similar to: Coda, HPDinterval and multiple chains

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

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:

Dear r-helpers, Following up on http://finzi.psych.upenn.edu/R/Rhelp02a/archive/ 81159.html where Douglas Bates gives a helpful application of lmer() to data(sleepstudy, package = 'lme4'), I need a bit more help in order to plot the correct confidence intervals of a designed experiment such as: > data(ratdrink, package = 'faraway') I follow the steps Douglas took in

Hi, Can anyone tell me why I am not getting the correct intervals for fixed effect terms for the following generalized linear mixed model from HPDinterval: > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

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

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

Hi all R mailing listers: I am using the coda package. I tried to view the source of HPDinterval code by typing fix(HPDinterval), it dispalys as follows: function (obj, prob = 0.95, ...) UseMethod("HPDinterval") Then I search the answers about this case (see below), it still failed. Thank you in advance! David > getAnywhere('HPDinterval')2 differing objects matching

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 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 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

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 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

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 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