[R] problem with plots with short example.
Duncan Mackay
mackay at northnet.com.au
Fri Mar 29 05:58:38 CET 2013
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")
> >> >
> >> >
> >> > ############################
> >> >
> >> >
> >> >
> >> >
> >> > [[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.
> >
> > ______________________________________________
> > 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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