similar to: Geweke Diagnostic in CODA package

Intermittently I'm getting this error from the geweke.diag function of the coda package. Would anyone be kind enough to enlighten me as to the possible source of such an error, or how to debug/locate it? Error in { : task 22 failed - "inner loop 1; cannot correct step size" Thanks a bunch. J -- Dr. Jim Maas University of East Anglia

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,

Dear R-users, I have some problems with the geweke.diag-Function of the coda-package. I try to obtain the Geweke-diagnostic by using the following, simple code: library(coda) input.geweke = as.mcmc(input.matrix) #input.matrix is a 25.000 x 35 matrix with the 25.000 saved draws of the 35 parameters of interest output = geweke.diag(input.geweke) However, I get the following

Doese anyone know a R function to find the median of a gamma distribution? [[alternative HTML version deleted]]

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 I m a student in PARIS X university (France).I m preparing a working paper dealing with the presence of long memory in finantial markets. I have programs computing the hurst exponent by the rescaled range method and the GPH method (Geweke Porter-Hudak). I want to apply the modified rescaled range method proposed by A.Lo (1991). AS i m beggining with RATS i couldn't do the progam . can

Dear R users: I am using hierchical modeling for a response varible (ordinal) given by patients for each doctor. My MCMC run with MCMMCglmm ( thin=20,nitt=208000,burnin=24000, family='ordinal') still can't have all the parameters pass the GEWEKE diagnosis test. I am trying to find the reason for the slow convergence. Can the reason be 20 out of 50 doctors having 5 or less response

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>

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]]

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

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

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 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

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)

I'm trying to read CODA/mcmc files (see the coda package), as generated by jags/WinBUGS/OpenBUGS, into a big.matrix. I can't load the whole mcmc object produced by read.coda() into memory since I'm using a laptop for this analysis (currently I'm unfunded). Right now I'm doing it by creating the filebacked.big.matrix, reading a chunk of data at a time from the chain