search for: codas

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

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 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'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

...along the lines of c.bugs<-coda2bugs (n.burnin=1000) coda2bugs<-function(codafile="jags.out", indexfile="jags.ind", n.chains=1, n.iter=NA, n.burnin=NA, n.thin=1, DIC=FALSE, file.rm=T, ...){ require(R2WinBUGS) #first, split up the coda file for R2WinBUGS codaSplit(codafile, indexfile) #get the parameter names index.table<-read.table(indexfile) varNames<-as.vector(index.table[,1]) #determine the n.iter if(is.na(n.iter)){n.iter<-index.table[1,3]} #you will need to put the n.burnin in yourself #for the cypraea example, it is...

Hello, in case somebody wants to test Theora without compilation, feel free to use konvalo.org's setup. It includes mplayer with theora from svn 2004-09-21 with Wim Taymans' mmx-patches from August 2004 applied (there are mplayer and mplayer.theora-mmx, the latter with decoder mmx-patches from VP3HoSwiYO) and a theora-encoder script (a bit slower than ffmpeg2theora as it runs several

Hello, in case somebody wants to test Theora without compilation, feel free to use konvalo.org's setup. It includes mplayer with theora from svn 2004-09-21 with Wim Taymans' mmx-patches from August 2004 applied (there are mplayer and mplayer.theora-mmx, the latter with decoder mmx-patches from VP3HoSwiYO) and a theora-encoder script (a bit slower than ffmpeg2theora as it runs several

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

Here's a set of patches that inserts a step into the build process to make sure that the UAPI headers can all be built together with C++ (if the compiler being used supports C++). Note that it's based on a commit from the sound tree to fix usage of u32 and co.. Most of the patches perform fixups, including: (1) Fix member names that conflict with C++ reserved words by providing

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 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, 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

All, I have just installed Samba on a Solaris 8 server and am trying to share two unix directories to an NT domain. The smb.conf file is set up as follows :- [spain]/usr/local/samba/lib $ more smb.conf [global] workgroup = coda username map = /usr/local/samba/lib/users.map hosts equiv = /etc/hosts.equiv [build] comment = autobuild path = /users/osproc/autobuild public = yes

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

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

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

> 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

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