[R] rjags error. Error parsing model file:,syntax error on line 5 near
Greetings, I am running a factor analysis model in rjags and have
received the following error
Error parsing model file: syntax error on line 5 near
Line 5 is model {
Here is my syntax. Any insight would be greatly appreciated.
require(rjags)
modelstring =
model {
for (i in 1 : nData) {
for (j in 1 : nIndicators) {
y[i,j] ~ dnorm(mu[i,j],psi[j])
ephat[i,j] - y[i,j] - mu[i,j]
}
mu[i,1] - alpha[1]+xi[i,1] # Factor 1
mu[i,2] - alpha[2]+lam[2]*xi[i,1]
mu[i,3] - alpha[3]+lam[3]*xi[i,1]
mu[i,4] - alpha[4]+lam[4]*xi[i,1]
mu[i,5] - alpha[5]+lam[5]*xi[i,1]
mu[i,6] - alpha[6]+lam[6]*xi[i,1]
mu[i,7] - alpha[7]+lam[7]*xi[i,1]
mu[i,8] - alpha[8]+lam[8]*xi[i,1]
mu[i,9] - alpha[9]+xi[i,2]# Factor 2
mu[i,10] - alpha[10]+lam[10]*xi[i,2]
mu[i,11] - alpha[11]+lam[11]*xi[i,2]
mu[i,12] - alpha[12]+lam[12]*xi[i,2]
mu[i,13] - alpha[13]+lam[13]*xi[i,2]]
mu[i,14] - alpha[14]+lam[14]*xi[i,2]
mu[i,15] - alpha[15]+lam[15]*xi[i,2]
xi[i,1:2] ~ dmnorm(u[1:2],phi[1:2,1:2])
}
for (j in 1:nIndicators) {
alpha[j] ~ dnorm(0.0, 1.0)
}
#---
# Distributions and Priors
#Priors on Loadings
lam[2] ~ dnorm(0,psi[2])
lam[3] ~ dnorm(0,psi[3])
lam[4] ~ dnorm(0,psi[4])
lam[5] ~ dnorm(0,psi[5])
lam[6] ~ dnorm(0,psi[6])
lam[7] ~ dnorm(0,psi[7])
lam[8] ~ dnorm(0,psi[8])
lam[10] ~ dnorm(0,psi[10])
lam[11] ~ dnorm(0,psi[11])
lam[12] ~ dnorm(0,psi[12])
lam[13] ~ dnorm(0,psi[13])
lam[14] ~ dnorm(0,psi[14])
lam[15] ~ dnorm(0,psi[15])
#---
#Priors on Precisions
for(j in 1:nIndicators) {
psi[j] ~ dgamma(9.0, 4.0) # Error variances
sgm[j] - 1/psi[j]
}
phi[1:2,1:2] ~ dwish(R[1:2,1:2], 5) # Precision matrix
phx[1:2,1:2] - inverse(phi[1:2,1:2]) # Variance/Covariance matrix
}
writeLines(modelstring,con=model.txt)
#
# READ IN DATA AND PREPARE FOR JAGS
cfadata = read.csv(~/Desktop/rjags stuff/nelsdata.csv,header=T)
nData = NROW(cfadata)
yname = c(getalong, spirit, discfair, friends, tchgood,
tcherint, tchprais, tlisten,
studisr, tputdown, strict, sputdown, notsafe,
dislrn, getaway)
y = as.matrix(cfadata)
nData=NROW(y)
nIndicators = NCOL(y)
cfadata - list(y=y, nData=nData)
#---
# A set of init statements goes here, but I haven't done that.
#---
# RUN CHAIN
parameters = c(lam[2],lam[3],lam[4])
adaptSteps = 500
burnInSteps = 500
nChains = 3
numSavedSteps = 5
thinSteps = 1
cfaModel = jags.model(model.txt,data=cfadata,
n.chains=nChains, n.adapt=adaptSteps)
# Burn-in:
cat(Burning in the MCMC chain ...\n)
update(cfaModel, n.iter=burnInSteps)
cat(Sampling from the final MCMC chain ... \n)
codaSamples = coda.samples(cfaModel, variable.names=parameters,
n.iter=nPerChain, thin=thinSteps)
--
==
David Kaplan, Ph.D.
Professor and Chair
Department of Educational Psychology
University of Wisconsin - Madison
Educational Sciences, Room, 880B
1025 W. Johnson Street
Madison, WI 53706
email: dkap...@education.wisc.edu
homepage: edpsych.education.wisc.edu/people/faculty-staff/david-kaplan
Project page: bise.wceruw.org
Phone: 608-262-0836
__
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and provide commented, minimal, self-contained, reproducible code.
