An alternative to null-hypothesis significance tests

The statistic p(rep) estimates the probability of replicating an effect. It captures traditional publication criteria for signal-to-noise ratio, while avoiding parametric inference and the resulting Bayesian dilemma. In concert with effect size and replication intervals, p(rep) provides all of the information now used in evaluating research, while avoiding many of the pitfalls of traditional statistical inference.     

A tutorial on Bayesian nonparametric models

A key problem in statistical modeling is model selection, that is, how to choose a model at an appropriate level of complexity. This problem appears in many settings, most prominently in choosing the number of clusters in mixture models or the number of factors in factor analysis. In this tutorial, we describe Bayesian nonparametric methods, a class of methods that side-steps this issue by allowing the data to determine the complexity of the model. This tutorial is a high-level introduction to Bayesian nonparametric methods and contains several examples of their application.     

A tutorial on approximate Bayesian computation

This tutorial explains the foundation of approximate Bayesian computation (ABC), an approach to Bayesian inference that does not require the specification of a likelihood function, and hence that can be used to estimate posterior distributions of parameters for simulation-based models. We discuss briefly the philosophy of Bayesian inference and then present several algorithms for ABC. We then apply these algorithms in a number of examples. For most of these examples, the posterior distributions are known, and so we can compare the estimated posteriors derived from ABC to the true posteriors and verify that the algorithms recover the true posteriors accurately. We also consider a popular simulation-based model of recognition memory (REM) for which the true posteriors are unknown. We conclude with a number of recommendations for applying ABC methods to solve real-world problems.     

A tutorial introduction to Bayesian models of cognitive development

We present an introduction to Bayesian inference as it is used in probabilistic models of cognitive development. Our goal is to provide an intuitive and accessible guide to the what, the how, and the why of the Bayesian approach: what sorts of problems and data the framework is most relevant for, and how and why it may be useful for developmentalists. We emphasize a qualitative understanding of Bayesian inference, but also include information about additional resources for those interested in the cognitive science applications, mathematical foundations, or machine learning details in more depth. In addition, we discuss some important interpretation issues that often arise when evaluating Bayesian models in cognitive science.     

Four reasons to prefer Bayesian analyses over significance testing

Inference using significance testing and Bayes factors is compared and contrasted in five case studies based on real research. The first study illustrates that the methods will often agree, both in motivating researchers to conclude that H1 is supported better than H0, and the other way round, that H0 is better supported than H1. The next four, however, show that the methods will also often disagree. In these cases, the aim of the paper will be to motivate the sensible evidential conclusion, and then see which approach matches those intuitions. Specifically, it is shown that a high-powered non-significant result is consistent with no evidence for H0 over H1 worth mentioning, which a Bayes factor can show, and, conversely, that a low-powered non-significant result is consistent with substantial evidence for H0 over H1, again indicated by Bayesian analyses. The fourth study illustrates that a high-powered significant result may not amount to any evidence for H1 over H0, matching the Bayesian conclusion. Finally, the fifth study illustrates that different theories can be evidentially supported to different degrees by the same data; a fact that P-values cannot reflect but Bayes factors can. It is argued that appropriate conclusions match the Bayesian inferences, but not those based on significance testing, where they disagree.     

Bayesian inference with Stan: A tutorial on adding custom distributions

When evaluating cognitive models based on fits to observed data (or, really, any model that has free parameters), parameter estimation is critically important. Traditional techniques like hill climbing by minimizing or maximizing a fit statistic often result in point estimates. Bayesian approaches instead estimate parameters as posterior probability distributions, and thus naturally account for the uncertainty associated with parameter estimation; Bayesian approaches also offer powerful and principled methods for model comparison. Although software applications such as WinBUGS (Lunn, Thomas, Best, & Spiegelhalter, Statistics and Computing, 10, 325–337, 2000) and JAGS (Plummer, 2003) provide “turnkey”-style packages for Bayesian inference, they can be inefficient when dealing with models whose parameters are correlated, which is often the case for cognitive models, and they can impose significant technical barriers to adding custom distributions, which is often necessary when implementing cognitive models within a Bayesian framework. A recently developed software package called Stan (Stan Development Team, 2015) can solve both problems, as well as provide a turnkey solution to Bayesian inference. We present a tutorial on how to use Stan and how to add custom distributions to it, with an example using the linear ballistic accumulator model (Brown & Heathcote, Cognitive Psychology, 57, 153–178. doi: 10.1016/j.cogpsych.2007.12.002, 2008).     

