood-ratio tests for normality

When using maximum likelihood methods to estimate genetic and environmental components of (co)variance, it is common to test hypotheses using likelihood ratio tests, since such tests have desirable asymptotic properties. In particular, the standard likelihood ratio test statistic is assumed asymptotically to follow a χ2distribution with degrees of freedom equal to the number of parameters tested. Using the relationship between least squares and maximum likelihood estimators for balanced designs, it is shown why the asymptotic distribution of the likelihood ratio test for variance components does not follow a χ2distribution with degrees of freedom equal to the number of parameters tested when the null hypothesis is true. Instead, the distribution of the likelihood ratio test is a mixture of χ2distributions with different degrees of freedom. Implications for testing variance components in twin designs and for quantitative trait loci mapping are discussed. The appropriate distribution of the likelihood ratio test statistic should be used in hypothesis testing and model selection.

Likelihood ratio tests for many groups in high dimensions

This paper studies the applications of extreme value theory on analysis for closing price data of the Dow-Jones industrial index and Danish fire insurance claims data. The generalized extreme value (GEV) distribution is considered in analyzing the real data, and the hypothesis testing problem for the shape parameter of GEV distribution is investigated based on a new test statistic—the $$L_q$$ -likelihood ratio ( $$L_q$$ R) statistic. The $$L_q$$ R statistic can be treated as a generalized form of the classical likelihood ratio (LR) statistic. We show that the asymptotic behavior of proposed statistic is characterized by the degree of distortion $$q$$ . For small and modest sample sizes, the $$L_q$$ R statistic is still available when $$q$$ is properly chosen. By simulation studies, the proposed statistic not only performs the asymptotic properties, but also outperforms the classical LR statistic as the sample sizes are modest or even small. Meanwhile, the test power based on the new statistic is also simulated by Monte Carlo methods. At last, the models are diagnosed by graphical methods.

DrGaP: A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies

4 - A moments-based procedure for evaluating risk forecasting models

Multivariate linear regressions are widely used statistical tools in many applications to model the associations between multiple related responses and a set of predictors. To infer such associations, it is often of interest to test the structure of the regression coefficients matrix, and the likelihood ratio test (LRT) is one of the most popular approaches in practice. Despite its popularity, it is known that the classical $\chi^2$ approximations for LRTs often fail in high-dimensional settings, where the dimensions of responses and predictors $(m,p)$ are allowed to grow with the sample size $n$. Though various corrected LRTs and other test statistics have been proposed in the literature, the fundamental question of when the classic LRT starts to fail is less studied, an answer to which would provide insights for practitioners, especially when analyzing data with $m/n$ and $p/n$ small but not negligible. Moreover, the power performance of the LRT in high-dimensional data analysis remains underexplored. To address these issues, the first part of this work gives the asymptotic boundary where the classical LRT fails and develops the corrected limiting distribution of the LRT for a general asymptotic regime. The second part of this work further studies the test power of the LRT in the high-dimensional setting. The result not only advances the current understanding of asymptotic behavior of the LRT under alternative hypothesis, but also motivates the development of a power-enhanced LRT. The third part of this work considers the setting with $p>n$, where the LRT is not well-defined. We propose a two-step testing procedure by first performing dimension reduction and then applying the proposed LRT. Theoretical properties are developed to ensure the validity of the proposed method. Numerical studies are also presented to demonstrate its good performance.

From first principles, we derive a quadratic nonlinear, first-order dynamical system capable of performing exact Bayes-Markov inferences for a wide class of biologically plausible stimulus-dependent patterns of activity while simultaneously providing an online estimate of model performance. This is accomplished by constructing a dynamical system that has solutions proportional to the probability distribution over the stimulus space, but with a constant of proportionality adjusted to provide a local estimate of the probability of the recent observations of stimulus-dependent activity-given model parameters. Next, we transform this exact equation to generate nonlinear equations for the exact evolution of log likelihood and log-likelihood ratios and show that when the input has low amplitude, linear rate models for both the likelihood and the log-likelihood functions follow naturally from these equations. We use these four explicit representations of the probability distribution to argue that, in contrast to the arguments of previous work, the dynamical system for the exact evolution of the likelihood (as opposed to the log likelihood or log-likelihood ratios) not only can be mapped onto a biologically plausible network but is also more consistent with physiological observations.

In this paper, we examine by Monte Carlo experiments the small sample properties of the W (Wald), LM (Lagrange Multiplier) and LR (Likelihood Ratio) tests for equality between sets of coefficients in two linear regressions under heteroscedasticity. The small sample properties of the size-corrected W, LM and LR tests proposed by Rothenberg (1984) are also examined and it is shown that the performances of the size-corrected W and LM tests are very good. Further, we examine the two-stage test which consists of a test for homoscedasticity followed by the Chow (1960) test if homoscedasticity is indicated or one of the W, LM or LR tests if heteroscedasticity should be assumed. It is shown that the pretest does not reduce much the bias in the size when the sizecorrected citical values are used in the W, LM and LR tests.