[R] Question about error message
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Re: [R] Simple ordering or sorting question
That did it. Thanks!! David === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1082B 1025 W. Johnson Street Madison, WI 53706 email: dkap...@education.wisc.edu homepage: http://www.education.wisc.edu/edpsych/default.aspx?content=kaplan.html Phone: 608-262-0836 === On 5/18/11 1:50 PM, jim holtman wrote: It looks like your row numbers are characters because that is the sort sequence you are getting. Try df- df[order(as.numeric(rownames(df))), ] On Wed, May 18, 2011 at 2:42 PM, David Kaplan dkap...@education.wisc.edu wrote: Greetings, I'm trying to simply reorder a data frame on the row numbers. So, for example, instead of getting 1,2,3,4,5,6,7,8,9,10,11, ... 100 ..., I get instead 1, 10, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 11, ... I've tried commands such as df- df[order(rownames(df)),] and and have substituted the order command with sort and sort.list to no avail. Any advice would be appreciated. Thanks in advance. David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1082B 1025 W. Johnson Street Madison, WI 53706 email: dkap...@education.wisc.edu homepage: http://www.education.wisc.edu/edpsych/default.aspx?content=kaplan.html Phone: 608-262-0836 === [[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. [[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.
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Re: [R] Filling in a uniform dist plot
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--
===
David Kaplan, Ph.D.
Professor
Department of Educational Psychology
University of Wisconsin - Madison
Educational Sciences, Room, 1061
1025 W. Johnson Street
Madison, WI 53706
email: [EMAIL PROTECTED]
homepage:
http://www.education.wisc.edu/edpsych/default.aspx?content=kaplan.html
Phone: 608-262-0836
__
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.
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Re: [R] Identify command in R]
Let me try to be more specific. The x y coordinates are different because of NAs in the dataset. In this analysis, a set of hat values (a measure of influence in regression) is given for each observation. On the basis of the regression that was run to get these hat values, the sample size was 1164 (one removed due to NA). The length of the data set is 1165. If I remove the NA from the data set, I can get identify to run. What I would like to know is if there is a way to get identify to ignore the NAs? Thanks in advance, -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] homepage: http://www.education.wisc.edu/edpsych/default.aspx?content=kaplan.html Phone: 608-262-0836 __ 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.
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Re: [R] Merging nested files
I think this will work. Thanks. But, is there a command to merge on a string variable. All I have is the country 3 letter designation. Thanks again, David === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] homepage: http://www.education.wisc.edu/edpsych/default.aspx?content=kaplan.html Phone: 608-262-0836 === Erik Iverson wrote: Hello - David Kaplan wrote: Greetings all, I have three files that I would like to merge. The first is a student level file that contains the student ID, their school ID, and their country ID. The second is the school file that contains the school ID and country ID. The third is the country file with a country ID. I would like to merge the three together using the common country ID. Of course, what this would mean is that school data be repeated for every student in their school, and country data repeated for every school and student in that country. Any direction would be helpful. I believe what you are after is to use the merge function. 'merge' takes two data.frames, so to merge 3 data.frames, you'll have to use it twice. You may want the all = TRUE argument to merge also. Example, with your data.frames, it might look like: tmp - merge(student, school, all = TRUE) df - merge(tmp, country, all = TRUE) One thing to watch out for is that the merge function will merge on the common names in each data.frame, in your case country ID. Sometimes I check before the merge what variables it will attempt to merge on by using intersect(names(student), names(school)) and making sure it is what I expect, i.e. ususally only one common name. Hope that helps. Thanks in advance, David __ 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.
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Re: [R] Handling complex sampling designs in R
This looks fantastic. Thanks! David === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] homepage: http://www.education.wisc.edu/edpsych/default.aspx?content=kaplan.html Phone: 608-262-0836 === Tobias Verbeke wrote: Dear professor Kaplan, I typically need to analyze data from large scale surveys obtained under complex sampling designs and where sampling weights are provided. I suspect that weights can be handled for some, but not all, packages. Can someone point me to information about which packages can incorporate sampling weights? The most feature-rich package to analyze data originating from complex sampling designs is the survey package by Thomas Lumley. A feature list (as well as a wide assortment of package documentation) can be found at http://faculty.washington.edu/tlumley/survey/ The package itself can be installed from CRAN install.packages(survey) Kind regards, Tobias Verbeke __ 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] derivatives and integrals in R
__ 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] Handling complex sampling designs in R
__ 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.
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__ 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.
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[R] Error message got a real'
Hi all, I'm running the program sem on a Mac, but I'm getting a message that I think is quite general. The error reads Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got '10652)' The 10652 is the sample size coming from a .csv file where I have header = TRUE. Any thoughts would be appreciated. David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: dkaplan at education dot wisc dot edu homepage: [1]http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 === References 1. http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm __ 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.
