Questions tagged [winbugs]
Questions about BUGS language for defining Bayesian models that can be run by the WinBUGS software package. It is advised to supplement your question with a reproducible BUGS example (http://stackoverflow.com/q/5963269).
91
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2
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Missing data imputation in univariate meta analysis with binary data using WinBUGS
I want to impute missing data in univariate meta-analysis. My outcome (no. fractures) is a binary variable. Below is the WinBUGS code I have tried. The code is ...
- 11
0
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0
answers
79
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How to correctly include an offset in a bernouli model in JAGS/WINBUGS (Only one success, but number of choices can change)
I am trying to fit a Bernoulli model in Jags. This is for mate choice - whether a male interacts with a given female out of a selection of females. For the purpose of the model they only get one ...
1
vote
1
answer
63
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Zero and One tricks for INLA?
The Zero and One tricks are used to sample from a model not included in the basic functions in BUGS:
http://www.medicine.mcgill.ca/epidemiology/Joseph/courses/common/Tricks.html
I have a general and ...
1
vote
1
answer
77
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how to overcome error while defining multiple loops for model specification in OpenBUGS?
I'm using following program for MCMC simulation. While compiling this code, I am getting error message which is multiple definition of node s[1]. I am not able to ...
2
votes
1
answer
698
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How many chains should i run in winBUGS?
i am relatively new to winBUGS and i am running a meta-regression model for bayesian meta-analysis. This model tracks the posterior distributions of the parameters mean and tau-square. Moreover,which ...
- 43
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1
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875
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How to correctly include offset in Bayesian Zero-Inflated Poisson model in winbugs
I am trying to fit a Bayesian Zero-inflated model and I want to include an offset term.
When I compared the output of the pscl package; the result of the count model from the winbugs and pscl package ...
- 23
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votes
0
answers
622
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Posterior Predictive Check for Hierarchical Logistic Regression Model
I need to apply Posterior Predictive Check (PPC) on Hierarchical Logistic Regression Model (so I have binary outcome) to validate my model (to see goodness of fit of my model). I know that I need to ...
- 125
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0
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49
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Is there something wrong with my Bayesian hierarchical spatio-temporal model?
I built a Bayesian spatio-temporal model and one of the parameters to be estimated is the random spatial effects s. The random spatial effect is assigned an intrinsic conditional autoregressive prior (...
- 123
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2
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662
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Are "improper uniform priors" in Bayesian analysis equivalent to maximum likelihood estimations?
The improper uniform distribution for parameter $\theta$ is :
$p(\theta)=1,\ for -\infty<\theta<\infty$.
It is called "improper" since it does not integrate to 1. Because Bayesian theorem is ...
- 1,017
0
votes
1
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933
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How to interpret Zero-Inflated Poisson in WINBUGS?
I have Winbugs code for a zero-inflated Poisson (ZIP) model. I obtained this code from my lab at university and the person who wrote it is not accessible for me to ask questions. Here is the code:
<...
- 309
2
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1
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150
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How to interpret zero-inflation model for Bayesian regression?
I am trying to understand the zero-inflated poisson (ZIP) model used in Bayesian regression modelling. I came across code here for the ZIP model. My question is related to the 3rd line of code within ...
- 309
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198
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How to specify a new joint prior distribution restricted to (0,1) interval in WinBUGS?
I am doing some Bayesian analysis in OpenBUGS and I need to specify a joint prior distribution for parameters $\gamma_1$ and $\gamma_2$ (the Jeffreys prior related to my model), such that
$$\pi(\...
2
votes
1
answer
352
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How does WINBUGS determine the posterior density of a parameter with multiple chains?
I am a new user to WINBUGS. I am running a model with 2 chains. When my model has finished running I have the following posterior density plot of my parameter:
The plot only shows one distribution (i....
- 309
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1
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320
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How do interpret a vague prior for hierarchical modeling?
I am new to Bayesian analysis and using the following WINBUGS example to understand Bayesian hierarchical modeling:
I have 2 questions:
1) For the fixed effects terms, i.e., the beta0 and beta1 ...