This study aims to compare normality tests in different sample sizes in data with normal distribution under different kurtosis and skewness coefficients obtained simulatively. To this end, firstly, simulative data were produced using the MATLAB program for different skewness/kurtosis coefficients and different sample sizes. The normality analysis of each data type was conducted using the MATLAB program and ten different normality tests; namely, (Kolmogorov Smirnov (KS) Test, KS Stephens Modification, KS Marsaglia, KS Lilliefors Modification, Anderson-Darling Test, Cramer- Von Mises Test, Shapiro-Wilk Test, Shapiro-Francia Test, Jarque-Bera Test, and D’Agostino & Pearson Test). As a result of the analyses conducted according to ten different normality tests, it was found that normality tests were not affected by the sample size when the skewness and kurtosis coefficients were equal to or close to zero; however, in cases where the skewness and kurtosis coefficients moved away from zero, it was found that normality tests are affected by the sample size, and such tests tend to give significant results. Therefore, in large samples, it may be suggested that critical values for skewness and kurtosis coefficients’ z-scores as proposed by Kim (2013) and Mayers (2013) or the histogram graphs be used.

Summary The mixed linear model is a popular method for analysing unbalanced repeated measurement data. The classical statistical tests for parameters in this model are based on asymptotic theory that is unreliable in the small samples that are often encountered in practice. For testing a given fixed effect parameter with a small sample, we develop and investigate refined likelihood ratio (LR) tests. The refinements considered are the Bartlett correction and use of the Cox–Reid adjusted likelihood; these are examined separately and in combination. We illustrate the various LR tests on an actual data set and compare them in two simulation studies. The conventional LR test yields type I error rates that are higher than nominal. The adjusted LR test yields rates that are lower than nominal, with absolute accuracy similar to that of the conventional LR test in the first simulation study and better in the second. The Bartlett correction substantially improves the accuracy of the type I error rates with either the conventional or the adjusted LR test. In many cases, error rates that are very close to nominal are achieved with the refined methods.

BackgroundThe detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association study is to compare the observed median association test statistic to the expected median test statistic. This ratio is inflated in the presence of cryptic population structure. However, inflation may also be caused by the properties of the association test itself particularly in the analysis of rare variants. We compared the properties of the three most commonly used association tests: the likelihood ratio test, the Wald test and the score test when testing rare variants for association using simulated data.ResultsWe found evidence of inflation in the median test statistics of the likelihood ratio and score tests for tests of variants with less than 20 heterozygotes across the sample, regardless of the total sample size. The test statistics for the Wald test were under-inflated at the median for variants below the same minor allele frequency.ConclusionsIn a genetic association study, if a substantial proportion of the genetic variants tested have rare minor allele frequencies, the properties of the association test may mask the presence or absence of bias due to population structure. The use of either the likelihood ratio test or the score test is likely to lead to inflation in the median test statistic in the absence of population structure. In contrast, the use of the Wald test is likely to result in under-inflation of the median test statistic which may mask the presence of population structure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0496-1) contains supplementary material, which is available to authorized users.

The limit distributions of likelihood ratio and cumulative sum tests for a change in a binomial probability

A simple iterative procedure is found for the exact null and alternative distributions of likelihood ratio, cumulative sum and related statistics for testing for a change in probability of a sequence of independent binomial random variables. It is concluded that the likelihood ratio test is slightly less powerful than the cumulative sum test near the middle of the sequence, but that the likelihood ratio test is much more powerful near the ends. An example from epidemiology is used to illustrate the results. Under certain conditions the cumulative sum test is identical to a two-sample Kolmogorov-Smirnov test and so the iterative procedure can be used to find the null distribution of Kolmogorov-Smirnov and related statistics.

Several approaches to hypothesis testing for coefficients in least absolute value regression are compared using a Monte Carlo simulation: likelihood ratio test, Lagrange multiplier test, and three versions of the bootstrap hypothesis test. Factors considered that might influence test performance include the disturbance distribution, the type of independent variable, and the sample size. Overall, the likelihood ratio and the bootstrap tests perform best, with the likelihood ratio test being marginally more powerful. Least absolute value tests are also compared to the standard t test and three versions of the bootstrapped t test for least squares regression.

This article extends the validity of the conditional likelihood ratio (CLR) test developed by Moreira (2003, Econometrica 71(4), 1027-–1048) to instrumental variable regression models with unknown homoskedastic error variance and many weak instruments. We argue that the conventional CLR test with estimated error variance loses exact similarity and is asymptotically invalid in this setting. We propose a modified critical value function for the likelihood ratio (LR) statistic with estimated error variance, and prove that our modified test achieves asymptotic validity under many weak instruments asymptotics. Our critical value function is constructed by representing the LR using four statistics, instead of two as in Moreira (2003, Econometrica 71(4), 1027-–1048). A simulation study illustrates the desirable finite sample properties of our test.