rjags is a R interface to the JAGS MCMC library for Bayesian graphical models.

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Bayesian random effects meta-analysis on the risk ratio with r2jags

Following the work of Warn 2002 I am trying to set up the model for a Bayesian meta-analysis on the risk ratio and the odds ratio. I am using R together with R2jags to fit a simple RE MA model. ...
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2answers
22 views

JAGS choosing a random subset of a vector

I would like to allow the subset of a vector I am summing over to be a random quantity. My model is of the form (albeit more complex): ...
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9 views

Alpha Parameter Specification Dirichlet Prior

I have a straightforward Dirichlet-Multinomial model with code that is running in RJAGS. The data are a collection of 200 2 x 2 contingency tables. The multinomial counts are those of a 2 x 2 ...
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1answer
45 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. ...
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1answer
83 views

JAGS Error: Invalid Parent Values on last observation

I am using R2jags to fit a model in R using JAGS. Here is my code: ...
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1answer
48 views

Jags - estimates are same as true values of y?

Lets say I have the following state space model: $y_t = \beta_t x_t + \epsilon_t$ $\beta_{t+1} = \mu_t + \beta_t \eta_t$ $\mu_{t+1} = \mu_t + \omega_t$ All my true values for $y$ are known, but I ...
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1answer
36 views

Can Jags be used to fit classical inference state space models?

Can Jags be used to fit classical inference state space models (that is without using a Bayesian approach by specifying a prior)? To be fully clear: can I estimate a state space model such as the ...
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1answer
75 views

Translating a bayesian model from MCMCpack (hregress) to JAGS

I am trying to convert a hierarchical model that currently works with the R package MCMCpack, into a JAGS version. I have experience working with regular models in JAGS, but not with hierarchical ...
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1answer
38 views

Estimating von Mises Parameters for Angular Data

I want to model some angular data. Any input on how to incorporate the von Mises distribution and suggestions on appropriate priors in RJAGS for von Mises mean and concentration would be greatly ...
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22 views

generating a sequence of indicators based on variable boundaries in JAGS

Suppose I have a vector of indices 1:N, and data y[1], ..., y[N]. I have three variable center points in ...
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1answer
112 views

RJAGS Multinomial-Dirichlet – Observed node inconsistent with unobserved parents at initialization

I am trying to model a simple 2x2 contingency table with a multinomial-Dirichlet model. A snippet of my data z[i,1:4] look like this: ...
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1answer
162 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: ...
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53 views

“Observed node inconsistent ” when binomial success rate exactly one

I observed some curious behavior in JAGS (rjags). There probably is a good reason for it, but I can't figure it out: As part of a more complex model I have these statements: ...
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72 views

JAGS prior-based prediction

I'm trying to use rjags to predict what the curve-maximums will be for different groups of incomplete data (one metric x and one metric y). Here is an example of the indata: ...
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272 views

Specifying a Normal-Log-Normal Mixture (Skew Normal) in WINBUGS/JAGS

I am an actuary working on a Bayesian loss reserve model using incremental average severity data. Exploratory analysis of the response seems to suggest a skew normal distribution of some sort would be ...
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1answer
402 views

JAGS array indexing [closed]

I have a relatively simple multivariate response problem that seems to causing me problems with array indexing. I've scraped/rewworked the model program down to the bare essentials and hopefully ...
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583 views

Help with JAGS model using matrix multiplication and Dirichlet prior

I want to set up a simple JAGS model using matrix multiplication, but I am not sure how to set up the matrices. My overall equation is $c=yx$ where $c$ is a 2x1 matrix defined in R of observed data ...
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2answers
400 views

How to conditionally run element of JAGS script based on user supplied variable?

Background: I often find that when working with JAGS that I end up with a lot of JAGS scripts as I explore different models. After a while I might settle on a set of models that I'm going to report, ...
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1answer
148 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!! ...
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2answers
193 views

How to analyze this data using rjags, or any other way?

