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JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling

Published on Jan 1, 2003
Martyn Plummer1
Estimated H-index: 1
Abstract
JAGS is a program for Bayesian Graphical modelling which aims for compatibility with Classic BUGS. The program could eventually be developed as an R package. This article explains the motivations for this program, briefly describes the architecture and then discusses some ideas for a vectorized form of the BUGS language.
  • References (5)
  • Citations (1690)
References5
Newest
Published on Oct 1, 2003in Scandinavian Actuarial Journal 1.55
Mogens Bladt13
Estimated H-index: 13
,
Antonio Gonzalez1
Estimated H-index: 1
,
Steffen L. Lauritzen39
Estimated H-index: 39
In this paper we present a method for estimation of functionals depending on one or several phase-type distributions. This could for example be the ruin probability in a risk reserve process where claims are assumed to be of phase-type. The proposed method uses a Markov chain Monte Carlo simulation to reconstruct the Markov jump processes underlying the phase-type variables in combination with Gibbs sampling to obtain a stationary sequence of phase-type probability measures from the posterior di...
35 Citations Source Cite
Published on Mar 10, 2002in Journal of Statistical Software 22.74
Gregory R. Warnes5
Estimated H-index: 5
(Pfizer)
Hydra is an open-source, platform-neutral library for performing Markov Chain Monte Carlo. It implements the logic of standard MCMC samplers within a framework designed to be easy to use, extend, and integrate with other software tools. In this paper, we describe the problem that motivated our work, outline our goals for the Hydra pro ject, and describe the current features of the Hydra library. We then provide a step-by-step example of using Hydra to simulate from a mixture model drawn from can...
14 Citations Source Cite
Published on Sep 1, 2000in Biometrics 1.52
Chantal Guihenneuc-Jouyaux10
Estimated H-index: 10
(University of Paris),
Sylvia Richardson53
Estimated H-index: 53
(French Institute of Health and Medical Research),
Ira M. Longini61
Estimated H-index: 61
(Emory University)
Summary. Multistate models have been increasingly used to model natural history of many diseases as well as to characterize the follow-up of patients under varied clinical protocols. This modeling allows describing disease evolution, estimating the transition rates, and evaluating the therapy effects on progression. In many cases, the staging is defined on the basis of a discretization of the values of continuous markers (CD4 cell count for HIV application) that are subject to great variability ...
50 Citations Source Cite
Published on Jun 1, 1993in Statistics in Medicine 1.93
Linda Sharples51
Estimated H-index: 51
Coronary occlusive disease following cardiac transplantation is monitored using serial angiography, and graded on a 3 point scale according to the amount of narrowing observed in major vessels. Disease progression is modelled as a continuous time Markov process. The Gibbs sampler is used to estimate the marginal posterior distributions of the transition rates between grades of disease and from each grade to death.
27 Citations Source Cite
Published on Jan 1, 1993
David J. Spiegelhalter76
Estimated H-index: 76
,
Andrew Thomas9
Estimated H-index: 9
+ 2 AuthorsDarren Lunn3
Estimated H-index: 3
576 Citations
Cited By1690
Newest
Published on May 1, 2019in Scientific Reports 4.12
Nora Mitchell1
Estimated H-index: 1
(University of New Mexico),
Gregory L. Owens1
Estimated H-index: 1
(University of California, Berkeley)
+ 2 AuthorsKenneth D. Whitney26
Estimated H-index: 26
(University of New Mexico)
Hybridization is a common phenomenon, yet its evolutionary outcomes remain debated. Here, we ask whether hybridization can speed adaptive evolution using resynthesized hybrids between two species of Texas sunflowers (Helianthus annuus and H. debilis) that form a natural hybrid in the wild (H. annuus ssp. texanus). We established separate control and hybrid populations and allowed them to evolve naturally in a field evolutionary experiment. In a final common-garden, we measured fitness and a suit...
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Published on Feb 19, 2019in Scientific Reports 4.12
Katie O'Brien2
Estimated H-index: 2
(University of Cambridge),
R. Andrew Atkinson20
Estimated H-index: 20
(King's College London)
+ 11 AuthorsMonty Mythen45
Estimated H-index: 45
(National Institute for Health Research)
At high altitude oxygen delivery to the tissues is impaired leading to oxygen insufficiency (hypoxia). Acclimatisation requires adjustment to tissue metabolism, the details of which remain incompletely understood. Here, metabolic responses to progressive environmental hypoxia were assessed through metabolomic and lipidomic profiling of human plasma taken from 198 human participants before and during an ascent to Everest Base Camp (5,300 m). Aqueous and lipid fractions of plasma were separated an...
