search for: coda

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: "mi...

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) > co...

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 patch...

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 ru...

...#39;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 adapting and updating, I run the following command: coda_odp_gini_only <- coda.samples(odp_gini_only, variable.names=c("beta","sigma2.u2", "deviance"),...

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 have had no luck as of yet. I've attempted to adapt Yu-Sung Su's method over at http:// yusung.blogspot.com/2007/01/analyzing-coda-statistics...

...he latter with decoder mmx-patches from VP3HoSwiYO) and a theora-encoder script (a bit slower than ffmpeg2theora as it runs several processes, but also a bit more universal) The program names with a .reference suffix relate to the versions without any mmx-related patches applied. You will need a Coda client which is available at http://www.konvalo.org/pub/coda-client-setup (see http://www.konvalo.org/?pagename=Main.Software) and then either run "/coda/konvalo.org/start" to get a shell session with these programs in the PATH or "/coda/konvalo.org/start mplayer [args]" a...

...he latter with decoder mmx-patches from VP3HoSwiYO) and a theora-encoder script (a bit slower than ffmpeg2theora as it runs several processes, but also a bit more universal) The program names with a .reference suffix relate to the versions without any mmx-related patches applied. You will need a Coda client which is available at http://www.konvalo.org/pub/coda-client-setup (see http://www.konvalo.org/?pagename=Main.Software) and then either run "/coda/konvalo.org/start" to get a shell session with these programs in the PATH or "/coda/konvalo.org/start mplayer [args]" a...

...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 mcmc.list to perform some diagnostics but it doesn't work with functions from the BRugs package such as samplesBgr. Can you explain what should I do to read coda files with BRugs ? Thanking you in advance Guillaume --...

...(3) Remove the use of internal kernel structs in UAPI structures. (4) Fix symbol collisions. (5) Fix use of sparsely initialised arrays (which g++ doesn't implement). (6) Remove some use of PAGE_SIZE since this isn't valid outside of the kernel. There's also: (7) Move the coda_psdev.h header file to fs/coda/. And lastly: (8) Compile all of the UAPI headers (with a few exceptions) together as C++ to catch new errors occurring as part of the regular build process. Changes for v2: - Merge commit from sound tree to fix u32 usage issues - Use a switch to fix...

...ease 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: lattice > summary(rd.mc) Length Class Mode 1 merMCMC S4 > HPDinterval(rd.mc) Error in UseMethod("HPDinterval") : no applicable method for "HPDinterval" > str(rd.mc) Formal class 'merMCMC' [package "lme4"...

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 th...

...r: 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 message: "no applicable method for 'HPDinterval' applied to an object of class "merMCMC"" Should I be coercing A6post to another type, or am I missing other steps altogether? Thanks :) Doug Adams ----- Doug Adams MStat Student...

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 s...

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 writable = yes [source] comment = autosource path = /users/osproc/autosource public = yes writable = yes However I...

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...

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 <j.logsdon at lancaster.ac.uk> Subject: RE: [R] First (well second) CODA hurdle problem Cc: r-help at stat.math.ethz.ch, BUGS <bugs at mailbase.ac.uk> On 0...

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 locked binding for '.Coda.Options' Quiting codamenu...

> 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 f...