bridgesampling: An R Package for Estimating Normalizing Constants

Statistical procedures such as Bayes factor model selection and Bayesian model averaging require the computation of normalizing constants (e.g., marginal likelihoods). These normalizing constants are notoriously difficult to obtain, as they usually involve high-dimensional integrals that cannot be solved analytically. Here we introduce an R package that uses bridge sampling (Meng & Wong, 1996; Meng & Schilling, 2002) to estimate normalizing constants in a generic and easy-to-use fashion. For models implemented in Stan, the estimation procedure is automatic. We illustrate the functionality of the package with three examples

Informed Bayesian T-Tests

Across the empirical sciences, few statistical procedures rival the popularity of the frequentist t-test. In contrast, the Bayesian versions of the t-test have languished in obscurity. In recent years, however, the theoretical and practical advantages of the Bayesian t-test have become increasingly apparent and various Bayesian t-tests have been proposed, both objective ones (based on general desiderata) and subjective ones (based on expert knowledge). Here we propose a flexible t-prior for standardized effect size that allows computation of the Bayes factor by evaluating a single numerical integral. This specification contains previous objective and subjective t-test Bayes factors as special cases. Furthermore, we propose two measures for informed prior distributions that quantify the departure from the objective Bayes factor desiderata of predictive matching and information consistency. We illustrate the use of informed prior distributions based on an expert prior elicitation effort

A Tutorial on Fisher Information

In many statistical applications that concern mathematical psychologists, the concept of Fisher information plays an important role. In this tutorial we clarify the concept of Fisher information as it manifests itself across three different statistical paradigms. First, in the frequentist paradigm, Fisher information is used to construct hypothesis tests and confidence intervals using maximum likelihood estimators; second, in the Bayesian paradigm, Fisher information is used to define a default prior; lastly, in the minimum description length paradigm, Fisher information is used to measure model complexity

Fitting the Cusp Catastrophe in R: A cusp Package Primer

Of the seven elementary catastrophes in catastrophe theory, the âÂÂcuspâ model is the most widely applied. Most applications are however qualitative. Quantitative techniques for catastrophe modeling have been developed, but so far the limited availability of flexible software has hindered quantitative assessment. We present a package that implements and extends the method of Cobb (Cobb and Watson'80; Cobb, Koppstein, and Chen'83), and makes it easy to quantitatively fit and compare different cusp catastrophe models in a statistically principled way. After a short introduction to the cusp catastrophe, we demonstrate the package with two instructive examples.

Evidential Calibration of Confidence Intervals

We present a novel and easy-to-use method for calibrating error-rate based confidence intervals to evidence-based support intervals. Support intervals are obtained from inverting Bayes factors based on a parameter estimate and its standard error. A $k$ support interval can be interpreted as "the observed data are at least $k$ times more likely under the included parameter values than under a specified alternative". Support intervals depend on the specification of prior distributions for the parameter under the alternative, and we present several types that allow different forms of external knowledge to be encoded. We also show how prior specification can to some extent be avoided by considering a class of prior distributions and then computing so-called minimum support intervals which, for a given class of priors, have a one-to-one mapping with confidence intervals. We also illustrate how the sample size of a future study can be determined based on the concept of support. Finally, we show how the bound for the type I error rate of Bayes factors leads to a bound for the coverage of support intervals. An application to data from a clinical trial illustrates how support intervals can lead to inferences that are both intuitive and informative

A Comparison of Reinforcement Learning Models for the Iowa Gambling Task Using Parameter Space Partitioning

The Iowa gambling task (IGT) is one of the most popular tasks used to study decisionmaking deficits in clinical populations. In order to decompose performance on the IGT in its constituent psychological processes, several cognitive models have been proposed (e.g., the Expectancy Valence (EV) and Prospect Valence Learning (PVL) models). Here we present a comparison of three models—the EV and PVL models, and a combination of these models (EV-PU)—based on the method of parameter space partitioning. This method allows us to assess the choice patterns predicted by the models across their entire parameter space. Our results show that the EV model is unable to account for a frequency-of-losses effect, whereas the PVL and EV-PU models are unable to account for a pronounced preference for the bad decks with many switches. All three models underrepresent pronounced choice patterns that are frequently seen in experiments. Overall, our results suggest that the search of an appropriate IGT model has not yet come to an end