1 Citations Source Cite
Published on Jan 3, 2019in Nature Communications 12.35
Jan Gläscher24
Estimated H-index: 24
(California Institute of Technology),
Ralph Adolphs93
Estimated H-index: 93
(California Institute of Technology),
Daniel Tranel97
Estimated H-index: 97
(University of Iowa)
The role of the frontal lobes in cognition and behavior has long been enigmatic. Over the past decade, computational models have provided a powerful approach to understanding cognition and decision-making. Here, we used a model-based approach to analyze data from a classical task used to assess frontal lobe function, the Wisconsin Card Sorting Test. We applied computational modeling and voxel-based lesion-symptom mapping in 328 patients with focal lesions, to uncover cognitive processes and neur...
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Published on Apr 15, 2019in BMC Cancer 3.29
Adrian D. Vickers1
Estimated H-index: 1
,
Katherine B. Winfree8
Estimated H-index: 8
(Eli Lilly and Company)
+ 5 AuthorsDavid P. Carbone67
Estimated H-index: 67
(Ohio State University)
Background Locally advanced or metastatic non-small cell lung cancer (NSCLC) that has progressed after first-line treatment has a poor prognosis. Recent randomized clinical trials (RCTs) have demonstrated survival benefits of alternative treatments to docetaxel. However, information is lacking on which patients benefit the most and what drug or regimen is optimal. We report a systematic review and network meta-analysis (NMA) of second-line treatments in all subgroup combinations determined by hi...
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Published on Apr 3, 2018in Scientific Reports 4.12
Robert Miller18
Estimated H-index: 18
(Dresden University of Technology)
To date, there is only scarce evidence for a considerable association of subjective and objective stress measures, which might be attributable to method bias (e.g., confounding) and/or asynchrony of their temporal changes. To validate different subjective stress measures by a physiological measure of long-term stress (hair cortisol concentrations; HCC), 37 heterosexual couples (N = 74) completed a 12-week internet-based assessment protocol comprised of a weekly hassle scale (WHS; once per week),...
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Published on Mar 5, 2019in Scientific Reports 4.12
Hideyuki Doi30
Estimated H-index: 30
(University of Hyogo),
Keiichi Fukaya1
Estimated H-index: 1
(National Institute for Environmental Studies)
+ 3 AuthorsMasaki Miya56
Estimated H-index: 56
(American Museum of Natural History)
Environmental DNA (eDNA) metabarcoding is a recently developed method to assess biodiversity based on a high-throughput parallel DNA sequencing applied to DNA present in the ecosystem. Although eDNA metabarcoding enables a rapid assessment of biodiversity, it is prone to species detection errors that may occur at sequential steps in field sampling, laboratory experiments, and bioinformatics. In this study, we illustrate how the error rates in the eDNA metabarcoding-based species detection can be...
1 Citations Source Cite
Published on Feb 28, 2019in Scientific Reports 4.12
Denis Valle11
Estimated H-index: 11
(University of Florida),
Kok Ben Toh (University of Florida)+ 1 AuthorsQing Zhao1
Estimated H-index: 1
(University of Florida)
Count data commonly arise in natural sciences but adequately modeling these data is challenging due to zero-inflation and over-dispersion. While multiple parametric modeling approaches have been proposed, unfortunately there is no consensus regarding how to choose the best model. In this article, we propose a ordinal regression model (MN) as a default model for count data given that this model is shown to fit well data that arise from several types of discrete distributions. We extend this model...
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Published on Aug 1, 2019in NeuroImage 5.43
Michael D. Nunez3
Estimated H-index: 3
(University of California, Irvine),
Aishwarya Gosai2
Estimated H-index: 2
(Harvard University)
+ 1 AuthorsRamesh Srinivasan31
Estimated H-index: 31
(University of California, Irvine)
Encoding of a sensory stimulus is believed to be the first step in perceptual decision making. Previous research has shown that electrical signals recorded from the human brain track evidence accumulation during perceptual decision making (Gold and Shadlen, 2007; O'Connell et al., 2012; Philiastides et al., 2014). In this study we directly tested the hypothesis that the latency of the N200 recorded by EEG (a negative peak occurring between 150 and 275 ms after stimulus presentation in human part...
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Carlos Daniel Paulino10
Estimated H-index: 10
(University of Lisbon),
Giovani L. Silva10
Estimated H-index: 10
(Instituto Superior Técnico)
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