scholarly journals An omnibus test for the global null hypothesis

2018 ◽  
Vol 28 (8) ◽  
pp. 2292-2304 ◽  
Author(s):  
Andreas Futschik ◽  
Thomas Taus ◽  
Sonja Zehetmayer
Keyword(s):  
Null Hypothesis ◽  
A Priori ◽  
R Package ◽  
Test Statistics ◽  
Omnibus Test ◽  
Genetic Studies ◽  
Global Tests ◽  
Overall Performance ◽  
The Individual ◽  
Meta Analyses

Global hypothesis tests are a useful tool in the context of clinical trials, genetic studies, or meta-analyses, when researchers are not interested in testing individual hypotheses, but in testing whether none of the hypotheses is false. There are several possibilities how to test the global null hypothesis when the individual null hypotheses are independent. If it is assumed that many of the individual null hypotheses are false, combination tests have been recommended to maximize power. If, however, it is assumed that only one or a few null hypotheses are false, global tests based on individual test statistics are more powerful (e.g. Bonferroni or Simes test). However, usually there is no a priori knowledge on the number of false individual null hypotheses. We therefore propose an omnibus test based on cumulative sums of the transformed p-values. We show that this test yields an impressive overall performance. The proposed method is implemented in an R-package called omnibus.

The Orchard Plot: Cultivating a Forest Plot for Use in Ecology, Evolution and Beyond

2019 ◽  
Author(s):  
Shinichi Nakagawa ◽  
Malgorzata Lagisz ◽  
Rose E O'Dea ◽  
Joanna Rutkowska ◽  
Yefeng Yang ◽  
...  
Keyword(s):  
Meta Analysis ◽  
R Package ◽  
Effect Sizes ◽  
Forest Plot ◽  
Point Estimates ◽  
Aggregate Effect ◽  
The Individual ◽  
Meta Analyses ◽  
Heterogeneous Effect ◽  
Intuitive Interpretation

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, showing point estimates (with 95% confidence intervals; CIs) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the ‘orchard plot’. Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also includes 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.

scholarly journals Integrative analysis of relative abundance data and presence-absence data of the microbiome using the LDM

2022 ◽  
Author(s):  
Zhengyi Zhu ◽  
Glen A Satten ◽  
Yi-Juan Hu
Keyword(s):  
Relative Abundance ◽  
R Package ◽  
Data Types ◽  
Omnibus Test ◽  
Testing Hypotheses ◽  
Abundance Data ◽  
Optimal Power ◽  
Wide Range ◽  
Individual Taxon ◽  
The Individual

We previously developed LDM for testing hypotheses about the microbiome that performs the test at both the community level and the individual taxon level. LDM can be applied to relative abundance data and presence-absence data separately, which work well when associated taxa are abundant and rare, respectively. Here we propose an omnibus test based on LDM that allows simultaneous consideration of data at different scales, thus offering optimal power across scenarios with different association mechanisms. The omnibus test is available for the wide range of data types and analyses that are supported by LDM. The omnibus test has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM .

scholarly journals Testing hypotheses about the microbiome using the linear decomposition model (LDM)

2017 ◽  
Author(s):  
Yi-Juan Hu ◽  
Glen A. Satten
Keyword(s):  
Multiple Testing ◽  
Type I Error ◽  
Type I ◽  
Omnibus Test ◽  
Global Test ◽  
Decomposition Model ◽  
Interaction Terms ◽  
Global Tests ◽  
The Individual ◽  
Continuous And Discrete Variables

