Re: [R] problem with plots with short example.
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 ###
[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$numstate
))
###
### code chunk number 3: exchange
###
exchange.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu, tau)
}
mu ~ dnorm(0,.001)
tau ~ dgamma(.1,.1)
}
exchange.out - run.jags(exchange.mod,
data=dat, burnin=1, sample=5,
thin=5, monitor=c(mu, tau),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 4: exchange
###
FE.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]])
}
for(j in 1:J){
mu[j] ~ dnorm(0,.001)
tau[j] ~ dgamma(.1,.1)
}
}
FE.out - run.jags(FE.mod,
data=dat, burnin=1, sample=5,
thin=5, monitor=c(mu, tau),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 5: exchange
###
hier.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]])
}
for(j in 1:J){
mu[j] ~ dnorm(theta,nu)
tau[j] ~ dgamma(a,b)
}
theta ~ dnorm(0,.01)
nu ~ dgamma(.1,.1)
a ~ dunif(0,1000)
b ~ dunif(0,1000)
}
hier.out - run.jags(hier.mod,
data=dat, burnin=1, sample=10,
thin=10, monitor=c(mu, tau, theta, nu, a, b),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 6: sums
###
hier.chains - combine.mcmc(hier.out$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]]
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Re: [R] problem with plots with short example.
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=1, sample=5,
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=1, sample=5,
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=1, sample=10,
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$stateabb), length)
plot(mu.bar, mu.bar2, cex=sqrt(ns[,2])/3,
xlab = FE mu[j],
ylab = Hierarchical mu[j])
abline(a=0, b=1)
###
### code chunk number 7: dotchart
###
fe.mu - FE.chains[,grep(mu\\[, colnames(FE.chains))]
fe.ci - t(apply(fe.mu, 2, quantile, c(.5,.025,.975)))
rownames(fe.ci) - unstate
fe.ci - fe.ci[order(fe.ci[,1]), ]
dotchart(fe.ci[order(fe.ci[,1]),1], lcolor=white, pch=16,
xlim=range(c(fe.ci)))
segments(fe.ci[,2], 1:34, fe.ci[,3], 1:34)
mu.ci - quantile(exchange.chains[,1], c(.5,.025,.975))
polygon(x=mu.ci[c(2,3,3,2)],
y = c(-1,-1,36,36),
col=rgb(128,128,128,100, maxColorValue=255),
border=NA)
abline(v=mu.ci[1], lty=2, lwd=2)
axis(4, at=1:34, labels=ns[match(rownames(fe.ci), ns[,1]),2],
cex.axis=.75, las=2)
###
### code chunk number 8: femeans
###
library(sm)
sm.density(mu.bar, model=normal)
[[alternative HTML version
Re: [R] problem with plots with short example.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Nicole Ford
Sent: Thursday, March 28, 2013 4:55 PM
To: r-help help
Subject: [R] problem with plots with short example.
i am having problem running my own data. yesterday it was working just
fine. today it is not. this is the code i was using as an example to
follow. this code ALSO worked just fine yesterday, and is no longer
working at all. i suspect it is a problem with either my computer or
the software, at this point. if THIS won't even run something is
wrong.
i can assure you this isn't HW i know dave, but i am no longer at
UW-M and i have never learned HLMs and i am learning this on my own for
my own research.
his code is here, along with data. it is short, quick, etc.
http://www.quantoid.net/936/Lecture7.R
### R code from vignette source 'Lecture7.Rnw'
###
### code chunk number 1: opts
###
options(useFancyQuotes=F)
###
### code chunk number 2: data1
###
library(foreign)
therms -
na.omit(read.dta(http://quantoid.net/936/2008_difftherm.dta;))
unstate - unique(therms[,1])
therms$numstate - match(therms$state, unstate)
library(runjags)
dat - dump.format(list(
N = nrow(therms), J=length(unstate),
y = therms$difftherm,
numstate = therms$numstate
))
###
### code chunk number 3: exchange
###
exchange.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu, tau)
}
mu ~ dnorm(0,.001)
tau ~ dgamma(.1,.1)
}
exchange.out - run.jags(exchange.mod,
data=dat, burnin=1, sample=5,
thin=5, monitor=c(mu, tau),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 4: exchange
###
FE.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]])
}
for(j in 1:J){
mu[j] ~ dnorm(0,.001)
tau[j] ~ dgamma(.1,.1)
}
}
FE.out - run.jags(FE.mod,
data=dat, burnin=1, sample=5,
thin=5, monitor=c(mu, tau),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 5: exchange
###
hier.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]])
}
for(j in 1:J){
mu[j] ~ dnorm(theta,nu)
tau[j] ~ dgamma(a,b)
}
theta ~ dnorm(0,.01)
nu ~ dgamma(.1,.1)
a ~ dunif(0,1000)
b ~ dunif(0,1000)
}
hier.out - run.jags(hier.mod,
data=dat, burnin=1, sample=10,
thin=10, monitor=c(mu, tau, theta, nu, a, b),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 6: sums
###
hier.chains - combine.mcmc(hier.out$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
Re: [R] problem with plots with short example.
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-boun...@r-project.org [mailto:r-help-bounces@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=1, sample=5,
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=1, sample=5,
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=1, sample=10,
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
Re: [R] problem with plots with short example.
