The exponential growth of social data both in volume and complexity has increasingly exposed many of the shortcomings of the conventional frequentist approach to statistics. The scientific community has called for careful usage of the approach and its inference. Meanwhile, the alternative method, Bayesian statistics, still faces considerable barriers toward a more widespread application. The bayesvl R package is an open program, designed for implementing Bayesian modeling and analysis using the Stan language’s no-U-turn (NUTS) sampler. The (...) package combines the ability to construct Bayesian network models using directed acyclic graphs (DAGs), the Markov chain Monte Carlo (MCMC) simulation technique, and the graphic capability of the ggplot2 package. As a result, it can improve the user experience and intuitive understanding when constructing and analyzing Bayesian network models. A case example is offered to illustrate the usefulness of the package for Big Data analytics and cognitive computing. (shrink)

Critics of Bayesianism often assert that scientists are not Bayesians. The widespread use of Bayesian statistics in the field of radiocarbon calibration is discussed in relation to this charge. This case study illustrates the willingness of scientists to use Bayesian statistics when the approach offers some advantage, while continuing to use orthodox methods in other contexts. The case of radiocarbon calibration, therefore, suggests a picture of statistical practice in science as eclectic and pragmatic rather than rigidly (...) adhering to any one theoretical position. (shrink)

A comparison of Neyman's theory of interval estimation with the corresponding subjective Bayesian theory of credible intervals shows that the Bayesian approach to the estimation of statistical parameters allows experimental procedures which, from the orthodox objective viewpoint, are clearly biased and clearly inadmissible. This demonstrated methodological difference focuses attention on the key difference in the two general theories, namely, that the orthodox theory is supposed to provide a known average frequency of successful estimates, whereas the Bayesian account (...) provides only a coherent ordering of degrees of belief and a subsequent maximization of subjective expected utilities. To rebut the charge of allowing biased procedures, the Bayesian must attack the foundations of orthodox, objectivist methods. Two apparently popular avenues of attack are briefly considered and found wanting. The first is that orthodox methods fail to apply to the single case. The second is that orthodox methods are subject to a typical Humean regress. The conclusion is that orthodox objectivist methods remain viable in the face of the subjective Bayesian alternative — at least with respect to the problem of statistical estimation. (shrink)

Increasingly, clinical research is evaluated on the quality of its statistical analysis. Traditionally, statistical analyses in clinical research have been carried out from a ‘frequentist’ perspective. The presence of an alternative paradigm – the Bayesian paradigm – has been relatively unknown in clinical research until recently. There is currently a growing interest in the use of Bayesian statistics in health care research. This is due both to a growing realization of the limitations of frequentist methods and to (...) the ability of Bayesian methods explicitly to incorporate prior expert knowledge and belief into the analyses. This is in contrast to frequentist methods, where prior experience and beliefs tend to be incorporated into the analyses in an ad hoc fashion. This paper outlines the frequentist and Bayesian paradigms. Acute myocardial infarction mortality data are then analysed from both a Bayesian and a frequentist perspective. In some analyses, the two methods are seen to produce comparable results; in others, they produce different results. It is noted that in this example, there are clinically relevant questions that are more easily addressed from a Bayesian perspective. Finally, areas in clinical research where Bayesian ideas are increasingly common are highlighted. (shrink)

In statistics, there are two main paradigms: classical and Bayesian statistics. The purpose of this article is to investigate the extent to which classicists and Bayesians can agree. My conclusion is that, in certain situations, they cannot. The upshot is that, if we assume that the classicist is not allowed to have a higher degree of belief in a null hypothesis after he has rejected it than before, then he has to either have trivial or incoherent credences (...) to begin with or fail to update his credences by conditionalization. (shrink)

