problem with plots with short example.

within.mod <- lm(wvsAB$dem ~ wvsAB$cpi + as.factor(wvsAB$country), data=wvsAB)

summary(within.mod)

Hi Nicole

My code works using source file if I put

 library(runjags)
 x = testjags(findjags("windows",look_in = "c:/Program Files/JAGS"))
source("G:/Sweave/Bayes.R")

works ok

Further developments with Sweave. Putting this in the Sweave file

 library(runjags)
 x = testjags(findjags("windows",look_in = "c:/Program Files/JAGS"))

x
...
$JAGS.available
[1] TRUE

$JAGS.path
[1] "\"c:/Program Files/JAGS/JAGS-3.3.0/i386/bin/jags-terminal.exe\""
...

If I do not setwd() everything works fine for runjags but have not tried to plot any plots as pdf
Unfortunately it comes up in my  default
c:\Users\d mackay\Documents\

############################
Using setwd() before Sweave("G:/Sweave/Bayes.Rnw")
and in the Sweave file

# \Sweave file before run.jags call
 x = testjags(findjags("windows",look_in = "c:/Program Files/JAGS"))

It returns this error in the R command window

Error:  chunk 7 (label = JAGS2)
Error in run.jags(model = mod, monitor = "p", init = list(init1, init2),  :
 Unable to call JAGS

However x shows that it is finding JAGS
x
...
$JAGS.available
[1] TRUE

$JAGS.path
[1] "\"c:/Program Files/JAGS/JAGS-3.3.0/i386/bin/jags-terminal.exe\""

...

Latex tex file
You are currently logged on as d mackay, on a windows machine
You are using R version 2.15.3 (2013-03-01), with the Rgui GUI
JAGS version 3.3.0 found successfully using the command "c:/Program
Files/JAGS/JAGS-3.3.0/i386/bin/jags-terminal.exe"

So do not use setwd or change directory from the gui menu and it works but things end up where your default directory is

I am not sure what is going on but any assistance to fix it would be appreciated.

Regards

Duncan

At 12:45 29/03/2013, you wrote:

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: 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")


############################




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