scholarly journals A unified approach to permutation testing for equivalence

2020 ◽  
Author(s):  
Rosa Arboretti ◽  
Fortunato Pesarin ◽  
Luigi Salmaso
Keyword(s):  
Quality Control ◽  
Clinical Trials ◽  
Comparative Analysis ◽  
Null Hypothesis ◽  
Mirror Image ◽  
Permutation Testing ◽  
Unified Approach ◽  
Published Paper

AbstractThe notion of testing for equivalence of two treatments is widely used in clinical trials, pharmaceutical experiments, bioequivalence and quality control. It is traditionally operated within the intersection–union principle (IU). According to this principle the null hypothesis is stated as the set of effects the differences $$\delta$$ δ of which lie outside a suitable equivalence interval and the alternative as the set of $$\delta$$ δ that lie inside it. In the literature related solutions are essentially based on likelihood techniques, which in turn are rather difficult to deal with. A recently published paper goes beyond most of likelihood limitations by using the IU approach within the permutation theory. One more paper, based on Roy’s union–intersection principle (UI) within the permutation theory, goes beyond some limitations of traditional two-sided tests. Such UI approach, effectively a mirror image of IU, assumes a null hypothesis where $$\delta$$ δ lies inside the equivalence interval and an alternative where it lies outside. Since testing for equivalence can rationally be analyzed by both principles but, as the two differ in terms of the mirror-like roles assigned to the hypotheses under study, they are not strictly comparable. The present paper’s main goal is to look into these problems and provide a sort of comparative analysis of both by highlighting the related requirements, properties, limitations, difficulties, and pitfalls so as to get practitioners properly acquainted with their correct use in practical contexts.

scholarly journals Power and False Negatives in Qualitative Comparative Analysis: Foundations, Simulation and Estimation for Empirical Studies

2018 ◽  
Vol 26 (1) ◽  
pp. 72-89 ◽  
Author(s):  
Ingo Rohlfing
Keyword(s):  
Comparative Analysis ◽  
Null Hypothesis ◽  
Empirical Studies ◽  
False Negative ◽  
Qualitative Comparative Analysis ◽  
Truth Table ◽  
Permutation Testing ◽  
Ex Post ◽  
Table Analysis ◽  
Sole Criterion

In Qualitative Comparative Analysis (QCA), empirical researchers use the consistency value as one, if not sole, criterion to decide whether an association between a term and an outcome is consistent with a set-relational claim. Braumoeller (2015) points out that the consistency value is unsuitable for this purpose. We need to know the probability of obtaining it under the null hypothesis of no systematic relation. He introduces permutation testing for estimating the $p$ value of a consistency score as a safeguard against false positives. In this paper, I introduce permutation-based power estimation as a safeguard against false-negative conclusions. Low power might lead to the false exclusion of truth table rows from the minimization procedure and the generation and interpretation of invalid solutions. For a variety of constellations between an alternative and null hypothesis and numbers of cases, simulations demonstrate that power estimates can range from 1 to 0. Ex post power analysis for 63 truth table analyses shows that even under the most favorable constellation of parameters, about half of them can be considered low-powered. This points to the value of estimating power and calculating the required number of cases before the truth table analysis.

Guidelines for publishing papers on cancer clinical trials: responsibilities of editors and authors.

1983 ◽  
Vol 1 (2) ◽  
pp. 164-169 ◽  
Author(s):  
M Zelen
Keyword(s):  
Quality Control ◽  
Clinical Trials ◽  
Study Design ◽  
Journal Editor ◽  
Cancer Clinical Trials ◽  
Journal Editors ◽  
Early Results ◽  
Published Paper ◽  
Statistical Results

Guidelines are proposed for the reporting of clinical trials. These are meant to be used for both authors and journal editors. Specific proposals are made for: reporting the population under study, actual therapy used, describing the study design, accounting of patients, follow-up statistics, and describing the quality control of the data. Nonrandomized studies require special discussion. Such studies potentially have substantial biases which can lead to incorrect conclusions. Six areas of biases arising in nonrandomized studies are pointed out which should require a discussion in an acceptable published paper. The presentation of statistical results and the reporting of early studies present unusually difficult problems. Guidelines are presented for statistical analyses which, although simple to implement in practice, are not generally used. A proposal is made for the publication of early results of a study which require that the authors agree to follow and periodically report on their trial to the journal editor. If the early conclusions change with additional follow-up, the editor should notify its readers. The adoption of these guidelines can be an important force in raising the scientific level of the reporting of clinical trials.

scholarly journals Genotype Pattern Mining for Pairs of Interacting Variants Underlying Digenic Traits