ABSTRACTIn this article, we discuss the benefits of Bayesian statistics and how to utilize them in studies of moral education. To demonstrate concrete examples of the applications of Bayesian statistics to studies of moral education, we reanalyzed two data sets previously collected: one small data set collected from a moral educational intervention experiment, and one big data set from a large-scale Defining Issues Test-2 survey. The results suggest that Bayesian analysis of data sets collected from (...) moral educational studies can provide additional useful statistical information, particularly that associated with the strength of evidence supporting alternative hypotheses, which has not been provided by the classical frequentist approach focusing on P-values. Finally, we introduce several practical guidelines pertaining to how to utilize Bayesian statistics, including the utilization of newly developed free statistical software, Jeffrey’s Amazing Statistics Program, and thresholding based on Bayes Factors, to scholars in the field of moral education. (shrink)

Scientists and Bayesian statisticians often study hypotheses that they know to be false. This creates an interpretive problem because the Bayesian probability of a hypothesis is supposed to represent the probability that the hypothesis is true. I investigate whether Bayesianism can accommodate the idea that false hypotheses are sometimes approximately true or that some hypotheses or models can be closer to the truth than others. I argue that the idea that some hypotheses are approximately true in an absolute (...) sense is hard to square with Bayesianism, but that the notion that some hypotheses are comparatively closer to the truth than others can be made compatible with Bayesianism, and that this provides an adequate and potentially useful solution to the interpretive problem. Finally, I compare my ``verisimilitude'' solution to the interpretive problem with a ``counterfactual'' solution recently proposed by Jan Sprenger. (shrink)

This paper addresses the problem that Bayesian statistical inference cannot accommodate theory change, and proposes a framework for dealing with such changes. It first presents a scheme for generating predictions from observations by means of hypotheses. An example shows how the hypotheses represent the theoretical structure underlying the scheme. This is followed by an example of a change of hypotheses. The paper then presents a general framework for hypotheses change, and proposes the minimization of the distance between hypotheses as (...) a rationality criterion. Finally the paper discusses the import of this for Bayesian statistical inference. (shrink)

From the outside, Bayesian statistics may seem like a closed little corner of probability. Once a prior is specified you compute! From the inside the field is filled with problems, conceptual and otherwise. This paper surveys some of what remains to be done and gives examples of the work in progress via a Bayesian peek into Feller volume I.

At a very fundamental level an individual (or a computer) can process only a finite amount of information in a finite time. We can therefore model the possibilities facing such an observer by a tree with only finitely many arcs leaving each node. There is a natural field of events associated with this tree, and we show that any finitely additive probability measure on this field will also be countably additive. Hence when considering the foundations of Bayesian statistics (...) we may as well assume countable additivity over a σ-field of events. (shrink)

What justifies the use of Bayesian statistics in science? The traditional answer is that Bayesian statistics is simply an instance of orthodox expected utility theory. Thus, Bayesian statistical methods, like principles of utility theory, are justified by norms of individual rationality. In particular, most Bayesians argue that a scientist's credences must satisfy the probability axioms if she adheres to norms of practical and epistemic rationality. We argue that, to justify Bayesian statistics as a (...) tool for science, it is necessary that a scientist's public credences obey the probability axioms. We claim that norms of collective science help justify this restricted view, termed public probabilism. (shrink)

In the Bayesian framework, a language learner should seek a grammar that explains observed data well and is also a priori probable. This paper proposes such a measure of prior probability. Indeed it develops a full statistical framework for lexicalized syntax. The learner's job is to discover the system of probabilistic transformations (often called lexical redundancy rules) that underlies the patterns of regular and irregular syntactic constructions listed in the lexicon. Specifically, the learner discovers what transformations apply in the (...) language, how often they apply, and in what contexts. It considers simpler systems of transformations to be more probable a priori. Experiments show that the learned transformations are more effective than previous statistical models at predicting the probabilities of lexical entries, especially those for which the learner had no direct evidence. (shrink)

According to the Bayesian view, scientific hypotheses must be appraised in terms of their posterior probabilities relative to the available experimental data. Such posterior probabilities are derived from the prior probabilities of the hypotheses by applying Bayes'theorem. One of the most important problems arising within the Bayesian approach to scientific methodology is the choice of prior probabilities. Here this problem is considered in detail w.r.t. two applications of the Bayesian approach: (1) the theory of inductive probabilities (TIP) (...) developed by Rudolf Carnap and other epistomologists and (2) the analysis of the multinational inferences provided by Bayesian statstics (BS). ... Zie: Summary. (shrink)