Bayesian inference using WBDev: A tutorial for social scientists

Over the last decade, the popularity of Bayesian data analysis in the empirical sciences has greatly increased. This is partly due to the availability of WinBUGS, a free and flexible statistical software package that comes with an array of predefined functions and distributions, allowing users to build complex models with ease. For many applications in the psychological sciences, however, it is highly desirable to be able to define one’s own distributions and functions. This functionality is available through the WinBUGS Development Interface (WBDev). This tutorial illustrates the use of WBDev by means of concrete examples, featuring the expectancyvalence model for risky behavior in decision making, and the shifted Wald distribution of response times in speeded choice.     

A tutorial on hierarchically structured constructs

Many psychological constructs are conceived to be hierarchically structured and thus to operate at various levels of generality. Alternative confirmatory factor analytic (CFA) models can be used to study various aspects of this proposition: (a) The one-factor model focuses on the top of the hierarchy and contains only a general construct, (b) the first-order factor model focuses on the intermediate level of the hierarchy and contains only specific constructs, and both (c) the higher order factor model and (d) the nested-factor model consider the hierarchy in its entirety and contain both general and specific constructs (e.g., bifactor model). This tutorial considers these CFA models in depth, addressing their psychometric properties, interpretation of general and specific constructs, and implications for model-based score reliabilities. The authors illustrate their arguments with normative data obtained for the Wechsler Adult Intelligence Scale and conclude with recommendations on which CFA model is most appropriate for which research and diagnostic purposes.     

A tutorial on adaptive design optimization

Experimentation is ubiquitous in the field of psychology and fundamental to the advancement of its science, and one of the biggest challenges for researchers is designing experiments that can conclusively discriminate the theoretical hypotheses or models under investigation. The recognition of this challenge has led to the development of sophisticated statistical methods that aid in the design of experiments and that are within the reach of everyday experimental scientists. This tutorial paper introduces the reader to an implementable experimentation methodology, dubbed Adaptive Design Optimization, that can help scientists to conduct “smart” experiments that are maximally informative and highly efficient, which in turn should accelerate scientific discovery in psychology and beyond.     

A tutorial on how to do a Mokken scale analysis on your test and questionnaire data

Over the past decade, Mokken scale analysis (MSA) has rapidly grown in popularity among researchers from many different research areas. This tutorial provides researchers with a set of techniques and a procedure for their application, such that the construction of scales that have superior measurement properties is further optimized, taking full advantage of the properties of MSA. First, we define the conceptual context of MSA, discuss the two item response theory (IRT) models that constitute the basis of MSA, and discuss how these models differ from other IRT models. Second, we discuss dos and don'ts for MSA; the don'ts include misunderstandings we have frequently encountered with researchers in our three decades of experience with real‐data MSA. Third, we discuss a methodology for MSA on real data that consist of a sample of persons who have provided scores on a set of items that, depending on the composition of the item set, constitute the basis for one or more scales, and we use the methodology to analyse an example real‐data set.     

A tutorial on kernel methods for categorization

The abilities to learn and to categorize are fundamental for cognitive systems, be it animals or machines, and therefore have attracted attention from engineers and psychologists alike. Modern machine learning methods and psychological models of categorization are remarkably similar, partly because these two fields share a common history in artificial neural networks and reinforcement learning. However, machine learning is now an independent and mature field that has moved beyond psychologically or neurally inspired algorithms towards providing foundations for a theory of learning that is rooted in statistics and functional analysis. Much of this research is potentially interesting for psychological theories of learning and categorization but also hardly accessible for psychologists. Here, we provide a tutorial introduction to a popular class of machine learning tools, called kernel methods. These methods are closely related to perceptrons, radial-basis-function neural networks and exemplar theories of categorization. Recent theoretical advances in machine learning are closely tied to the idea that the similarity of patterns can be encapsulated in a positive definite kernel. Such a positive definite kernel can define a reproducing kernel Hilbert space which allows one to use powerful tools from functional analysis for the analysis of learning algorithms. We give basic explanations of some key concepts—the so-called kernel trick, the representer theorem and regularization—which may open up the possibility that insights from machine learning can feed back into psychology.     

A tutorial on partially observable Markov decision processes

The partially observable Markov decision process (POMDP) model of environments was first explored in the engineering and operations research communities 40 years ago. More recently, the model has been embraced by researchers in artificial intelligence and machine learning, leading to a flurry of solution algorithms that can identify optimal or near-optimal behavior in many environments represented as POMDPs. The purpose of this article is to introduce the POMDP model to behavioral scientists who may wish to apply the framework to the problem of understanding normative behavior in experimental settings. The article includes concrete examples using a publicly-available POMDP solution package.