[R] problem with plots with short example.
Duncan Mackay
mackay at northnet.com.au
Fri Mar 29 03:37:41 CET 2013
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: mackay at 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 at 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 at 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.
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