[R] problem with plots with short example.

[Nicole Ford]

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-bounces at r-project.org [mailto:r-help-bounces at 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
> 
>