AbstractMotivationMethods for analyzing microbiome data generally fall into one of two groups: tests of the global hypothesis of any microbiome effect, which do not provide any information on the contribution of individual operational taxonomic units (OTUs); and tests for individual OTUs, which do not typically provide a global test of microbiome effect. Without a unified approach, the findings of a global test may be hard to resolve with the findings at the individual OTU level. Further, many tests of individual OTU effects do not preserve the false discovery rate (FDR).ResultsWe introduce the linear decomposition model (LDM), that provides a single analysis path that includes global tests of any effect of the microbiome, tests of the effects of individual OTUs while accounting for multiple testing by controlling the FDR, and a connection to distance-based ordination. The LDM accommodates both continuous and discrete variables (e.g., clinical outcomes, environmental factors) as well as interaction terms to be tested either singly or in combination, allows for adjustment of confounding covariates, and uses permutation-based p-values that can control for correlation. The LDM can also be applied to transformed data, and an “omnibus” test can easily combine results from analyses conducted on different transformation scales. We also provide a new implementation of PERMANOVA based on our approach. For global testing, our simulations indicate the LDM provided correct type I error and can have comparable power to existing distance-based methods. For testing individual OTUs, our simulations indicate the LDM controlled the FDR well. In contrast, DESeq2 often had inflated FDR; MetagenomeSeq generally had the lowest sensitivity. The flexibility of the LDM for a variety of microbiome studies is illustrated by the analysis of data from two microbiome studies. We also show that our implementation of PERMANOVA can outperform existing implementations.

scholarly journals Symptom Cluster-Matching Antidepressant Treatment: A Case Series Pilot Study

2021 ◽  
Vol 14 (6) ◽  
pp. 526
Author(s):  
Sławomir Murawiec ◽  
Marek Krzystanek
Keyword(s):  
Depressive Symptoms ◽  
Pilot Study ◽  
Antidepressant Treatment ◽  
Case Series ◽  
Symptom Cluster ◽  
Study Results ◽  
Cluster Matching ◽  
The Individual ◽  
Meta Analyses ◽  
Effectiveness Studies

Despite treating depression with antidepressants, their effectiveness is often insufficient. Comparative effectiveness studies and meta-analyses show the effectiveness of antidepressants; however, they do not provide clear indications as to the choice of a specific antidepressant. The rational choice of antidepressants may be based on matching their mechanisms of action to the symptomatic profiles of depression, reflecting the heterogeneity of symptoms in different patients. The authors presented a series of cases of patients diagnosed with depression in whom at least one previous antidepressant treatment was shown to be ineffective before drug targeted symptom cluster-matching treatment (SCMT). The presented pilot study shows for the first time the effectiveness of SCMT in the different clusters of depressive symptoms. All the described patients obtained recovery from depressive symptoms after introducing drug-targeted SCMT. Once validated in clinical trials, SCMT might become an effective and rational method of selecting an antidepressant according to the individual profile of depressive symptoms, the mechanism of their formation, and the mechanism of drug action. Although the study results are preliminary, SCMT can be a way to personalize treatment, increasing the likelihood of improvement even in patients who meet criteria for treatment-resistant depression.

scholarly journals A Systematic Review and Qualitative Synthesis Resulting in a Typology of Elementary Classroom Movement Integration Interventions

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Spyridoula Vazou ◽  
Collin A. Webster ◽  
Gregory Stewart ◽  
Priscila Candal ◽  
Cate A. Egan ◽  
...  
Keyword(s):  
Physical Activity ◽  
Teacher Collaboration ◽  
A Priori ◽  
Real Life ◽  
Dose Intensity ◽  
Routine Practice ◽  
Qualitative Synthesis ◽  
Wide Range ◽  
Meta Analyses ◽  
Movement Integration

Abstract Background/Objective Movement integration (MI) involves infusing physical activity into normal classroom time. A wide range of MI interventions have succeeded in increasing children’s participation in physical activity. However, no previous research has attempted to unpack the various MI intervention approaches. Therefore, this study aimed to systematically review, qualitatively analyze, and develop a typology of MI interventions conducted in primary/elementary school settings. Subjects/Methods Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed to identify published MI interventions. Irrelevant records were removed first by title, then by abstract, and finally by full texts of articles, resulting in 72 studies being retained for qualitative analysis. A deductive approach, using previous MI research as an a priori analytic framework, alongside inductive techniques were used to analyze the data. Results Four types of MI interventions were identified and labeled based on their design: student-driven, teacher-driven, researcher-teacher collaboration, and researcher-driven. Each type was further refined based on the MI strategies (movement breaks, active lessons, other: opening activity, transitions, reward, awareness), the level of intrapersonal and institutional support (training, resources), and the delivery (dose, intensity, type, fidelity). Nearly half of the interventions were researcher-driven, which may undermine the sustainability of MI as a routine practice by teachers in schools. An imbalance is evident on the MI strategies, with transitions, opening and awareness activities, and rewards being limitedly studied. Delivery should be further examined with a strong focus on reporting fidelity. Conclusions There are distinct approaches that are most often employed to promote the use of MI and these approaches may often lack a minimum standard for reporting MI intervention details. This typology may be useful to effectively translate the evidence into practice in real-life settings to better understand and study MI interventions.