- 309
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1
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815
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2
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1
answer
397
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"Undefined real result" with inverse() function in WinBUGS
Using WinBUGS, I'd like to generate the posterior distribution for a function of several other variables (stochastic nodes). One step in building up this function involves taking the inverse of a ...
- 41
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0
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387
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How do I specify a random effect in Bayesian beta regression model?
My response data are proportions that I want to model with one continuous predictor and a random effect of group.
Here's my winbugs code:
...
- 21
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1
answer
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How do I calculate the posterior predictive distribution in WinBUGS?
I would like to work out the posterior predictive distribution from the following multilevel (mixed effect) model in WinBUGS. The example is taken from an example I found online for illustrative ...
- 25
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1
answer
128
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Winbugs fixed effects stats output: mean or median?
I am running a fixed effects hazard ratios model with WinBUGS and I can't tell if I've run into a potential problem.
In the stats output, my mean and median are similar, but generally differ by ...
- 111
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1
answer
585
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Winbugs beta distribution
I have fitted a likelihood function with a dbeta function in WinBUGs as follows
...
- 147
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0
answers
185
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Left or right skewed prior in WinBUGS
I am trying to find a proper way of defining a right or left skewed continuous (0...100) distribution for my priors in a simple linear regression.
Furthermore, I expect to find some outliers in my ...
- 147
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2
answers
4k
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Bayesian t-test assumptions
I know that the traditional independent t-test assumes homoscedasticity (i.e., equal variances across groups) and normality of the residuals.
They are usually checked by using levene's test for ...
- 147
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1
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107
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Reference for modeling with WinBugs
Does anyone have any good reference for beginners in WinBUGS about modeling?
I already have some familiarity with R, but I had never used R2WinBUGS before. I'm interested in making beta, beta ...
2
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1
answer
2k
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Learning WinBUGS programming for network meta-analysis
I'm currently interested in learning NMA using WinBUGS. I studied the general concepts behind multiple treatment comparisons and i have a good base on classic pair-wise meta-analysis. I can also do a ...
0
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1
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426
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Simple explanation of a WinBUGS code
Can anyone give me a quick walkthrough of what this code is doing?
I think the line
log( mu[i] ) <- alpha + beta * (year[i]-1970) + log( pop[i] )
is updating ...
- 47
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1
answer
4k
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WinBUGS error - undefined real result
I am trying to run this WinBUGS code to get a prediction for the number of fatalities in 1975
...
- 47
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0
answers
94
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Change a random effects model into a fixed effects model in *BUGS
I want to manipulate this RE model into a FE model for sensitivity analysis. The model is described here: Baseline natural history model
...
12
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1
answer
2k
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Which is the best method for network meta-analysis?
There are now several different approaches to perform a network meta-analysis or mixed treatment comparison.
The most commonly used and accessible ones are probably the following:
in a Bayesian ...
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3
votes
0
answers
763
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Modeling quadratic function parameters as a function of variables
I'm modeling a response variable that varies seasonally. The pattern is relatively well described by a quadratic function. As the data have been collected over many (~50) years, I'm interested to ...
- 303
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1
answer
2k
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Priors for Truncated Parameters - RJAGS
I would like to estimate the parameters of a specific model.
The model specification is as follows:
$p_t = k_t + B_t/(1-B_t) + \eta_t$, where $ \eta_t \sim N(0, \sigma^2)$
$R_{t+1} = R_{t} + R_t (...
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1
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2k
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"Multiple definitions of node p[1]" Error using WinBUGS [closed]
I have written the following code in WinBUGS and every time I try to compile the data after loading in the data I get the same error which is "Multiple definitions of node ...
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783
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code works in jags but not winbugs [closed]
I have band-recovery data from several areas, and am trying to get survival rates for adult and juvenile for each area. Brownie model is used. The model is:
...
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2
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221
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(Failure) probability calculation
I am working on mortality in 12 hospitals performing cardiac surgery in babies. The dataset is available here: Surg dataset. The dataset is structured in this way:
...
