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Behavior Research Methods

, Volume 46, Issue 1, pp 15–28 | Cite as

Extending JAGS: A tutorial on adding custom distributions to JAGS (with a diffusion model example)

  • Dominik Wabersich
  • Joachim Vandekerckhove
Article

Abstract

We demonstrate how to add a custom distribution into the general-purpose, open-source, cross-platform graphical modeling package JAGS (“Just Another Gibbs Sampler”). JAGS is intended to be modular and extensible, and modules written in the way laid out here can be loaded at runtime as needed and do not interfere with regular JAGS functionality when not loaded. Writing custom extensions requires knowledge of C++, but installing a new module can be highly automatic, depending on the operating system. As a basic example, we implement a Bernoulli distribution in JAGS. We further present our implementation of the Wiener diffusion first-passage time distribution, which is freely available at https://sourceforge.net/projects/jags-wiener/.

Keywords

Custom distributions JAGS Bayesian Diffusion model HDM 

Notes

Author note

This project was partially supported by grant 1230118 from the National Science Foundation’s Measurement, Methods, and Statistics panel to J.V., and by a travel grant from the German Academic Exchange Service (PROMOS) to D.W. We are indebted to Martyn Plummer for helpful comments on the manuscript and for helping us with compiling issues. We also thank two anonymous reviewers and the action editor for constructive comments on an earlier draft of this article.

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Copyright information

© Psychonomic Society, Inc. 2013

Authors and Affiliations

  1. 1.Department of Cognitive SciencesUniversity of CaliforniaIrvineUSA
  2. 2.Department of PsychologyUniversity of TübingenTübingenGermany

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