The current paper highlights a new, interactive Shiny App that can be used to aid in understanding and teaching the important task of conducting a prior sensitivity analysis when implementing Bayesian estimation methods. In this paper, we discuss the importance of examining prior distributions through a sensitivity analysis. We argue that conducting a prior sensitivity analysis is equally important when so-called diffuse priors are implemented as it is with subjective priors. As a proof of concept, we conducted a small (...) simulation study, which illustrates the impact of priors on final model estimates. The findings from the simulation study highlight the importance of conducting a sensitivity analysis of priors. This concept is further extended through an interactive Shiny App that we developed. The Shiny App allows users to explore the impact of various forms of priors using empirical data. We introduce this Shiny App and thoroughly detail an example using a simple multiple regression model that users at all levels can understand. In this paper, we highlight how to determine the different settings for a prior sensitivity analysis, how to visually and statistically compare results obtained in the sensitivity analysis, and how to display findings and write up disparate results obtained across the sensitivity analysis. The goal is that novice users can follow the process outlined here and work within the interactive Shiny App to gain a deeper understanding of the role of prior distributions and the importance of a sensitivity analysis when implementing Bayesian methods. The intended audience is broad and can include those with limited exposure to Bayesian methods or the specific model presented here. (shrink)

Unfortunately, reading Chow's work is likely to leave the reader more confused than enlightened. My preferred solutions to the “controversy” about null- hypothesis testing are: (1) recognize that we really want to test the hypothesis that an effect is “small,” not null, and (2) use Bayesian methods, which are much more in keeping with the way humans naturally think than are classical statistical methods.

Many biologists, especially in ecology and evolution, analyze their data by estimating fits to a set of candidate models and selecting the best model according to the Akaike Information Criterion (AIC) or the Bayesian Information Criteria (BIC). When the candidate models represent alternative hypotheses, biologists may want to limit the chance of a false positive to a specified level. Existing model selection methodology, however, allows for only indirect control over error rates by setting a threshold for the difference in (...) AIC scores. We present a novel theoretical framework for parametric Neyman-Pearson (NP) model selection using information criteria that does not require a pre-data null and applies to three or more non-nested models simultaneously. We apply the theoretical framework to the Error Control for Information Criteria (ECIC) procedure introduced by Cullan et al. (J Appl Stat 47: 2565–2581, 2019), and we show it shares many of the desirable properties of AIC-type methods, including false positive and negative rates that converge to zero asymptotically. We discuss implications for the compatibility of evidentialist and severity-based approach to evidence in philosophy of science. (shrink)

The debates between Bayesian, frequentist, and other methodologies of statistics have tended to focus on conceptual justifications, sociological arguments, or mathematical proofs of their long run properties. Both Bayesian statistics and frequentist (“classical”) statistics have strong cases on these grounds. In this article, we instead approach the debates in the “Statistics Wars” from a largely unexplored angle: simulations of different methodologies’ performance in the short to medium run. We conducted a large number of simulations (...) using a straightforward decision problem based around tossing a coin with unknown bias and then placing bets. In this simulation, we programmed four players, inspired by Bayesian statistics, frequentist statistics, Jon Williamson’s version of Objective Bayesianism, and a player who simply extrapolates from observed frequencies to general frequencies. The last player functions as a benchmark: a statistical methodology should at least outperform a crude form of induction. We focused on the performance of these methodologies in guiding the players towards good decisions. Unlike an earlier simulation study of this type, we found no systematic difference in performance between the Bayesian and frequentist players, provided the Bayesian used a flat prior and the frequentist used a low confidence level. Unlike that study, we were able to use Big Data methods to mitigate problems of random error in the simulation results. The Williamsonian player, who is a novel element of our study, also had no systematic differences in their performance, provided that they use a low confidence level. These players performed similarly even in the very short run, when players were making different decisions. Our study indicates that all three methodologies should be taken seriously by philosophers and practitioners of statistics. However, the frequentist and Williamsonian performed poorly when their confidence levels were high, and the Bayesian was surprisingly harmed by biased priors, providing some unexpected lessons for these methodologies when facing this type of decision problem. (shrink)

The Bayesian Approach and the Classical Approach are two very different families of approaches to statistical inference. There are many different versions of each view, often with very substantial differences among them. But I will here endeavor to explain the philosophical core of each family of approaches, as well as to identify four main philosophical differences between them.