Re: [R] Error message got a real'
Thanks, I'm not sure why it wasn't saved as a .csv. I posted it to the R Mac list and the general R list because in the past when I've posted to the R Mac list I was told it wasn't a R question. Because this problem didn't appear with the windows verson of R, I wasn't sure which list was appropriate. There was no intention to be inconsiderate. David === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: dkaplan at education dot wisc dot edu homepage: [1]http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 === Duncan Murdoch wrote: David Kaplan wrote: Yea, I checked that, but that wasn't the problem. I'm sending the input and a much smaller file. It's in .csv format. The input is for the Mac, and I'm beginning to think it might be a Mac issue. The program input lines come from John Fox's program sem The test.csv file isn't a csv file (which is a text format, with comma separated columns). It looks like your spreadsheet let you name it with extension .csv, but didn't save it in that format. By the way, posting the same question 6 minutes apart on two mailing lists is quite inconsiderate; please don't do that. Duncan Murdoch David === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: dkaplan at education dot wisc dot edu homepage: [1][2]http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 === Duncan Murdoch wrote: David Kaplan wrote: Hi all, I'm running the program sem on a Mac, but I'm getting a message that I think is quite general. The error reads Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got '10652)' The 10652 is the sample size coming from a .csv file where I have header = TRUE. It appears to be finding a parenthesis too. That's not a real. Duncan Murdoch References 1. [3]http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm __ [EMAIL PROTECTED] mailing list [5]https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide [6]http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. References 1. http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm 2. http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm 3. http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm 4. mailto:R-help@r-project.org 5. https://stat.ethz.ch/mailman/listinfo/r-help 6. http://www.R-project.org/posting-guide.html __ 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] Markov and Hidden Markov models
Hi, Is there a package that will estimate simple Markov models and hidden Markov models for discrete time processes in R? Thanks in advance, David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] homepage: http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 __ 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] Moving to a Mac environment - quick question
Hi all, I'm moving to a Mac platform and have installed R and all seems fine. My question concerns moving my R objects over. On my pc, which file contains my R objects and once I copy that, where do I copy it within the Mac? I hope that was clear. Thanks in advance, David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] homepage: [2]http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 === References 1. mailto:[EMAIL PROTECTED] 2. http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm __ 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] White's test again
Hi all, It seems that I can get White's (HC3) test using MASS. The syntax I used for the particular problem is anova(scireg3, white.adjust=hc3) where scireg3 is an object from the lm function. But, the anova summary table is all I get. I don't get the new estimates or standard errors correcting for heteroskedasticity. Is there a way to get that information? Thanks in advance, David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] homepage: http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 __ 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] A very simple question
Hi all, My apologies for a very simple question. I just downloaded R 2.6.0. I want to bring in all of the objects from 2.5.0 that I see when I type ls(). I have no idea how to do that. Thanks in advance. David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] Web: http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 Fax: 608-262-0843 __ 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] Fatal error message in Windows version of 2.6
Hi, I opened up R 2.6 and now I am receiving a message that says Fatal Error: Unable to restore saved data in .RData When I look at the console I see a message that says Error in .Call(R_lazyLoadDBfetch,...) Any thoughts? David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] Web: http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 Fax: 608-262-0843 __ 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.
Re: [R] Question re matplot
Yea, sorry, that was a typo when I copied into my emal. Here it is again matplot(battingagg$X, battingagg[, c(HR,RBI,X2B, BB, R, SB)], type=b,lty=4,lwd=2, col=1:4,xlab = Year, ylab = (1)HRs, (2)RBIs, (3)DOUBLES,(4)BB,(5)Runs,(6) BB, pty=m,sub = Figure 2. Plot of Selected Offensive Baseball Statistics: 1901 - 2005) David === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] Web: http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 Fax: 608-262-0843 === Marc Schwartz wrote: On Sat, 2007-10-13 at 22:00 -0500, David Kaplan wrote: Hi, I have the following script for matplot matplot(battingagg$X, battingagg[, c(HR,RBI,X2B, BB, R, SB)], type=b,lty=4,lwd=2, col=1:4,xlab = Year, ylab (1)HRs, (2)RBIs, (3)DOUBLES,(4)BB,(5)Runs,(6) BB, pty=m,sub = Figure 2. Plot of Selected Offensive Baseball Statistics: 1901 - 2005,) The problem I'm having is with ylab. It seems not to be giving the entire label, but rather cuts of the first 3 variables giving me only (4)BB,(5)Runs,(6) BB. How can I get it to print the entire label? Thanks in advance. David Is the above an exact copy of your script? If yes, what happens when you remember to put an '=' sign after 'ylab'? :-) Also, you appear to have a superfluous ',' at the end of the function call, prior to the final close paren. HTH, Marc Schwartz __ 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.
Re: [R] Missing data
I did. If you don't want to answer, then your unhelpful suggestions to yourself. === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room 1061 1025 W. Johnson Street Madison, WI 53706 email: [EMAIL PROTECTED] Web: http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 Fax: 608-262-0843 === Bert Gunter wrote: Please use R's existing search tools before posting: RsiteSearch(imputation) RsiteSearch(missing data imputation) etc. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David Kaplan Sent: Tuesday, September 11, 2007 2:36 PM To: [EMAIL PROTECTED] Subject: [R] Missing data Hi all, I'm looking for a contributed package that can provide a detailed account of missing data patterns and perhaps also provide imputation procedures, such as mean imputation or hot deck imputation and the like. Is there anything out there? Thanks in advance, David __ 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.