- 153
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0
answers
80
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OpenBUGS and coda library
I've fitted a hierarchical model with OpenBUGS using R2WinBUGS package of R. Now, I'd like to use the functions contained in the ...
- 2,097
5
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1
answer
943
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Can improper priors be implemented in some way?
I'm new to bayesian inference. I've just discovered that improper priors can't be specified in WinBUGS/OpenBUGS. I was wondering if this is common or not in bayesian inference.
Are there same cases ...
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3
votes
2
answers
3k
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Defining prior on variance and not precision
I know that WinBugs uses precision as a parameter in dnorm instead of variance
...
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1
answer
2k
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Is multinomial the same as multiple binomial?
I wonder, if I write - in JAGS, WinBUGS, or in a paper:
x[] ~ dmulti(p[], N)
is it the same as if I write:
...
- 6,133
5
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1
answer
603
views
How can regression trees be fit in WinBUGS/OpenBUGS/JAGS?
There is an R package called BayesTree which can fit regression trees in Bayesian environment. However, this way only simple regression is possible. I would like to use regression trees as a part of a ...
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1
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1
answer
790
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WinBUGS: multiple definitions of node [duplicate]
I wrote this code in WinBUGS but I can't run it! It says 'multiple definitions of node tau'
...
- 47
1
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0
answers
232
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Confidence intervals of proportions for clustered data
I am trying to compute the proportion of "yes"'s in data that is clustered (participants within cities). If I ignore the cities, I get very nice and narrow confidence intervals. If I compute the ...
- 171
2
votes
1
answer
3k
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Undefined real result error at WinBUGS
I am currently working on my thesis and interested in estimating a multilevel differential item functioning model and I using at WinBUGS. Until I had done model check-up, there are no errors. However, ...
- 21
1
vote
1
answer
174
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Measurements from two raters. Should I use multilevel/"random-effects" model?
I have several variables that were measured on patients, for most patients the variables of interest were measured by 2 independent "raters". Most of the variables are binary. I need to compute the ...
- 171
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0
answers
1k
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Is my OpenBUGS / WinBUGS model well specified?
I've just started trying to use OpenBUGS for Bayesian analysis of stochastic volatility models. In particular, I'm trying to calculate stochastic covariance, similar to the DC-MSV model specified by ...
- 771
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votes
0
answers
2k
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What is the form of link function in this BUGS multinomial regression example?
The alligators example from openbugs examples repository is the same example that comes with winbugs.
Basically this is a multinomial logistic regression example in which the outcome variable has 5 ...
- 1,111
18
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2
answers
4k
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Bayesian estimation of $N$ of a binomial distribution
This question is a technical follow-up of this question.
I have trouble understanding and replicating the model presented in Raftery (1988): Inference for the binomial $N$ parameter: a hierarchical ...
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3
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0
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226
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Dawid Skene model for BUGS
I'm a beginner in BUGS. I'm trying to code the Dawid Skene model in BUGS. The model is as follows:
Currently, I'm adapting the code from Stan, here.
Here is the code:
...
- 131
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0
answers
729
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Longitudinal data format in WinBUGS or OpenBUGS, different number of items per time point
I am working with longitudinal data, where there are a different number of "items" per time point. I am working with the MCMCdynamicIRT1d function in ...
- 11
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0
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311
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WinBUGS multinomial all parameters are random variables
everyone here.
I want to use multinomial distribution, but p[] and N are all random. model is correct and data loaded , model compilied, but it can't still run , it says:value of binomial f[1] must be ...
- 11
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0
answers
1k
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Zero trick in WinBUGS for truncation
I am using the Zero-trick to create a prior for correlation parameter. Data y is a bi-variate normal with covariance matrix with same diagonal elements and ...
- 21
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0
answers
263
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How are deterministic/logical nodes represented mathematically in directed graphical models?
Various software for performing inference on graphical models support logical(a.k.a deterministic) nodes. PyMc, Winbugs, Smile are the ones I'm aware of.
Based on the different inference methods ...
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