I was up till 4 am with this sucker trying to figure it out- I thought i lost my mind/ screwed it up somehow. I guess it's nice to know it really wasn't me. Though, I AM sad R is messing up- first time in over 3 years, so I guess it isn't so bad. But timing couldn't have been worse, as I have a conference coming up.
Thanks very much, Duncan! I am going to give that a whirl tomorrow! On Mar 28, 2013, at 10:37 PM, Duncan Mackay wrote: > Hi Nicole > > I just upgraded to 2.15.3 today > I was just having similar problems with run.jags and it stopping dead in its > tracks with an error message pointing to somewhere else > > See > > ?run.jags > and the second paragraph of it. > > I then got it to run using a run.jags script using Rterm and saved the model. > By accident I copied and pasted a script to R with run.jags in it and it now > runs. > > see also ?test.jags > > Do not know what will happen after a reboot. > > > HTH > > Duncan > > Duncan Mackay > Department of Agronomy and Soil Science > University of New England > Armidale NSW 2351 > Email: home: mac...@northnet.com.au > > > > At 10:24 29/03/2013, you wrote: >> To be clear everything "runs" with no error message... the only hint of a >> problem is at the end of the code: the plot will not fill out/ it is empty. >> >> if anyone has any idea why something like this might happen, i would greatly >> appreciate it... so i can handle it quickly. >> >> thanks in advance. >> On Mar 28, 2013, at 7:55 PM, Nicole Ford wrote: >> >> > 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") >> > >> > >> > ############################ >> > >> > >> > >> > >> > [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > 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. >> >> ______________________________________________ >> 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. > > ______________________________________________ > 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. ______________________________________________ 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.