There are three groups that received different treatments and then learn a task which they are scored on over the course of 60 sessions. 1) How to choose a function to fit? -The best choice in this ...
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1answer
670 views

Define Priors for Dirichlet Distribution parameters in JAGS

I'm defining a Multinomial-Dirichlet model in JAGS and want to assign some hyperpriors to the parameters of the Dirichlet distribution. In the WinBugs manual I read that "the parameters of Dirichlet ...
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1answer
171 views

Autoregressive prior distributions

I have a set of 50 (P) time series' and each one is on a slightly different but should be influenced by the same effects of time. To get the time effects I have ...
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1answer
981 views

How to specify the Wishart distribution scale matrix

I'm running the below Bayesian mixing model in R using the rjags package, but I am having difficultly in specifying the scale matrix for the Wishart distribution. Essentially, I want Sigma.inv to be a ...
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281 views

Specifying Dirichlet prior in rjags

I am running the below mixing model using the rjags package in R, but I keep getting the error message ...
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350 views

Should coin flips be modeled as Bernoulli or binomial draws in RJags?

What is the best way to model coin flips as a hierarchical model? Do you say coin draws are a series of draws from Bernoulli trials or as one draw from a binomial distribution? That is something like ...
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1answer
66 views

Simulated single value based on multiple chains in RJAGS

I am using RJAGS to simulate the posterior distribution of event that a certain candidate will win the presidential election. I need to find the actual percentage that one of the candidates will have. ...
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650 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 ...
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166 views

How to define CDF of bivariate normal distribution in rjags?

I am trying to define my own likelihood in rjags. I want to define the CDF of bivariate normal distribution under rjags. Does anyone know how to define the CDf of bivariate normal in rjags?
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889 views

JAGS - problem with taking submatrices

I'm trying to use JAGS for clustering mixtures of multivariate normal distributions. In order to model different covariance structures in each cluster I wanted to use one big (C*D)xD matrix (C - ...
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2answers
851 views

Compilation error in JAGS

With this data: ...
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2answers
2k views

jags missing data error

I am estimating a probit in jags on a time series cross sectional data set (country years) with 5 covariates, 4 of which are lagged, so the first observation for each country will be missing on those ...
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384 views

Generating and analyzing predicted data in JAGS

I am trying to model a logistic regression on data predicted from the results of a previous logistic regression, and am having trouble figuring out how to do it, either in OpenBUGS (BRugs) or JAGS ...
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251 views

How to sample from the prior predictive distribution in jags?

Is there an example available of how I can sample from the prior predictive distribution (without data) in jags? I would like to get a better sense for the contribution of the prior in a multilevel ...
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1answer
1k 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)? ...
2
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1answer
2k views

JAGS: unobserved parents and intialization

I have a very simple multinomial logistic regression problem; it's a simplified version of the alligator lake/food/size BUGS example. In my case I have (effectively) lake/food and have just stripped ...
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1answer
1k 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 ...
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1answer
909 views

How to combine step(x) and dbern(p) in JAGS/WinBUGS?

The problem involves trying to characterize the probability: P.f = Pd*Pr{t1 < t2} using jags or WinBUGS. The issue is the last term where both t1 and t2 are ...
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1answer
261 views

Data and model blocks in JAGS

I am trying to model a function of observed data in JAGS. For example x[i,t]/phi ~ dpois(mu) where x is observed and phi is a parameter in the model. I can't ...
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1answer
3k views

Ordered logit in JAGS

I am trying to code a simple model with JAGS: ...
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2answers
605 views

How to run JAGS as fast as possible on Mac?

I am running lots of simulations in JAGS 3.1.0 , which I have compiled from source. I am using a mid-2009 Macbook Pro 13 2.53GHz. Is there any step by step tutorial (from scratch) to compile ATLAS or ...
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1answer
575 views

How does dinterval() for interval censored data work in JAGS?

I am trying to understand how dinterval() works in JAGS for censored data. I am modeling coarse data where I only have upper and lower bounds for each data point (not the true value). Here is a ...
10
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1answer
406 views

MCMC converging to a single value?

I'm trying to fit a hierarchical model using jags, and the rjags package. My outcome variable is y, which is a sequence of bernoulli trials. I have 38 human subjects which are performing under two ...