Questions tagged [coda]

Coda is an R package to perform analysis and diagnostics for Markov Chain Monte Carlo simulations.

Filter by
Sorted by
Tagged with
3
votes
0answers
34 views

How to make correlation test with compositional data?

I have a compositional data set ...
4
votes
1answer
512 views

Effective sample size for MCMC with multimodal target

I am trying to evaluate an adaptive MCMC algorithm on a multimodal target density. Among other performance measures, I would like to evaluate the sampler in terms of Effective Sample Size (ESS). The ...
4
votes
1answer
337 views

Can a Markov chain be approximated with an AR process?

In some MCMC literature/source code, a Markov chain is often approximated with an AR(1) process. There is some theory to suggest that such an approximation is somewhat valid for a finite state space, ...
2
votes
2answers
811 views

Suspiciously high Multivariate PSRF from gelman.diag()

I am using "Multivariate PSRF" statistics from gelman.diag() function to analyze my MCMC chains. Now I analyzed convergence 471 variables (parameters for each site)....
4
votes
0answers
360 views

What convergence diagnostics are appropriate for a Bayesian hierarchical logistic regression model?

Using WinBUGS, I fit several Bayesian hierarchical logistic regression models for the mean of a binary response variable conditional on a set of criteria. I am now using CODA in R to determine if my ...
1
vote
1answer
864 views

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. ...
3
votes
0answers
86 views

Coda output, joint quantile

I am running a hierarchical model in JAGS. It is a piecewise constant survival regression model. So I have 4 sets of regression coefficients and baseline hazard rates. I would like to plot a mean ...
7
votes
2answers
486 views

First iteration in MCMC coda chain is different from initial values

I have my jags output object. In order to understand how MCMC coda chains work, I tried to see if first iteration in each MCMC chain is equal to the initial values supplied. And it is different! The ...