scholarly journals Communities and the individual: Beyond the liberal–communitarian divide

2021 ◽  
Vol 47 (4) ◽  
pp. 392-401
Author(s):  
Volker Kaul
Keyword(s):  
Personal Autonomy ◽  
A Priori ◽  
Significant Others ◽  
The Self ◽  
Global Perspective ◽  
Self And Identity ◽  
Default Position ◽  
The Individual

Liberalism believes that individuals are endowed a priori with reason or at least agency and it is up to that reason and agency to make choices, commitments and so on. Communitarianism criticizes liberalism’s explicit and deliberate neglect of the self and insists that we attain a self and identity only through the effective recognition of significant others. However, personal autonomy does not seem to be a default position, neither reason nor community is going to provide it inevitably. Therefore, it is so important to go beyond the liberal–communitarian divide. This article is analysing various proposals in this direction, asks about the place of communities and the individual in times of populism and the pandemic and provides a global perspective on the liberal–communitarian debate.

scholarly journals Computer-assisted contralateral side comparison of the ankle joint using flat panel technology

2021 ◽  
Author(s):  
Sarina Thomas ◽  
Lisa Kausch ◽  
Holger Kunze ◽  
Maxim Privalov ◽  
André Klein ◽  
...  
Keyword(s):  
Information Gain ◽  
Contralateral Side ◽  
Computer Assisted ◽  
Ankle Joints ◽  
Additional Radiation ◽  
Median Position ◽  
Operative Evaluation ◽  
Overall Performance ◽  
The Individual ◽  
Segmentation Problem

Abstract Purpose Reduction and osteosynthesis of ankle fractures is a challenging surgical procedure when it comes to the verification of the reduction result. Evaluation is conducted using intra-operative imaging of the injured ankle and depends on the expertise of the surgeon. Studies suggest that intra-individual variance of the ankle bone shape and pose is considerably lower than the inter-individual variance. It stands to reason that the information gain from the healthy contralateral side can help to improve the evaluation. Method In this paper, an assistance system is proposed that provides a side-to-side view of the two ankle joints for visual comparison and instant evaluation using only one 3D C-arm image. Two convolutional neural networks (CNN) are employed to extract the relevant image regions and pose information of each ankle so that they can be aligned with each other. A first U-Net uses a sliding window to predict the location of each ankle. The standard plane estimation is formulated as segmentation problem so that a second U-Net predicts the three viewing planes for alignment. Results Experiments were conducted to assess the accuracy of the individual steps on 218 unilateral ankle datasets as well as the overall performance on 7 bilateral ankle datasets. The experiments on unilateral ankles yield a median position-to-plane error of $$0.73\pm 1.36$$ 0.73 ± 1.36 mm and a median angular error between 2.98$$^\circ $$ ∘ and 3.71$$^\circ $$ ∘ for the plane normals. Conclusion Standard plane estimation via segmentation outperforms direct pose regression. Furthermore, the complete pipeline was evaluated including ankle detection and subsequent plane estimation on bilateral datasets. The proposed pipeline enables a direct contralateral side comparison without additional radiation. This has the potential to ease and improve the intra-operative evaluation for the surgeons in the future and reduce the need for revision surgery.

scholarly journals Statistical Uncertainty of DNS in Geometries without Homogeneous Directions

2021 ◽  
Vol 11 (4) ◽  
pp. 1399
Author(s):  
Jure Oder ◽  
Cédric Flageul ◽  
Iztok Tiselj
Keyword(s):  
Channel Flow ◽  
A Priori ◽  
Time Integration ◽  
Navier Stokes ◽  
Statistical Uncertainty ◽  
Time Step ◽  
Order Of Magnitude ◽  
Averaging Time ◽  
The Individual ◽  
Time Required

