BUGS is an acronym for Bayesian inference Using Gibbs Sampling; BUGS is also a software package for doing this.
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Help with Bayesian inference in OpenBugs
I have a task that involved Bayesian inference and could use some pointers and hints. I've already got some parts figured out but others remain blurred. Also, my OpenBUGS abilities are frankly limited ...
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A better bayesian way of modelling autoregressive mixtures
I have a JAGS hierarchical model which includes a temporal sub-model for the primary vote share between four party groups (LNP, Labor, Green, and Other). For each day in the temporal model, the vote ...
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What is the difference between these very simple normal and hierarchical normal BUGS models?
Consider these basic JAGS models, each having the same input. The question concerns only the first two, I include the other two for completeness.
Model 1 ("normal")
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How many chains should we choose in multi-treatment meta-analysis using MCMC and WinBugs
I am learning to undertake multiple treatment comparison meta-analysis (aka network meta-analysis or MTM) using WinBugs. One of the specifications are choosing the number of chains to run in the MCMC ...
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How to model repeated measures' results in meta-analysis?
I am developing network meta-analysis BUGS model that I will use to compare Hazard Ratios in studies that assume Box Proportional Hazard model.
As input I am given pairs: (log HR, its standard ...
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CODA gleman.diag, Error in chol.default(W): [closed]
I'd like to use gelman.diag for an MCMC chain I ran in JAGS. It is very large, so I can't provide it.
The chain contains several MVN distributions, and I use a wishart prior on the precision matrix.
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39 views
Multiplying a matrix by a scalar which has a prior distribution in OpenBUGS
So I am having a problem specifying my model in OpenBUGS. A set of vectors in a linear regression model is given a multivariate normal prior with a constant mean vector and a constant precision matrix ...
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Thinning chains in BUGS/JAGS
Hi I have a quick question about the details of running a model in JAGS and BUGS.
Say I run a model with n.burnin=5000, n.iter=5000 and thin=2. Does this mean that the program will
run 5,000 ...
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158 views
Results Difference: Frequentist vs. Bayesian
I fit a lognormal model on some data points using both frequentist and Bayesian (using a non-informative prior) approaches. However, I got different results. Here are my codes and outputs:
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Calculating the likelihood of time series data when there are missing data
I am trying to calculate the log-likelihood of some time series data given parameter sets estimated in BUGS. I can not figure out how to handle some missing values at random points in time.
For the ...
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Extracting values from R output of bugs command [closed]
I asked this question on http://stackoverflow.com/, but I couldn't get what I want. So, I am asking it here.
I am running winbugs from R and I need to use some variables in R output. When I type ...
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113 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 ...
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25 views
Experiment to find bug elimination rates
I am really new to experiments and I have been trying to read all the books I can from the library about designing my experiment. What I want to determine is: which is more common in a new software ...
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87 views
How to make inferences on group SD and and the SD of the group SD in a hierarchical Bayesian model?
The hierarchical model specified below is quite "standard" and easy to implement in for example JAGS/BUGS. It has an hierarchical gamma prior on the subject's precisions ($\tau_j$) which in turn has ...
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231 views
What's the Bayesian counterpart to Pearson product-moment correlation?
I was wondering what the counterpart to Pearson product-moment correlation would be in a Bayesian framework. Or if there are many alternatives, what would be the most convenient or conventional ...
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Is it possible to compute integrals in JAGS?
Is it possible to specify a model that uses an integral in the JAGS dialect of BUGS? (I believe this is possible in *BUGS, but I use a Mac, on which it seems JAGS is better supported.)
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Non-conventional form for a full conditional
I have a full-conditional of the form :
$$
p(X|...) \propto \exp(-(aX^2 +bX +c/X)),
$$
All of the other full-conditionals of my model simplify to a simpler form and for a sake of simplicity, I would ...
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252 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 ...
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error of No data node in Bugs
I have the following model in which Out, Fs, N and CyclNum come from the data file. The model compilation does not proceed successfully with an error saying that one of the node (j[1]) has no data.
I ...
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54 views
Latent groups in Bayes net with BUGS
I'm modeling a Bayes net with OpenBUGS, and I find problems to specify some of the parameters and their priors.
The aim of the model is to identify latent groups in the data from a sample of human ...
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3answers
122 views
Bayesian meta analysis of residual standard deviation using BUGS
I have a small number of studies where the same model was calculated and want to infer the typical standard residual deviation. I have the degrees of freedom, the sum of the squares SSR and the mean ...
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99 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 ...
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3answers
292 views
Winbugs and other MCMC without information for prior distribution
What happens when you don't have an idea of the parameters distribution? What approach should we use?
Most of the time we aim to undersatnd if a certain variable has any influence over the ...
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1answer
109 views
Crazy divergence in mixed model - chains start well but go crazy later
I'm trying to compute a mixed model using jags (R2jags) and I got very strange divergence. The chains started so well, very well according to the results expected (also see ...
