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Questions tagged [jags]

"JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS." (http://mcmc-jags.sourceforge.net/)

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5
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1answer
5k views

Prediction based on bayesian model

I have created a bayesian model that estimates 6 parameters using rjags from R. Now i want to do some predictions based on new data in R. Can anyone help me with an example. ...
8
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1answer
1k views

When making inferences about group means, are credible Intervals sensitive to within-subject variance while confidence intervals are not?

This is a spin off of this question: How to compare two groups with multiple measurements for each individual with R? In the answers there (if I understood correctly) I learned that within-subject ...
2
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1answer
962 views

Bayesian errors-in-variables model definition in JAGS and symbolically

I'm fairly new to probability theory and am attempting to understand and implement an errors-in-variables simple linear regression model. I am assuming a model of the form $$ Y=\theta X_a+\epsilon_Y ...
31
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1answer
6k views

For which distributions are the parameterizations in BUGS and R different?

I have found some distributions for which BUGS and R have different parameterizations: Normal, log-Normal, and Weibull. For each of these, I gather that the second parameter used by R needs to be ...
9
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1answer
5k views

Missing values in response variable in JAGS

Gelman & Hill (2006) say: In Bugs, missing outcomes in a regression can be handled easily by simply including the data vector, NA’s and all. Bugs explicitly models the outcome variable, and ...
1
vote
1answer
563 views

My MCMC do not overlap : Mixturemodel with JAGS and R

I fitted a JAGS model and I have those results : My questions are: Why do my chains not overlap, and how can I fix that? I used the following method: My model is a mixture Gaussian model of two ...
0
votes
2answers
781 views

Comparing a model with two rate parameters to a model with one. Conjugate priors?

I have a model which includes two exponential rate parameters. I would like to test whether a model with two individual rates describes some data better than a model for which both rates are the same. ...
10
votes
2answers
6k views

How can I model a proportion with BUGS/JAGS/STAN?

I am trying to build a model where the response is a proportion (it is actually the share of votes a party gets in constituencies). Its distribution is not normal, so I decided to model it with a beta ...
13
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1answer
5k views

Regularized bayesian logistic regression in JAGS

There are several math-heavy papers that describe the Bayesian Lasso, but I want tested, correct JAGS code that I can use. Could someone post sample BUGS / JAGS code that implements regularized ...
7
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6answers
2k views

R2jags does not remove the burn in part sometimes?

I found out that the function jags() in the R2jags package sometimes does not remove the burn in part even with the option ...
11
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2answers
4k views

How can I set up a zero-inflated poisson in JAGS?

I am trying to set up a zero-inflated poisson model in R and JAGS. I am new to JAGS and I need some guidance on how to do that. I've been trying with the following where y[i] is the observed ...
3
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1answer
1k views

Combining posterior distributions

I have 5 different posterior distributions (mcmc samples) which all estimate the same parameter beta. The 5 models are all obtained from 5 independent standardized datasets but estimate the same ...
41
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4answers
7k views

OpenBugs vs. JAGS

I am about to try out a BUGS style environment for estimating Bayesian models. Are there any important advantages to consider in choosing between OpenBugs or JAGS? Is one likely to replace the other ...
10
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3answers
3k views

Weighted generalized regression in BUGS, JAGS

In R we can "prior weight" a glm regression via the weights parameter. For example: ...
7
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2answers
7k views

How to use the SD of a normal sampling distribution to specify the gamma prior for the corresponding precision?

The gamma distribution is a commonly used prior distribution for the precision ($1/sd^2$) of a normal distribution in Bayesian hierarchical modeling. I want to use an informed prior for the variance ...
10
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1answer
1k views

Managing high autocorrelation in MCMC

I'm building a rather complex hierarchical Bayesian model for a meta-analysis using R and JAGS. Simplifying a bit, the two key levels of the model have $$ y_{ij} = \alpha_j + \epsilon_i$$ $$\alpha_j =...
8
votes
1answer
5k views

Specify a Zero-inflated (Hurdle) Gamma Model in JAGS/BUGS

I'm trying to use a zero-inflated gamma model (or a gamma 'hurdle' model). The model is a mixture of logistic regression and generalized linear modeling. I can do this analysis in two steps: 1) do a ...
6
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1answer
5k views

Ordered logit in JAGS

I am trying to code a simple model with JAGS: ...
8
votes
1answer
696 views

What level to use when comparing subjects in a hierarchical Bayesian analysis?