In this paper, we present uncertainties of statistical quantities of direct numerical simulations (DNS) with small numerical errors. The uncertainties are analysed for channel flow and a flow separation case in a confined backward facing step (BFS) geometry. The infinite channel flow case has two homogeneous directions and this is usually exploited to speed-up the convergence of the results. As we show, such a procedure reduces statistical uncertainties of the results by up to an order of magnitude. This effect is strongest in the near wall regions. In the case of flow over a confined BFS, there are no such directions and thus very long integration times are required. The individual statistical quantities converge with the square root of time integration so, in order to improve the uncertainty by a factor of two, the simulation has to be prolonged by a factor of four. We provide an estimator that can be used to evaluate a priori the DNS relative statistical uncertainties from results obtained with a Reynolds Averaged Navier Stokes simulation. In the DNS, the estimator can be used to predict the averaging time and with it the simulation time required to achieve a certain relative statistical uncertainty of results. For accurate evaluation of averages and their uncertainties, it is not required to use every time step of the DNS. We observe that statistical uncertainty of the results is uninfluenced by reducing the number of samples to the point where the period between two consecutive samples measured in Courant–Friedrichss–Levy (CFL) condition units is below one. Nevertheless, crossing this limit, the estimates of uncertainties start to exhibit significant growth.

scholarly journals Sartres Lösung zur Antinomie der sozialen Realität in der Kritik der dialektischen Vernunft

2020 ◽  
Vol 68 (6) ◽  
pp. 817-847
Author(s):  
Sebastian Gardner
Keyword(s):  
Ethical Theory ◽  
A Priori ◽  
Social Ontology ◽  
Human Freedom ◽  
Philosophical Foundation ◽  
A Posteriori ◽  
Political Reality ◽  
Dialectical Reason ◽  
The Individual

AbstractCritics have standardly regarded Sartre’s Critique of Dialectical Reason as an abortive attempt to overcome the subjectivist individualism of his early philosophy, motivated by a recognition that Being and Nothingness lacks ethical and political significance, but derailed by Sartre’s Marxism. In this paper I offer an interpretation of the Critique which, if correct, shows it to offer a coherent and highly original account of social and political reality, which merits attention both in its own right and as a reconstruction of the philosophical foundation of Marxism. The key to Sartre’s theory of collective and historical existence in the Critique is a thesis carried over from Being and Nothingness: intersubjectivity on Sartre’s account is inherently aporetic, and social ontology reproduces in magnified form its limited intelligibility, lack of transparency, and necessary frustration of the demands of freedom. Sartre’s further conjecture – which can be formulated a priori but requires a posteriori verification – is that man’s collective historical existence may be understood as the means by which the antinomy within human freedom, insoluble at the level of the individual, is finally overcome. The Critique provides therefore the ethical theory promised in Being and Nothingness.

scholarly journals A Frequentist Alternative to Significance Testing, p-Values, and Confidence Intervals

Econometrics ◽  
2019 ◽  
Vol 7 (2) ◽  
pp. 26 ◽  
Author(s):  
David Trafimow
Keyword(s):  
Present Article ◽  
Confidence Intervals ◽  
Null Hypothesis ◽  
A Priori ◽  
Significance Testing ◽  
Population Parameters ◽  
Null Hypothesis Significance Testing ◽  
P Values ◽  
Statistical Procedures ◽  
Major Section

There has been much debate about null hypothesis significance testing, p-values without null hypothesis significance testing, and confidence intervals. The first major section of the present article addresses some of the main reasons these procedures are problematic. The conclusion is that none of them are satisfactory. However, there is a new procedure, termed the a priori procedure (APP), that validly aids researchers in obtaining sample statistics that have acceptable probabilities of being close to their corresponding population parameters. The second major section provides a description and review of APP advances. Not only does the APP avoid the problems that plague other inferential statistical procedures, but it is easy to perform too. Although the APP can be performed in conjunction with other procedures, the present recommendation is that it be used alone.

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