yes I was also having something like this happen to me just before everything
blew up. i never set a working directory, but use file.choose() or call the
path directly. but the last few hours before it failed, it kept running older
datasets, when i clearly called the new data set, for example,
>within.mod <- lm(wvsAB$dem ~ wvsAB$cpi + as.factor(wvsAB$country), data=wvsAB)
would yeild in the summary immediately after: (with no error called on my
model!)
> summary(within.mod)
Call:
lm(formula = dat$dem ~ dat$cpi + as.factor(dat$country),
data = dat)
i was forced to do rm(data) more than once.
no idea what's goign on.
On Mar 29, 2013, at 12:58 AM, Duncan Mackay wrote:
> 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: 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.
______________________________________________
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.
