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PubMed1994

Bootstrap hypothesis tests for evolutionary trees and other dendrograms.

The bootstrap computer-intensive statistical technique is frequently applied to statistical analyses of phylogenetic trees. The widely used rule that a group is supported significantly if it appears in at least 95% of bootstrap trees is conservative in most situations. This paper describes three ways of using the bootstrap to carry out statistical inference on phylogenies. The first method tests whether there is nonrandom support for a single group or tree. The second method compares the support for two groups or trees. The third method tests whether a single group or tree has better support than the set of all possible alternatives; this may be a replacement for the "95% rule." These tests generally require fewer bootstrap trees to be estimated than do other methods of bootstrapping phylogenies. A simple, sequential statistical method can be used to increase the efficiency further. These methods can be applied to tests of multiple hypotheses about a single phylogeny. Parsimony analyses of 5S rRNA sequences of plants and cluster analyses of randomly amplified polymorphic DNA bands in three pathotypes of the cereal eyespot fungus are used as illustrative examples. The tests can be used to analyze dendrograms in subjects other than taxonomy.

Base Sequence↗
PubMed1994

Estimation and hypothesis testing of treatment effects in animal reproductive toxicology studies.

Healy (1) and Dempster et al. (8) proposed statistical methods to evaluate the treatment effects in animal reproductive toxicology research. Both methods assume homogeneous variance for the dams and the pups, respectively, in all the treatment groups. In this paper, via mixed effect modeling, we propose a method to estimate the treatment effects allowing heterogeneous variances for the dams and the pups, respectively, in different treatment groups. Covariates will also be included in the model. A procedure to test the fixed effects is also discussed. An example from an animal reproductive toxicological study is used to illustrate the procedures.

Animals↗
PubMed2002

Adjusting pairwise nonparametric equivalence hypothesis tests and confidence intervals for period effects in 3 x 3 crossover trials.

In pharmacokinetic and pharmacodynamic 3 x 3 crossover trials, average bioequivalence and noninferiority between treatments need to be only assessed pairwise in most cases. Due to the restricted number of subjects in such trials, normal distribution assumptions cannot be checked and frequently outliers are encountered, so that a nonparametric approach is more adequate. Therefore, to assess average bioequivalence or noninferiority, a new method is proposed to derive period adjusted nonparametric confidence intervals for pairwise treatment differences.

Chemistry, Pharmaceutical↗
PubMed1999

Study design and hypothesis testing: issues in the evaluation of evidence from research in nutritional epidemiology.

In addressing questions about the relations of dietary factors to disease in human populations, epidemiologic studies must account for the complexity of dietary habits, the intercorrelations among dietary habits, and the correlations of those habits with other behaviors. Furthermore, for studies of chronic disease, relevant dietary exposures may occur over decades. The classic epidemiologic study designs have been used to examine the associations between diet and disease; the strengths and weaknesses of those designs must be considered. Concerns have been raised regarding the validity of the measures of diet, the differential recall of diet by diseased individuals in case-control studies, and confounding by other related factors in both case-control and cohort studies. In clinical trials there may be difficulties in effecting the necessary dietary changes, especially for macronutrients, and there are also concerns about those circumstances in which participants cannot be blinded to their treatment. For case-control and cohort studies and for some clinical trials, intercorrelations among nutrients are a concern in the identification of factors that are important in the etiology of disease. It is important to understand these considerations when interpreting nutritional epidemiologic studies for the purpose of setting public policy. No one study can be considered definitive in the understanding of a diet-disease relation. However, epidemiologic findings from multiple studies taken together can contribute significantly to our understanding of diet in relation to disease in humans.

Bias↗
PubMed2004

HyPhy: hypothesis testing using phylogenies.

UNLABELLED: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution. AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org.

Algorithms↗
PubMed2003

Hypothesis testing in semiparametric additive mixed models.