This book analyzes the origins of statistical thinking as well as its related philosophical questions, such as causality, determinism or chance. Bayesian and frequentist approaches are subjected to a historical, cognitive and epistemological analysis, making it possible to not only compare the two competing theories, but to also find a potential solution. The work pursues a naturalistic approach, proceeding from the existence of numerosity in natural environments to the existence of contemporary formulas and methodologies to heuristic pragmatism, a concept (...) introduced in the book's final section. This monograph will be of interest to philosophers and historians of science and students in related fields. Despite the mathematical nature of the topic, no statistical background is required, making the book a valuable read for anyone interested in the history of statistics and human cognition. (shrink)

Abstract Based on recalling two characteristic features of Bayesian statistical inference in commutative probability theory, a stability property of the inference is pointed out, and it is argued that that stability of the Bayesian statistical inference is an essential property which must be preserved under generalization of Bayesian inference to the non?commutative case. Mathematical no?go theorems are recalled then which show that, in general, the stability can not be preserved in non?commutative context. Two possible interpretations of the (...) impossibility of generalization of Bayesian statistical inference to the non?commutative case are offered, none of which seems to be completely satisfying. (shrink)

The paper provides a formal proof that efficient estimates of parameters, which vary as as little as possible when measurements are repeated, may be expected to provide more accurate predictions. The definition of predictive accuracy is motivated by the work of Akaike (1973). Surprisingly, the same explanation provides a novel solution for a well known problem for standard theories of scientific confirmation — the Ravens Paradox. This is significant in light of the fact that standard Bayesian analyses of the (...) paradox fail to account for the predictive utility of universal laws like All ravens are black. (shrink)

To estimate causal relationships, time series econometricians must be aware of spurious correlation, a problem first mentioned by Yule (1926). To deal with this problem, one can work either with differenced series or multivariate models: VAR (VEC or VECM) models. These models usually include at least one cointegration relation. Although the Bayesian literature on VAR/VEC is quite advanced, Bauwens et al. (1999) highlighted that “the topic of selecting the cointegrating rank has not yet given very useful and convincing results”. (...) The present article applies the Full Bayesian Significance Test (FBST), especially designed to deal with sharp hypotheses, to cointegration rank selection tests in VECM time series models. It shows the FBST implementation using both simulated and available (in the literature) data sets. As illustration, standard non informative priors are used. (shrink)

I argue that the Bayesian Way of reconstructing Duhem's problem fails to advance a solution to the problem of which of a group of hypotheses ought to be rejected or "blamed" when experiment disagrees with prediction. But scientists do regularly tackle and often enough solve Duhemian problems. When they do, they employ a logic and methodology which may be called error statistics. I discuss the key properties of this approach which enable it to split off the task of (...) testing auxiliary hypotheses from that of appraising a primary hypothesis. By discriminating patterns of error, this approach can at least block, if not also severely test, attempted explanations of an anomaly. I illustrate how this approach directs progress with Duhemian problems and explains how scientists actually grapple with them. (shrink)

Statistical tests of the primality of some numbers look similar to statistical tests of many nonmathematical, clearly empirical propositions. Yet interpretations of probability prima facie appear to preclude the possibility of statistical tests of mathematical propositions. For example, it is hard to understand how the statement that n is prime could have a frequentist probability other than 0 or 1. On the other hand, subjectivist approaches appear to be saddled with ‘coherence’ constraints on rational probabilities that require rational agents to (...) assign extremal probabilities to logical and mathematical propositions. In the light of these problems, many philosophers have come to think that there must be some way to generalize a Bayesian statistical account. In this article I propose that a classical frequentist approach should be reconsidered. I conclude that we can give a conditional justification of statistical testing of at least some mathematical hypotheses: if statistical tests provide us with reasons to believe or bet on empirical hypotheses in the standard situations, then they also provide us with reasons to believe or bet on mathematical hypotheses in the structurally similar mathematical cases. (shrink)

