similar to: CODA or NFS

I have successfully installed coda in R, and I am also able to read output from a Bugs run into coda. When I try to plots from CODA Output Analysis Menu, I do however _get_ problems: CODA Output Analysis Menu ************************* 1:Plots 2:Statistics 3:List/Change Options 4:Return to Main Menu Selection: 1 Error: "missing" illegal use of missing Quitting CODA.... Do you

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 all, I'm not 100% sure if this question is best directed at the r-list, or a mailing list concerned with Bayesian analysis, so please accept my apologies if another audience may be more appropriate. I have been using the rjags package to run Jags models with multiple chains and store the results in a Coda based mcmc list. For instance, having created a jags model and done initial

Hi All, I am trying to figure out how to use R-Coda with the output from OpenBugs. I have installed and loaded the packages BRugs and R2WinBUGS. I have successfully run a simple Bayes model in WinBUGS using R2WinBUGS' "bugs" and have used "read.bugs" to build the coda object. I can successfully switch to OpenBugs and run the same model and get the basic summary

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

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

The object is a mcmc sample from lmer. I am using R v2.7.1. Please let me know what additional information I can provide, hopefully I am just making a simple mistake. Thanks in advance! > data(ratdrink, package = 'faraway') > rd.er <- lmer(wt ~ weeks*treat + (1 | subject), data = ratdrink) > rd.mc <- mcmcsamp(rd.er, 10000) > library(coda) Loading required package:

Hi everyone, The Linux Coda drivers and the ext3 patches don't seem to get along very well, at least in Linux 2.4.7. I've got a stock 2.4.7 kernel with a patch applied to the USB drivers (for a sony digital camera; see http://www.sujal.net/tech/linux/ just a change in unusual_devs.h). After I applied the ext3 patches from http://www.uow.edu.au/~andrewm/linux/ext3/ . Basically,

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 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

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

Hi list, our lab is divided in two sites and we would like to have a clone of the mail server on the second site for redundancy only (used in case of a lost of connectivity with the primary mail server, with the MX entries in the DNS the clone will receive the mails instead). The problem(s) comes with the mail partition who must be replicated and synchronized over the time (and over the net)

Hi all, I would like to compute ergodic mean using MCMC output from WinBUGS. I tried using CODA package, but it seems that it is not implemented yet. Could anyone help me to compute this? Attached to this email are my output and index files. Kind regards, Raquel -- Raquel Rangel de Meireles Guimar?es Doutoranda em Demografia raquel at cedeplar.ufmg.br

Dear R users: I am using the package coda (the last verison in CRAN) to analyse the output from a MCMC Bayesian analysis. And I get unconsitented results. I have export the chain using the read.table function and after I have transformed this data frame to an mcmc object using the mcmc function. I am interested in three variables, when I use the function effectiveSize I have these figures:

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

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

I'm currently using JAGS as my Bayesian program of choice due to working off of an older mac running OSX. I'd like to utilize some of the functions from R2WinBUGS, however. As such, I'm attempting to write something to go from coda output dumped by JAGS into the bugs object format - I've looked for functions that will convert from an mcmc object to a bugs object, but

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

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