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1160
Author(s):  
Atsuko Okazaki ◽  
Sukanya Horpaopan ◽  
Qingrun Zhang ◽  
Matthew Randesi ◽  
Jurg Ott
Keyword(s):  
Null Hypothesis ◽  
Pattern Mining ◽  
Genetic Diseases ◽  
Frequent Pattern Mining ◽  
Case Control ◽  
Frequent Pattern ◽  
Permutation Testing ◽  
Case Control Studies ◽  
P Values ◽  
Dna Variants

Some genetic diseases (“digenic traits”) are due to the interaction between two DNA variants, which presumably reflects biochemical interactions. For example, certain forms of Retinitis Pigmentosa, a type of blindness, occur in the presence of two mutant variants, one each in the ROM1 and RDS genes, while the occurrence of only one such variant results in a normal phenotype. Detecting variant pairs underlying digenic traits by standard genetic methods is difficult and is downright impossible when individual variants alone have minimal effects. Frequent pattern mining (FPM) methods are known to detect patterns of items. We make use of FPM approaches to find pairs of genotypes (from different variants) that can discriminate between cases and controls. Our method is based on genotype patterns of length two, and permutation testing allows assigning p-values to genotype patterns, where the null hypothesis refers to equal pattern frequencies in cases and controls. We compare different interaction search approaches and their properties on the basis of published datasets. Our implementation of FPM to case-control studies is freely available.

scholarly journals Genotype Pattern Mining for Pairs of Interacting Variants Underlying Digenic Traits

2021 ◽  
Author(s):  
Atsuko Okazaki ◽  
Sukanya Horpaopan ◽  
Qingrun Zhang ◽  
Matthew Randesi ◽  
Jurg Ott
Keyword(s):  
Null Hypothesis ◽  
Pattern Mining ◽  
Genetic Diseases ◽  
Frequent Pattern Mining ◽  
Case Control ◽  
Frequent Pattern ◽  
Permutation Testing ◽  
Case Control Studies ◽  
P Values ◽  
Dna Variants

Some genetic diseases (“digenic traits”) are due to the interaction between two DNA variants, which presumably reflects biochemical interactions. For example, certain forms of Retinitis Pigmentosa, a type of blindness, occur in the presence of two mutant variants, one each in the ROM1 and RDS genes, while occurrence of only one such variant results in a normal phenotype. Detecting variant pairs underlying digenic traits by standard genetic methods is difficult and is downright impossible when individual variants alone have minimal effects. Frequent Pattern Mining (FPM) methods are known to detect patterns of items. We make use of FPM approaches to find pairs of genotypes (from different variants) that can discriminate between cases and controls. Our method is based on genotype patterns of length two, and permutation testing allows assigning p-values to genotype patterns, where the null hypothesis refers to equal pattern frequencies in cases and controls. We compare different interaction search approaches and their properties on the basis of published datasets. Our implementation of FPM to case-control studies is freely available.

scholarly journals LEGAL REGULATION OF NOISE IMPACT ON THE ATMOSPHERIC AIR IN THE RUSSIAN FEDERATION: A COMPARATIVE ANALYSIS OF REGIONAL LEGISLATION

2020 ◽  
Vol 30 (2) ◽  
pp. 249-255
Author(s):  
S.A. Gagarin ◽  
M.B. Uage
Keyword(s):  
Comparative Analysis ◽  
Russian Federation ◽  
Legal Regulation ◽  
Unified Approach ◽  
Distinctive Features ◽  
Atmospheric Air ◽  
Noise Impact ◽  
The Russian Federation ◽  
Acoustic Impact ◽  
Physical Impact

The article examines the provisions of legislation on the sanitary and epidemiological welfare of the population, regulating the restrictions of negative physical impact on the environment. The article considers the provisions of regional legislation aimed at regulating the issues of ensuring the peace and quiet of citizens. The authors note that the Code of administrative offences of the Russian Federation does not contain a direct ban on actions that violate the peace and quiet of citizens at night, but the corresponding restrictions apply in almost every subject of the Russian Federation. The article analyzes the legal regulation of relations connected with ensuring peace and quiet in a number of subjects of the Russian Federation. Regional acts determine specific prohibited actions that are subject to administrative liability in the form of a fine. The article highlights common and distinctive features of the legislation of the subjects of the Russian Federation in the field of acoustic impact. It is concluded that it is necessary to develop a unified approach to ensuring silence in the Russian Federation.

Quality assurance in radiotherapy

2019 ◽  
pp. 520-536
Author(s):  
Patricia Díez ◽  
Edwin GA Aird
Keyword(s):  
Quality Control ◽  
Clinical Trials ◽  
Quality Assurance ◽  
Treatment Planning ◽  
Patient Pathway

Chapter 23 discusses quality assurance of the patient pathway, concentrating on quality control of treatment planning and delivery. There is also discussion on relevant legislation associated with the radiotherapy process as well as a section on quality assurance for clinical trials.

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