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$numstate
))
###
### code chunk number 3: exchange
###
exchange.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu, tau)
}
mu ~ dnorm(0,.001)
tau ~ dgamma(.1,.1)
}
exchange.out - run.jags(exchange.mod,
data=dat, burnin=1, sample=5,
thin=5, monitor=c(mu, tau),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 4: exchange
###
FE.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]])
}
for(j in 1:J){
mu[j] ~ dnorm(0,.001)
tau[j] ~ dgamma(.1,.1)
}
}
FE.out - run.jags(FE.mod,
data=dat, burnin=1, sample=5,
thin=5, monitor=c(mu, tau),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 5: exchange
###
hier.mod - model{
for(i in 1:N){
y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]])
}
for(j in 1:J){
mu[j] ~ dnorm(theta,nu)
tau[j] ~ dgamma(a,b)
}
theta ~ dnorm(0,.01)
nu ~ dgamma(.1,.1)
a ~ dunif(0,1000)
b ~ dunif(0,1000)
}
hier.out - run.jags(hier.mod,
data=dat, burnin=1, sample=10,
thin=10, monitor=c(mu, tau, theta, nu, a, b),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
###
### code chunk number 6: sums
###
hier.chains - combine.mcmc(hier.out$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)))
Re: [R] problem with plots with short example.
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=1, sample=5,
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=1, sample=5,
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=1, sample=10,
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
Re: [R] problem with plots with short example.
LOL dennis, thanks for the laugh at the end. I'm a PhD student... I had never used it before until this last semester when i started taking Bayes at my new university (transfer because of husband's job =\). My old dept offered bayes, but not the new one, so i am taking it in the psychology dept the application (lots of binary outcomes and t-test focused) isn't terribly useful for my own discipline (poli sci, where ALL i do is LM and logistic and now HLM!) but it -at least- has exposed me to how to use bayes, JAGS, etc. so it isn't completely foreign to me. I am on a mac and, for whatever reason (until the latest update), I was NEVER able to run any code on it. it was always always locking up on me everyone else in the class was using it (we use the Kruschke book and he has code, etc and recommnds it) so I was determinded to get it to work always ended in HOURS and HOURS of frustration and me just saying *screw it* and going to R and completing the task in 30 minutes. =b but like i said, since they have updated it (was in Jan of Feb?), i haven't had any issues but, MAN was that a frustrating 5/6 months. it really put a sour taste in my mouth. but, i will say- thank god for R-studio right now. lol totally saved my sanity. but i am determined to fix R... On Mar 28, 2013, at 10:45 PM, Dennis Murphy wrote: Hi Nicole: On Thu, Mar 28, 2013 at 7:25 PM, Nicole Ford nicole.f...@me.com wrote: thank you, dennis, but that's ok! i ran it all successfully yesterday, as well as my own any ideas why it would blow up like this and not plot? Sorry, no. Given the tenor of some of your posts today, I wondered if your computer had contracted a virus. Progressively weird behavior is often a sign, as is a noticeable slowdown in performance. what's interesting is: was able to run my own research just fine (JUST NOW finished) in R-studio (YUK), so something is definitely corrupt in the R environment. I wish I could figure it out! i HATE using R-studio. =\ I have certain issues with it, but I like RStudio for documentation writing and I'm about to start package development using RStudio projects in conjunction with Git. If you use script files instead of typing at the command line or copy/pasting from a text editor, it's easy to bounce back and forth between the two; the only thing I miss is the 'Run selection' feature in R GUI script shells running under Windows. If you're an R package developer, it's definitely the way to go, especially if you're using Git and devtools. Why do you hate RStudio so much? (I'm envisioning a Sanka commercial with Robert Young from the 70s where the commercial opens with the line: Hey, why so tense? :) [I can guess why, but I'll leave it at that.] To quote the great psychologist Cesar Millan, stay calm and assertive :) Dennis On Mar 28, 2013, at 10:13 PM, Dennis Murphy wrote: Hi Nicole: I, too, ran the script file without error, but a set of warnings. Here's the output from the R console: source(Lecture7.R.txt) Loading required package: coda Loading required package: lattice Loading required package: parallel Calling the simulation... (this may take some time) Simulation complete. Reading coda files... Coda files loaded successfully Abstracting pD ... 5 valid values Calculating the Gelman-Rubin statistic for 3 variables The Gelman-Rubin statistic is below 1.05 for all parameters Finished running the simulation Calling the simulation... (this may take some time) Simulation complete. Reading coda files... Coda files loaded successfully Abstracting pD ... 5 valid values Calculating the Gelman-Rubin statistic for 69 variables The Gelman-Rubin statistic is below 1.05 for all parameters Finished running the simulation Calling the simulation... (this may take some time) Simulation complete. Reading coda files... Coda files loaded successfully Abstracting pD ... 10 valid values Calculating the Gelman-Rubin statistic for 73 variables The Gelman-Rubin statistic is below 1.05 for all parameters Finished running the simulation Package `sm', version 2.2-4.1 Copyright (C) 1997, 2000, 2005, 2007, 2008, A.W.Bowman A.Azzalini Type help(sm) for summary information Loading required package: Matrix Attaching package: 'lme4' The following object(s) are masked from 'package:coda': HPDinterval The following object(s) are masked from 'package:stats': AIC, BIC Calling the simulation... (this may take some time) Simulation complete. Reading coda files... Coda files loaded successfully Calculating the Gelman-Rubin statistic for 9 variables The Gelman-Rubin statistic is below 1.05 for all parameters Finished running the simulation Calling the simulation... (this may take some time) Simulation complete. Reading coda files... Coda files loaded successfully Calculating the Gelman-Rubin statistic for 10 variables The
Re: [R] problem with plots with short example.
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=1, sample=5,
thin=5, monitor=c(mu, tau),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