Say that I have an experiment where I test the reaction time of a number of subjects where each subject makes many reaction time trials. In a Bayesian framework the reaction times ($y$) could be ...
6
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0answers
2k views

Hyper-prior for negative binomial in hierarchical model using JAGS/BUGS

Below I'm using a negative binomial because it is more flexible than a simple poisson model. The data are counts $y$ of events for 16 individuals $x$. There are 14 counts (i.e. counting periods) for ...
7
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1answer
2k views

Bayesian mixed model regression with a between subjects factor

I'm trying to specify a model in JAGS/rjags with one between subjects factor (a, with two levels - Y, N) interacting with one repeated measures continuous variable x plus subject varying slopes and ...
6
votes
1answer
4k views

How do I parameterize a Weibull distribution in JAGS / BUGS?

Based on the answer to a previous question, For which distributions are the parameterizations in BUGS and R different? I have been transforming R parameterizations to JAGS parameterizations, but I ...
12
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1answer
5k views

How to generate predictions with rjags?

I've used rjags to run MCMC on a model, specified in the JAGS language. Is there a good way to extract that model and perform predictions with it (using the posterior distributions of my parameters)? ...
4
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1answer
926 views

JAGS, cannot evaluate upper index of counter

I asked this question at the JAGS sourceforge help forum but didn't get response there. I have the following JAGS model: ...
1
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1answer
1k views

Binomial coefficient in JAGS

I'm trying to write such likelihood using JAGS in R (in order to estimate parameters $\xi$ and $\pi$, being $m$ fixed equal 7) using the "ones trick" and got stuck ...
5
votes
1answer
311 views

Difficulties with a Bayesian formulation of a model for human timing data

The Wing-Kristofferson model is a simple model of the behavior of a human trying to drum out a steady beat (that is, trying to mimic a metronome). Let $y_i$ be the $i$th interval between two drum ...
3
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0answers
2k views

Using JAGS for bayesian parameter estimation

I am using JAGS in R to construct a probabilistic graph model and estimate the corresponding parameters. The models is described as follows: ...
3
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2answers
751 views

Bounds on correlation to ensure covariance matrix is positive definite

UPDATED: I am constructing a correlation matrix for an MA(1) process, which would look something like... $$ C = \left( \begin{array}{cccccccccccccccccc} 1 & \rho & 0 & 0 & 0 & 0 &...
2
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0answers
669 views

Appropriate GLM when response variable is proportion, but not binomial

The response variable I'm dealing with is the proportion of a total area that is suitable habitat for a species of interest. So although the response variable is bounded between 0 and 1, my intuition ...
2
votes
1answer
684 views

error in JAGS beta-regression model R - value out of range in 'gammafn'

I am running a simple beta regression model in JAGS, following the example given here. Here is my JAGS model code as an R object: ...
1
vote
1answer
346 views

JAGS burn-in phase takes ZERO time? [duplicate]

My breath was taken away by this. I tried to run my JAGS model with different number burn-in samples but it still takes the same amout of time!! ...
1
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1answer
443 views

Random effect on scale parameter

I am trying to use random effects on both the location and scale parameters in a lognormal regression. As you can see in the JAGS code below, I am essentially fitting a accelerated failure time model ...
0
votes
1answer
221 views

Error metric for cross-validation on interval-censored data?

I want to compare crossvalidated model fit (of two Bayesian models, one using a normal distribution and the other a t-distribution) on interval-censored data - data where the exact point is not known, ...
0
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0answers
962 views

ANOVA with uncertain values - attempt to redefine node

I'm trying to do one-way ANOVA on uncertain (latent) input value YReal[i] (each input value is not exactly known, but it is given as normal distribution with mean <...