“Evidence” in the form of data collected and analysis thereof is fundamental to medicine, health and science. In this paper, we discuss the “evidence-based” aspect of evidence-based medicine in terms of statistical inference, acknowledging that this latter field of statistical inference often also goes by various near-synonymous names—such as inductive inference (amongst philosophers), econometrics (amongst economists), machine learning (amongst computer scientists) and, in more recent times, data mining (in some circles). Three central issues to this discussion of “evidence-based” are (i) (...) whether or not the statistical analysis can and/or should be objective and/or whether or not (subjective) prior knowledge can and/or should be incorporated, (ii) whether or not the analysis should be invariant to the framing of the problem (e.g. does it matter whether we analyse the ratio of proportions of morbidity to non-morbidity rather than simply the proportion of morbidity?), and (iii) whether or not, as we get more and more data, our analysis should be able to converge arbitrarily closely to the process which is generating our observed data. For many problems of data analysis, it would appear that desiderata (ii) and (iii) above require us to invoke at least some form of subjective (Bayesian) prior knowledge. This sits uncomfortably with the understandable but perhaps impossible desire of many medical publications that at least all the statistical hypothesis testing has to be classical non-Bayesian—i.e. it is not permitted to use any (subjective) prior knowledge. (shrink)

The replication crisis has prompted many to call for statistical reform within the psychological sciences. Here we examine issues within Frequentist statistics that may have led to the replication crisis, and we examine the alternative—Bayesian statistics—that many have suggested as a replacement. The Frequentist approach and the Bayesian approach offer radically different perspectives on evidence and inference with the Frequentist approach prioritising error control and the Bayesian approach offering a formal method for quantifying the relative (...) strength of evidence for hypotheses. We suggest that rather than mere statistical reform, what is needed is a better understanding of the different modes of statistical inference and a better understanding of how statistical inference relates to scientific inference. (shrink)

This article analyzes the role of entropy in Bayesian statistics, focusing on its use as a tool for detection, recognition and validation of eigen-solutions. “Objects as eigen-solutions” is a key metaphor of the cognitive constructivism epistemological framework developed by the philosopher Heinz von Foerster. Special attention is given to some objections to the concepts of probability, statistics and randomization posed by George Spencer-Brown, a figure of great influence in the field of radical constructivism.

We investigate the general properties of general Bayesian learning, where “general Bayesian learning” means inferring a state from another that is regarded as evidence, and where the inference is conditionalizing the evidence using the conditional expectation determined by a reference probability measure representing the background subjective degrees of belief of a Bayesian Agent performing the inference. States are linear functionals that encode probability measures by assigning expectation values to random variables via integrating them with respect to the (...) probability measure. If a state can be learned from another this way, then it is said to be Bayes accessible from the evidence. It is shown that the Bayes accessibility relation is reflexive, antisymmetric and non-transitive. If every state is Bayes accessible from some other defined on the same set of random variables, then the set of states is called weakly Bayes connected. It is shown that the set of states is not weakly Bayes connected if the probability space is standard. The set of states is called weakly Bayes connectable if, given any state, the probability space can be extended in such a way that the given state becomes Bayes accessible from some other state in the extended space. It is shown that probability spaces are weakly Bayes connectable. Since conditioning using the theory of conditional expectations includes both Bayes’ rule and Jeffrey conditionalization as special cases, the results presented generalize substantially some results obtained earlier for Jeffrey conditionalization. (shrink)

Education in statistics, the application of statistics in scientific research, and statistics itself as a scientific discipline are in crisis. Within science, the main cause of the crisis is the insufficiently clarified concept of probability. This article aims to separate the concept of probability which is scientifically based from other concepts that do not have this characteristic. The scientifically based concept of probability is Kolmogorov’s concept of probability models together with the conditions of their applicability. Bayesian (...) statistics is based on the subjective concept of probability, and as such can only have a heuristic value in searching for the truth, but it cannot and must not replace the truth. The way out of the crisis should take Kolmogorov and Bayesian analysis as elements, each of which has a well-defined and limited use. Only together with qualitative analysis and other types of quantitative analysis, and combined with experiments, they can contribute to reaching correct conclusions. (shrink)

