Nested sampling (NS) is an invaluable tool in data analysis in modern astrophysics, cosmology, gravitational wave astronomy and particle physics. We identify a previously unused property of NS related to order statistics: the insertion indexes of new live points into the existing live points should be uniformly distributed. This observation enabled us to create a novel cross-check of single NS runs. The tests can detect when an NS run failed to sample new live points from the constrained prior and plateaus in the likelihood function, which break an assumption of NS and thus leads to unreliable results. We applied our cross-check to NS runs on toy functions with known analytic results in 2 - 50 dimensions, showing that our approach can detect problematic runs on a variety of likelihoods, settings and dimensions. As an example of a realistic application, we cross-checked NS runs performed in the context of cosmological model selection. Since the cross-check is simple, we recommend that it become a mandatory test for every applicable NS run.
Searches for unknown physics and decisions between competing astrophysical models to explain data both rely on statistical hypothesis testing. The usual approach in searches for new physical phenomena is based on the statistical Likelihood Ratio Test (LRT) and its asymptotic properties. In the common situation, when neither of the two models under comparison is a special case of the other i.e., when the hypotheses are non-nested, this test is not applicable. In astrophysics, this problem occurs when two models that reside in different parameter spaces are to be compared. An important example i…
Hierarchically-organized data arise naturally in many psychology and neuroscience studies. As the standard assumption of independent and identically distributed samples does not hold for such data, two important problems are to accurately estimate group-level effect sizes, and to obtain powerful statistical tests against group-level null hypotheses. A common approach is to summarize subject-level data by a single quantity per subject, which is often the mean or the difference between class means, and treat these as samples in a group-level t-test. This 'naive' approach is, however, suboptimal …
In this paper, we apply Vuong's (1989) general approach of model selection to the comparison of nested and non-nested unidimensional and multidimensional item response theory (IRT) models. Vuong's approach of model selection is useful because it allows for formal statistical tests of both nested and non-nested models. However, only the test of non-nested models has been applied in the context of IRT models to date. After summarizing the statistical theory underlying the tests, we investigate the performance of all three distinct Vuong tests in the context of IRT models using simulation studies…
We develop a greedy algorithm that is fast and scalable in the detection of a nested partition extracted from a dendrogram obtained from hierarchical clustering of a multivariate series. Our algorithm provides a $p$-value for each clade observed in the hierarchical tree. The $p$-value is obtained by computing a number of bootstrap replicas of the dissimilarity matrix and by performing a statistical test on each difference between the dissimilarity associated with a given clade and the dissimilarity of the clade of its parent node. We prove the efficacy of our algorithm with a set of benchmarks…
We consider the problem of multiple hypothesis testing when there is a logical nested structure to the hypotheses. When one hypothesis is nested inside another, the outer hypothesis must be false if the inner hypothesis is false. We model the nested structure as a directed acyclic graph, including chain and tree graphs as special cases. Each node in the graph is a hypothesis and rejecting a node requires also rejecting all of its ancestors. We propose a general framework for adjusting node-level test statistics using the known logical constraints. Within this framework, we study a smoothing pr…
Risk assessments to help inform criminal justice decisions have been used in the United States since the 1920s. Over the past several years, statistical learning risk algorithms have been introduced amid much controversy about fairness, transparency and accuracy. In this paper, we focus on accuracy for a large department of probation and parole that is considering a major revision of its current, statistical learning risk methods. Because the content of each offender's supervision is substantially shaped by a forecast of subsequent conduct, forecasts have real consequences. Here we consider th…
Multivariate statistics are often available as well as necessary in hypothesis tests. We study how to use such statistics to control not only false discovery rate (FDR) but also positive FDR (pFDR) with good power. We show that FDR can be controlled through nested regions of multivariate $p$-values of test statistics. If the distributions of the test statistics are known, then the regions can be constructed explicitly to achieve FDR control with maximum power among procedures satisfying certain conditions. On the other hand, our focus is where the distributions are only partially known. Under …
We put forward an adaptive alpha (Type I Error) that decreases as the information grows, for hypothesis tests in which nested linear models are compared. A less elaborate adaptation was already presented in \citet{PP2014} for comparing general i.i.d. models. In this article we present refined versions to compare nested linear models. This calibration may be interpreted as a Bayes-non-Bayes compromise, of a simple translations of a Bayes Factor on frequentist terms that leads to statistical consistency, and most importantly, it is a step towards statistics that promotes replicable scientific fi…
Coarse Structural Nested Mean Models (SNMMs) provide useful tools to estimate treatment effects from longitudinal observational data with time-dependent confounders. Coarse SNMMs lead to a large class of estimators,within which an optimal estimator can be derived under the conditions of well-specified models for the treatment effect, for treatment initiation, and for nuisance regression outcomes (Lok & Griner, 2015). The key assumption lies in a well-specified model for the treatment effect; however, there is no existing guidance to specify the treatment effect model, and model misspecificatio…
Nested sampling (NS) is a popular algorithm for Bayesian computation. We investigate statistical errors in NS both analytically and numerically. We show two analytic results. First, we show that the leading terms in Skilling's expression using information theory match the leading terms in Keeton's expression from an analysis of moments. This approximate agreement was previously only known numerically and was somewhat mysterious. Second, we show that the uncertainty in single NS runs approximately equals the standard deviation in repeated NS runs. Whilst intuitive, this was previously taken for…
Nested sampling has emerged as a valuable tool for Bayesian analysis, in particular for determining the Bayesian evidence. The method is based on a specific type of random sampling of the likelihood function and prior volume of the parameter space. I study the statistical uncertainty in the evidence computed with nested sampling. I examine the uncertainty estimator from Skilling (2004, 2006) and introduce a new estimator based on a detailed analysis of the statistical properties of nested sampling. Both perform well in test cases and make it possible to obtain the statistical uncertainty in th…
Nested sampling is an iterative integration procedure that shrinks the prior volume towards higher likelihoods by removing a "live" point at a time. A replacement point is drawn uniformly from the prior above an ever-increasing likelihood threshold. Thus, the problem of drawing from a space above a certain likelihood value arises naturally in nested sampling, making algorithms that solve this problem a key ingredient to the nested sampling framework. If the drawn points are distributed uniformly, the removal of a point shrinks the volume in a well-understood way, and the integration of nested …
We present dynesty, a public, open-source, Python package to estimate Bayesian posteriors and evidences (marginal likelihoods) using Dynamic Nested Sampling. By adaptively allocating samples based on posterior structure, Dynamic Nested Sampling has the benefits of Markov Chain Monte Carlo algorithms that focus exclusively on posterior estimation while retaining Nested Sampling's ability to estimate evidences and sample from complex, multi-modal distributions. We provide an overview of Nested Sampling, its extension to Dynamic Nested Sampling, the algorithmic challenges involved, and the variou…
Many inference problems involve inferring the number $N$ of components in some region, along with their properties $\{\mathbf{x}_i\}_{i=1}^N$, from a dataset $\mathcal{D}$. A common statistical example is finite mixture modelling. In the Bayesian framework, these problems are typically solved using one of the following two methods: i) by executing a Monte Carlo algorithm (such as Nested Sampling) once for each possible value of $N$, and calculating the marginal likelihood or evidence as a function of $N$; or ii) by doing a single run that allows the model dimension $N$ to change (such as Marko…
