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

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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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rjags Compilation error. Cannot evaluate upper index of counter i [migrated]

I looked at a similar question but it did not help me. Here is my JAGS code (contained in a text file simulazione_vivek.txt): ...
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29 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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67 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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41 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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69 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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204 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
265 views

JAGS array indexing

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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427 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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260 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
127 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
172 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
538 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
131 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
802 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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236 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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2answers
302 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
65 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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523 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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158 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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798 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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699 views

Compilation error in JAGS

With this data: ...
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1answer
1k 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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352 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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237 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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912 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)? ...
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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
946 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
807 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
243 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
571 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
527 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 ...
9
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1answer
381 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 ...