similar to: Error in geweke.diag function of coda package

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

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 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

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

Since OMAP UART has a few distinct features than common 8250 UART, I re-implemented its driver rather than porting it based on ns16550.c. There are mainly two big differences between the implementations. First, OMAP UART introduces the concept of register access mode, which divides the register map into seperated space. Switching the access mode is then necessary when configuring it. Second, THRE

> > No, you have hit a known bug. The 'idmap config ' work done for 4.6.0 > seems to be causing this, you can safely ignore this error. Ok Rowland, thanks!! Mas mesmo conseguindo corrigir os problemas acima, não consigo ter acesso a aba security com o usuario administrator. Verificando nos logs, aparece a mensagem abaixo. On Wed, May 31, 2017 at 11:59 AM, Rowland Penny via

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, I used the MCMCirtKd function of MCMCpack: posterior2 <- MCMCirtKd(data, dimensions = 2, + burnin = 5000, mcmc = 50000, thin = 10, + verbose = 10000, B0 = .25, store.item = TRUE, item.constraints = beta.constraints) And after apply the comand summary() I got some erros and warnings that I could not understand: summary.posterior2 <- summary(posterior2)

Hi, >Is this the machine that you cannot set the permissions on ? Yes. >If so, what is the filesystem ? Ext4 for SO and Ext4 for shared files, but I have created a pool ZFS on this last filesystem (/dev/vdb1). Dispositivo Inicializar In?cio Fim Setores Tamanho Id Tipo /dev/vda1 * 2048 62912511 62910464 30G 83 Linux Disco /dev/vdb: 5 TiB, 5497568624640 bytes,

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