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How to model data in jags/bugs generated by taking the minimum of two random variables?
I have been thinking of modeling human timing data using jags where the data comes from an experiment where participants tap in time with a very slow metronome. The data is then a number of ...
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313 views
Can I get predictions from Winbugs/OpenBUGS?
I am new to WinBUGS and OpenBUGS.
I just fit a model to try an example. I was wondering whether I can get predictions generated by WinBUGS/OpenBUGS. If not, are there any convenient ways available ...
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394 views
Optimal software package for bayesian analysis
I was wondering which software statistical package do you guys recommend for performing Bayesian Inference.
For example, I know that you can run openBUGS or winBUGS as standalones or you can also ...
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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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322 views
How can I generate a plot similar to that produced by plot.bugs and plot.jags from an mcmc.list?
R seems to be able to output nice summary plots from the bugs and jags objects generated by the functions R2WinBUGS::bugs and ...
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542 views
How to get prediction for a specific variable in WinBUGS?
I am a new user of WinBUGS and have one question for your help. After running the following code, I got parameters of beta0 through ...
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530 views
Bayesian Analysis in R/WinBUGS and SAS (Proc MCMC)
I have a Bayesian model here in R/WinBUGS. This data "pumps" has two columns, time and fail. Each observation is a pump and fail[1] tells how many failures there were in time[1]. I want to know how I ...
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692 views
Problem with e1071 libsvm?
I have a dataset with two overlapping classes, seven points in each class, points are in two-dimensional space. In R, and I'm running svm from e1071 package to build separating hyperplane for these ...
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Priors for hierarchial Bayesian binomial model
I intend to use a hierarchical binomial model which would look like the following in BUGS language :
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765 views
WinBUGS error with zero values in binomial distribution: value of order of binomial <expr> must be greater than zero
It seems that WinBUGS has problems if it has only zero draws from one binomial distribution:
1. case - simple model
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1answer
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Computing 2 independent models at once leads to wrong results in WinBUGS
I wanted to compare how two different (independent) models perform under winbugs, So I created code like:
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1answer
222 views
How to create a loop without command “for” in Bugs?
I'll try to make an example to make it easier to understand the question.
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How do I specify priors for angle parameters in BUGS/JAGS?
I am writing a hierarchical BUGS model that involves both linear and angle variables. I want the hyper-parameters to be normally distributed, which is straight-forward for the linear variables, but ...
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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, ...
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Interaction terms and BUGS
It occurred to me that how one writes an interaction term in BUGS depends on the types of predictors that are "interacting". Suppose data that are long (rather than wide). Then, a model with an ...
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Identifying parameters in BUGS linear regression
With a linear regression defined in BUGS, how should one implement model identification constraints such as having the mean of a group of parameters be zero, or having the group of parameters sum to ...
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Vector multiplication in BUGS and JAGS
In R, c(3,1,0) * c(2,0,1) == c(6,0,0). This is not dot product and it's not cross product. First, what is the name for this product, and second, does it work in WinBUGS, OpenBUGS and/or JAGS?
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How to analyze longitudinal count data: accounting for temporal autocorrelation in GLMM?
Hello statistical gurus and R programming wizards,
I am interested in modeling animal captures as a function of environmental conditions and day of the year. As part of another study, I have counts ...
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2answers
374 views
Sampling variables and calculating likelihood in WinBUGS/OpenBUGS
I am trying to read some WinBUGS/OpenBUGS examples to figure out how to specify models. I can't seem to understand where the probabilistic dnorm, ...
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2answers
124 views
How to implement rounding in BUGS in a survey context?
In a traditional filtering context, you'd analyse polls coming in with something like
...
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39 views
How to read quantiles from R2WinBUGS? [duplicate]
Possible Duplicate:
Deciphering output from R2WinBUGS
How do I read in the quantiles from the following output? I am able to read in the mean, median and standard deviation by saying
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2answers
144 views
Deciphering output from R2WinBUGS
I have been struggling to figure out how to identify which output the parameter came from. For e.g. in the following code I run the model for 2 iterations. At the end of it I obtain 2 outputs named ...
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1answer
557 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 ...
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Does my multilevel modelling create false replication and spurious precision at the highest level?
I am fitting a 3-level model in Bugs. The data are in long format. The data consists of 885 Treatments in 1:3 COURSEs of treatment in 108 Patients (MRNs).
...
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How do I transform a data generation specification in R into a BUGS/JAGS specification
I am at a loss about what the BUGS/JAGS specification of the following should look like. The background is that one person has four measurements taken by four different instruments. Each instrument ...
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Is R's trimmed means function biased?
I've been trying to understand how R's trimmed mean function works. I suspect it might be biased, but would like to get feedback here before I file a bug-report (if this is an inappropriate forum for ...
