thank you, dan. any information, no matter how small, is helpful. i deleted R this moring and reinstalled it. outside of that i am not sure what else to delete/ reinstall. You mention you reinstalled JAGS- i will give that a try, as well. thanks!
On Mar 28, 2013, at 8:52 PM, Nordlund, Dan (DSHS/RDA) wrote: >> -----Original Message----- >> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- >> project.org] On Behalf Of Nicole Ford >> Sent: Thursday, March 28, 2013 4:55 PM >> To: r-help help >> Subject: [R] problem with plots with short example. >> >> i am having problem running my own data. yesterday it was working just >> fine. today it is not. this is the code i was using as an example to >> follow. this code ALSO worked just fine yesterday, and is no longer >> working at all. i suspect it is a problem with either my computer or >> the software, at this point. if THIS won't even run.... something is >> wrong. >> >> i can assure you this isn't HW.... i know dave, but i am no longer at >> UW-M and i have never learned HLMs and i am learning this on my own for >> my own research. >> >> his code is here, along with data. it is short, quick, etc. >> >> http://www.quantoid.net/936/Lecture7.R >> >> ### R code from vignette source 'Lecture7.Rnw' >> >> ################################################### >> ### code chunk number 1: opts >> ################################################### >> options(useFancyQuotes=F) >> >> >> ################################################### >> ### code chunk number 2: data1 >> ################################################### >> library(foreign) >> therms <- >> na.omit(read.dta("http://quantoid.net/936/2008_difftherm.dta";)) >> unstate <- unique(therms[,1]) >> therms$numstate <- match(therms$state, unstate) >> library(runjags) >> dat <- dump.format(list( >> N = nrow(therms), J=length(unstate), >> y = therms$difftherm, >> numstate = therms$numstate >> )) >> >> >> ################################################### >> ### code chunk number 3: exchange >> ################################################### >> exchange.mod <- "model{ >> for(i in 1:N){ >> y[i] ~ dnorm(mu, tau) >> } >> mu ~ dnorm(0,.001) >> tau ~ dgamma(.1,.1) >> }" >> exchange.out <- run.jags(exchange.mod, >> data=dat, burnin=10000, sample=50000, >> thin=5, monitor=c("mu", "tau"), >> monitor.deviance=T, monitor.pd=T, >> silent.jags=T) >> >> >> >> ################################################### >> ### code chunk number 4: exchange >> ################################################### >> FE.mod <- "model{ >> for(i in 1:N){ >> y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]]) >> } >> for(j in 1:J){ >> mu[j] ~ dnorm(0,.001) >> tau[j] ~ dgamma(.1,.1) >> } >> }" >> FE.out <- run.jags(FE.mod, >> data=dat, burnin=10000, sample=50000, >> thin=5, monitor=c("mu", "tau"), >> monitor.deviance=T, monitor.pd=T, >> silent.jags=T) >> >> >> ################################################### >> ### code chunk number 5: exchange >> ################################################### >> hier.mod <- "model{ >> for(i in 1:N){ >> y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]]) >> } >> for(j in 1:J){ >> mu[j] ~ dnorm(theta,nu) >> tau[j] ~ dgamma(a,b) >> } >> theta ~ dnorm(0,.01) >> nu ~ dgamma(.1,.1) >> a ~ dunif(0,1000) >> b ~ dunif(0,1000) >> }" >> hier.out <- run.jags(hier.mod, >> data=dat, burnin=10000, sample=100000, >> thin=10, monitor=c("mu", "tau", "theta", "nu", "a", "b"), >> monitor.deviance=T, monitor.pd=T, >> silent.jags=T) >> >> >> ################################################### >> ### code chunk number 6: sums >> ################################################### >> hier.chains <- combine.mcmc(hier.out$mcmc) >> FE.chains <- combine.mcmc(FE.out$mcmc) >> exchange.chains <- combine.mcmc(exchange.out$mcmc) >> >> mu.bar <- apply(FE.chains[, grep("mu\\[", colnames(FE.chains))], 2, >> mean) >> mu.bar2 <- apply(hier.chains[, grep("mu\\[", colnames(hier.chains))], >> 2, mean) >> ns <- aggregate(therms$numstate, list(therms$stateabb), length) >> plot(mu.bar, mu.bar2, cex=sqrt(ns[,2])/3, >> xlab = "FE mu[j]", >> ylab = "Hierarchical mu[j]") >> abline(a=0, b=1) >> >> >> ################################################### >> ### code chunk number 7: dotchart >> ################################################### >> fe.mu <- FE.chains[,grep("mu\\[", colnames(FE.chains))] >> fe.ci <- t(apply(fe.mu, 2, quantile, c(.5,.025,.975))) >> rownames(fe.ci) <- unstate >> fe.ci <- fe.ci[order(fe.ci[,1]), ] >> dotchart(fe.ci[order(fe.ci[,1]),1], lcolor="white", pch=16, >> xlim=range(c(fe.ci))) >> segments(fe.ci[,2], 1:34, fe.ci[,3], 1:34) >> mu.ci <- quantile(exchange.chains[,1], c(.5,.025,.975)) >> polygon(x=mu.ci[c(2,3,3,2)], >> y = c(-1,-1,36,36), >> col=rgb(128,128,128,100, maxColorValue=255), >> border=NA) >> abline(v=mu.ci[1], lty=2, lwd=2) >> axis(4, at=1:34, labels=ns[match(rownames(fe.ci), ns[,1]),2], >> cex.axis=.75, las=2) >> >> >> ################################################### >> ### code chunk number 8: femeans >> ################################################### >> library(sm) >> sm.density(mu.bar, model="normal") >> >> >> ############################ >> >> >> > > Nicole, > > I am not going to be much help, other than to say I just downloaded and > Installed the latest versions of JAGS for Windows, and the rjags and sm > packages. I am running 64-bit Windows 7 with R-2.15.3. I cut and pasted the > code from your email, and except for a couple of warnings early on about > deprecated some deprecated parameters, the code seems to have run fine. > > So something may have broken your environment, and you may need to do some > reinstallation. Maybe someone else will have some better news for you. > > Dan > > Daniel J. Nordlund > Washington State Department of Social and Health Services > Planning, Performance, and Accountability > Research and Data Analysis Division > Olympia, WA 98504-5204 > > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
