similar to: About Coda Package

Dear all, I recently started having some problemd with the coda package. I have also deleted it and then installed the package again. The problem is that I cant access the codamenu. That is ; ********************************************************************************************************************************************* > library(coda) > codamenu() Error in

I am having not a little difficulty in using R-CODA version 0.4 with R-Windows 0.64.2. Basically I want to produce some postscript plots from the updates. It seems the WinBugs output is OK for cut-and-paste operations but don't allow much flexibility for anything else. So far, I can produce the .ind and .out files from WinBugs 1.2 and these seem OK (in particular they are text files not

Dear List: the CODA and BOA packages for the analysis of MCMC output yield different results on two dignostic test of convergence: 1) Geweke's convergence diagnostic; 2) Heidelberger and Welch's convergence diagnostic. Does that imply that the CODA and BOA packages implement different ``flavors'' of the same test? I paste below an example. Geweke's test

Hello All, I'm trying to run a one-dimenional irt model using the packages MCMC and coda on a rather large set of roll-call voting data with many missing observations. Here's a sample of the code: Post10<- MCMCirt1d (Italy10, burnin = 1000, mcmc=50000, thin=100, verbose=TRUE, theta.constraints = list(V549=1, V443=-1)) The MCMCirt1d command seems to work fine, but when I try to

Dear R users: I am a newby to R, under Windows XP. Sorry if my question is too obvious, but I have not found any answer in the archives. I was using the R-Coda package with R version 2.4.1 and everything was going OK. After upgrading to R v.2.5.0, I receive the following error message when I'm trying to run codamenu(): "Error in coda.options(default = TRUE) : cannot change value of

My reply seems not to have made it to either list 24 hours after I sent it, so I'm sending it again. Apologies if you get this twice (or 4 times if you're on both lists, or 6 times if you're John) Martyn -----FW: RE: [R] First (well second) CODA hurdle problem----- Date: Thu, 05 Aug 1999 09:40:01 +0200 (CEST) From: Martyn Plummer <plummer at iarc.fr> To: John Logsdon

The document R-exts contains the following example of using mathematics in R documentation. \deqn{p(x) = {\lambda^x\ \frac{e^{-\lambda}}{x!}} {p(x) = lambda^x exp(-lambda)/x!} There is a syntax error in there, but that's not my point. The problem is that using "R CMD Rd2dvi" I find that putting the alternate forms of the equation on top of each other doesn't work.

Dear R users, I?d like to pose aquestion about pMCMC and HDP. I have performed a mixed logistic regression by MCMCglmm (a very good package) obtaining the following results: Iterations = 250001:799901 Thinning interval = 100 Sample size = 5500 DIC: 10.17416 G-structure: ~ID_an post.mean l-95% CI u-95% CIeff.samp ID_an 0.7023 0.0001367 3.678 2126 R-structure: ~units post.mean l-95%

HI Everybody Does anyone know of documentation about different ways of obtaining user input in R. I have used readline() but I wondered is there are sophisticated packages that does things like validate answers or generate selection lists. bets regards Christaan [[alternative HTML version deleted]]

Hi Friends.. Well, I have setting OpenLDAP on CentOS 4.4 on a Blade Server.. I am trying of setting a cluster.. But I don't know that use: NFS or CODA.. What is you opinion? -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.centos.org/pipermail/centos/attachments/20070206/62c12ffa/attachment.html>

Hi all: The CODA package provides Geweke Diagnostic method for convergence checking. The geweke.diag in CODA returns Z-score value but not give a conclustion that it is convergence or not. So I'd like to know how small/big the magnitude of Z-score is corresponding to the convergence of a chain. That is, Doese Z-score smaller or more than *threshold *determine the convergence? If so, how big

Hi R users, Does anybody knows for the following erro after running geweke.diag(MCMC.sampled, frac1=0.1, frac2=0.5) Erro em glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, : la??o interno 1; n??o ?? poss??vel corrigir o tamanho do passo Al??m disso: Warning messages: 1: algoritmo n??o convergiu in: glm.fit(x = X, y = Y, weights = weights, start = start,

I have just uploaded the R port of the CODA (Convergence Diagnostics and Output Analysis) package to CRAN. This is a suite of functions for analyzing the output of Markov Chain Monte Carlo simulations and diagnosing lack of convergence of the simulated output. It is designed to work with (but is not necessarily limited to) the BUGS program: http://www.mrc-bsu.cam.ac.uk/bugs/ I have made

I have just uploaded the R port of the CODA (Convergence Diagnostics and Output Analysis) package to CRAN. This is a suite of functions for analyzing the output of Markov Chain Monte Carlo simulations and diagnosing lack of convergence of the simulated output. It is designed to work with (but is not necessarily limited to) the BUGS program: http://www.mrc-bsu.cam.ac.uk/bugs/ I have made

Dear all, I just wrote a script to have each of my three mcmc chins running on a different computer core to improve computation speed. To do it I use the function sfLapply from the package snowfall. Before using parallell computation, I did my diagnostic analyses just after the model updating, but now I have to save the coda before. Using the CODA package, it is possible to load the outputs in a

Hi, I've got a linear mixed model created using lmer: A6mlm <- lmer(Score ~ division + (1|school), data=Age6m) (To those of you to whom this model looks familiar, thanks for your patience with this & my other questions.) Anyway, I was trying this to look at the significance of my fixed effects: A6post <- mcmcsamp(A6mlm, 50000) library(coda) HPDinterval(A6post) ..but I got this

I tried calculating pD as 1/2 variance of the deviance, but I got hugely inflated numbers. Does anybody know how to calculate pD from the coda files output from R2WinBUGS? By the way, 'set DIC' is greyed out for some reason within WinBUGS, so I can't monitor DIC. [[alternative HTML version deleted]]

Hello Everyone, Has anyone installed Markdown for Coda, Writeroom, Textwrangler, or OS X? I'm really interested in using this more but I'm interested in finding the best way to use. Biggest win for me would be for it to work from within Writeroom. Textwrangler would be next, followed by OS X, and Coda would be almost useless. I did see that MacPorts has 2 different distros of markdown

> I am looking for a syntax highlighter I can use with Panic's Coda (or > SubEthaEdit, which just work with Coda). Does this exist? > > -- > Puneet Kishor > It does. TheGeekInside has written it, I made a few modifications myself, and you can get it from me (Twitter: c_freitag) or him, I suppose (Twitter: thegeekinside). Christoph

Dear, I'm trying to run diagnostics on MCMC analysis (fitting a log-linear model to rates data). I'm getting an error message when trying Gelman-Rubin shrink factor plot: >gelman.plot(out) Error in chol.default(W) : the leading minor of order 2 is not positive definite I take it that somewhere, somehow a matrix is singular, but how can that be remedied? My code: library(rjags)