We consider testing whether the nonparametric function in a semiparametric additive mixed model is a simple fixed degree polynomial, for example, a simple linear function. This test provides a goodness-of-fit test for checking parametric models against nonparametric models. It is based on the mixed-model representation of the smoothing spline estimator of the nonparametric function and the variance component score test by treating the inverse of the smoothing parameter as an extra variance component. We also consider testing the equivalence of two nonparametric functions in semiparametric additive mixed models for two groups, such as treatment and placebo groups. The proposed tests are applied to data from an epidemiological study and a clinical trial and their performance is evaluated through simulations.

Anticonvulsants↗
PubMed2006

The influence of competing-risks setting on the choice of hypothesis test for treatment effect.

There is considerable debate regarding the choice of test for treatment difference in a randomized clinical trial in the presence of competing risks. This question arose in the study of standard and new antiepileptic drugs (SANAD) trial comparing new and standard antiepileptic drugs. This paper provides simulation results for the log-rank test comparing cause-specific hazard rates and Gray's test comparing cause-specific cumulative incidence curves. To inform the analysis of the SANAD trial, competing-risks settings were considered where both events are of interest, events may be negatively correlated, and the degree of correlation may differ in the 2 treatment groups. In settings where there are effects in opposite directions for the 2 event types, a likely situation for the SANAD trial, Gray's test has greater power to detect treatment differences than log-rank analysis. For the epilepsy application, conclusions were qualitatively similar for both log-rank and Gray's tests.

Anticonvulsants↗
PubMed1998

Prevalence proportion ratios: estimation and hypothesis testing.

BACKGROUND: Recent communications have argued that often it may not be appropriate to analyse cross-sectional studies of prevalent outcomes with logistic regression models. The purpose of this communication is to compare three methods that have been proposed for application to cross sectional studies: (1) a multiplicative generalized linear model, which we will call the log-binomial model, (2) a method based on logistic regression and robust estimation of standard errors, which we will call the GEE-logistic model, and (3) a Cox regression model. METHODS: Five sets of simulations representing fourteen separate simulation conditions were used to test the performance of the methods. RESULTS: All three models produced point estimates close to the true parameter, i.e. the estimators of the parameter associated with exposure had negligible bias. The Cox regression produced standard errors that were too large, especially when the prevalence of the disease was high, whereas the log-binomial model and the GEE-logistic model had the correct type I error probabilities. It was shown by example that the GEE-logistic model could produce prevalences greater than one, whereas it was proven that this could not happen with the log-binomial model. The log-binomial model should be preferred.

Cross-Sectional Studies↗
PubMed2006

Minimally invasive pharmacokinetic and pharmacodynamic technologies in hypothesis-testing clinical trials of innovative therapies.

Clinical trials of new cancer drugs should ideally include measurements of parameters such as molecular target expression, pharmacokinetic (PK) behavior, and pharmacodynamic (PD) endpoints that can be linked to measures of clinical effect. Appropriate PK/PD biomarkers facilitate proof-of-concept demonstrations for target modulation; enhance the rational selection of an optimal drug dose and schedule; aid decision-making, such as whether to continue or close a drug development project; and may explain or predict clinical outcomes. In addition, measurement of PK/PD biomarkers can minimize uncertainty associated with predicting drug safety and efficacy, reduce the high levels of drug attrition during development, accelerate drug approval, and decrease the overall costs of drug development. However, there are many challenges in the development and implementation of biomarkers that probably explain their disappointingly low implementation in phase I trials. The Pharmacodynamic/Pharmacokinetic Technologies Advisory committee of Cancer Research UK has found that submissions for phase I trials of new cancer drugs in the United Kingdom often lack detailed information about PK and/or PD endpoints, which leads to suboptimal information being obtained in those trials or to delays in starting the trials while PK/PD methods are developed and validated. Minimally invasive PK/PD technologies have logistic and ethical advantages over more invasive technologies. Here we review these technologies, emphasizing magnetic resonance spectroscopy and positron emission tomography, which provide detailed functional and metabolic information. Assays that measure effects of drugs on important biologic pathways and processes are likely to be more cost-effective than those that measure specific molecular targets. Development, validation, and implementation of minimally invasive PK/PD methods are encouraged.

Antineoplastic Agents↗