The data analyzed in this paper are part of the results described in Bueno et al. (2000). Three cytogenetics endpoints were analyzed in three populations of a species of wild rodent – Akodon montensis – living in an industrial, an agricultural, and a preservation area at the Itajaí Valley, State of Santa Catarina, Brazil. The polychromatic/normochromatic ratio, the mitotic index, and the frequency of micronucleated polychromatic erythrocites were used in an attempt to establish a genotoxic profile of each area. It (...) was assumed that the three populations were in the same conditions with respect to the influence of confounding factors such as animal age, health, nutrition status, presence of pathogens, and intra- and inter-populational genetic variability. Therefore, any differences found in the endpoints analyzed could be attributed to the external agents present in each area. The statistical models used in this paper are mixtures of negative-binomials and Poisson variables. The Poisson variables are used as approximations of binomials for rare events. The mixing distributions are beta densities. The statistical analyzes are under the bayesian perspective, as opposed to the frequentist ones often considered in the literature, as for instance in Bueno et al. (2000). (shrink)

Children acquiring languages with noun classes have ample statistical information available that characterizes the distribution of nouns into these classes, but their use of this information to classify novel nouns differs from the predictions made by an optimal Bayesian classifier. We use rational analysis to investigate the hypothesis that children are classifying nouns optimally with respect to a distribution that does not match the surface distribution of statistical features in their input. We propose three ways in which children's apparent (...) statistical insensitivity might arise, and find that all three provide ways to account for the difference between children's behavior and the optimal classifier. A fourth model combines two of these proposals and finds that children's insensitivity is best modeled as a bias to ignore certain features during classification, rather than an inability to encode those features during learning. These results provide insight into children's developing knowledge of noun classes and highlight the complex ways in which statistical information from the input interacts with children's learning processes. (shrink)

The three main approaches in statistical inference—classical statistics, Bayesian and likelihood—are in current use in phylogeny research. The three approaches are discussed and compared, with particular emphasis on theoretical properties illustrated by simple thought-experiments. The methods are problematic on axiomatic grounds, extra-mathematical grounds relating to the use of a prior or practical grounds. This essay aims to increase understanding of these limits among those with an interest in phylogeny.

With his new riddle of induction, Goodman raised a problem for enumerative induction which many have taken to show that only some ‘natural’ properties can be used for making inductive inferences. Arguably, however, (i) enumerative induction is not a method that scientists use for making inductive inferences in the first place. Moreover, it seems at first sight that (ii) Goodman’s problem does not affect the method that scientists actually use for making such inferences—namely, classical statistics. Taken together, this would (...) indicate that (iii) ‘naturalness’ is not such a relevant concept for the problem of induction, after all. I have no objections against (i) and (iii). But, contrary to (ii), I argue that classical statistics does face a version of Goodman’s problem, which I call the statistical riddle of induction. Given that his problem merely is an instance of the more general problem of underdetermination, this is hardly surprising. Perhaps more importantly, I also show how my riddle can be used for exposing a common fallacy in probabilistic reasoning, without relying on Bayesian assumptions. (shrink)

Otsuka (2023) argues for a correspondence between data science and traditional epistemology: Bayesian statistics is internalist; classical (frequentist) statistics is externalist, owing to its reliabilist nature; model selection is pragmatist; and machine learning is a version of virtue epistemology. Where he sees diversity, I see an opportunity for unity. In this article, I argue that classical statistics, model selection, and machine learning share a foundation that is reliabilist in an unconventional sense that aligns with internalism. Hence (...) a unification under internalist reliabilism. (shrink)

Chow's book makes a provocative contribution to the debate on the role of statistical significance, but it involves some important misconceptions in the presentation of the Fisher and Neyman/Pearson's theories. Moreover, the author's caricature-like considerations about “Bayesianism” are completely irrelevant for discarding the Bayesian statistical theory. These facts call into question the objectivity of his contribution.