Hi all,
I am currently in a Bayesian Modeling course and am trying to implement an
analog representation model using R, WinBUGS, and R2WinBUGS. I'm currently
stuck banging my head against an "expected collection operator c" error. I
am working off of a template code, and I swear I haven't moved any
collection operators from the original code.
Here is what my script looks like in R:
########################################################
# clears workspace:
rm(list=ls(all=TRUE))
# sets working directories:
setwd("C:\\Users\\Nick\\Desktop\\modeling")
library(R2WinBUGS)
bugsdir = "C:/Program Files/WinBUGS14"
# read the data
g = matrix(scan("g.txt", sep=","), ncol=144, nrow=3, byrow=T)
q = matrix(scan("q.txt", sep=","), ncol=144, nrow=3, byrow=T)
S = 3 # number of subjects
Q = 144 # number of questions for each child
N = 9 # maximum numbers of item list
data = list("g", "q", "S", "Q", "N") # to be passed on to WinBUGS
myinits = list(
list(sigma = rep(1,S), pitmp=rep(1/N, N)))
# parameters to be monitored:
parameters = c("pp","ppb","sigma")
# NB. even with only 1000 iterations, the sampling can take a long time!
# The following command calls WinBUGS with specific options.
# For a detailed description see Sturtz, Ligges, & Gelman (2005).
samples = bugs(data, inits=myinits, parameters,
model.file ="NumberConcept_2_data.txt",
n.chains=1, n.iter=1000, n.burnin=100, n.thin=1,
DIC=T, bugs.directory=bugsdir,
codaPkg=F, debug=T)
# Now the values for the monitored parameters are in the "samples" object,
# ready for inspection.
samples$summary
#######################################################
and here is the log file file from WinBUGS after R2WinBUGS passes it over:
#######################################################
display(log)
check(C:/Users/Nick/AppData/Local/Temp/RtmpIRZ1dh/NumberConcept_2_data.txt)
model is syntactically correct
data(C:/Users/Nick/AppData/Local/Temp/RtmpIRZ1dh/data.txt)
expected collection operator c
compile(1)
inits(1,C:/Users/Nick/AppData/Local/Temp/RtmpIRZ1dh/inits1.txt)
command #Bugs:inits cannot be executed (is greyed out)
gen.inits()
command #Bugs:gen.inits cannot be executed (is greyed out)
thin.updater(1)
update(100)
command #Bugs:update cannot be executed (is greyed out)
set(pp)
command #Bugs:set cannot be executed (is greyed out)
set(ppb)
command #Bugs:set cannot be executed (is greyed out)
set(sigma)
command #Bugs:set cannot be executed (is greyed out)
set(deviance)
command #Bugs:set cannot be executed (is greyed out)
dic.set()
command #Bugs:dic.set cannot be executed (is greyed out)
update(900)
command #Bugs:update cannot be executed (is greyed out)
coda(*,C:/Users/Nick/AppData/Local/Temp/RtmpIRZ1dh/coda)
command #Bugs:coda cannot be executed (is greyed out)
stats(*)
command #Bugs:stats cannot be executed (is greyed out)
dic.stats()
DIC
history(*,C:/Users/Nick/AppData/Local/Temp/RtmpIRZ1dh/history.odc)
command #Bugs:history cannot be executed (is greyed out)
save(C:/Users/Nick/AppData/Local/Temp/RtmpIRZ1dh/log.odc)
save(C:/Users/Nick/AppData/Local/Temp/RtmpIRZ1dh/log.txt)
#################################################################
WinBUGS also opens up a data window that looks like this:
#################################################################
list(g= structure(.Data= c(1.00000E+00, 1.00000E+00, 1.00000E+00,
1.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00,
1.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00,
1.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
1.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
1.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 1.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 2.00000E+00, 2.00000E+00), .Dim=c(3, 144)), q=
structure(.Data= c(4.00000E+00, 5.00000E+00, 3.00000E+00, 8.00000E+00,
1.00000E+00, 5.00000E+00, 4.00000E+00, 4.00000E+00, 3.00000E+00,
3.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 4.00000E+00,
5.00000E+00, 2.00000E+00, 3.00000E+00, 2.00000E+00, 1.00000E+00,
1.00000E+00, 2.00000E+00, 3.00000E+00, 7.00000E+00, 6.00000E+00,
5.00000E+00, 4.00000E+00, 7.00000E+00, 1.00000E+00, 1.00000E+00,
3.00000E+00, 6.00000E+00, 2.00000E+00, 6.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 3.00000E+00, 3.00000E+00, 4.00000E+00,
1.00000E+00, 7.00000E+00, 2.00000E+00, 2.00000E+00, 3.00000E+00,
4.00000E+00, 1.00000E+00, 3.00000E+00, 5.00000E+00, 6.00000E+00,
2.00000E+00, 6.00000E+00, 4.00000E+00, 2.00000E+00, 2.00000E+00,
5.00000E+00, 5.00000E+00, 1.00000E+00, 1.00000E+00, 4.00000E+00,
5.00000E+00, 3.00000E+00, 3.00000E+00, 1.00000E+00, 1.00000E+00,
7.00000E+00, 2.00000E+00, 1.00000E+00, 8.00000E+00, 4.00000E+00,
2.00000E+00, 1.00000E+00, 6.00000E+00, 4.00000E+00, 2.00000E+00,
3.00000E+00, 4.00000E+00, 2.00000E+00, 5.00000E+00, 1.00000E+00,
7.00000E+00, 2.00000E+00, 3.00000E+00, 5.00000E+00, 3.00000E+00,
6.00000E+00, 5.00000E+00, 1.00000E+00, 1.00000E+00, 3.00000E+00,
5.00000E+00, 1.00000E+00, 6.00000E+00, 2.00000E+00, 6.00000E+00,
4.00000E+00, 7.00000E+00, 4.00000E+00, 2.00000E+00, 1.00000E+00,
3.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 1.00000E+00,
3.00000E+00, 2.00000E+00, 4.00000E+00, 8.00000E+00, 1.00000E+00,
1.00000E+00, 5.00000E+00, 6.00000E+00, 4.00000E+00, 7.00000E+00,
1.00000E+00, 6.00000E+00, 7.00000E+00, 5.00000E+00, 3.00000E+00,
3.00000E+00, 4.00000E+00, 4.00000E+00, 3.00000E+00, 3.00000E+00,
2.00000E+00, 5.00000E+00, 3.00000E+00, 2.00000E+00, 6.00000E+00,
1.00000E+00, 2.00000E+00, 3.00000E+00, 1.00000E+00, 5.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 4.00000E+00, 2.00000E+00,
8.00000E+00, 2.00000E+00, 4.00000E+00, 1.00000E+00, 2.00000E+00,
1.00000E+00, 1.00000E+00, 3.00000E+00, 7.00000E+00, 3.00000E+00,
1.00000E+00, 3.00000E+00, 2.00000E+00, 4.00000E+00, 7.00000E+00,
4.00000E+00, 1.00000E+00, 1.00000E+00, 5.00000E+00, 3.00000E+00,
6.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 2.00000E+00, 6.00000E+00, 5.00000E+00, 8.00000E+00,
4.00000E+00, 3.00000E+00, 5.00000E+00, 3.00000E+00, 4.00000E+00,
6.00000E+00, 4.00000E+00, 5.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 3.00000E+00, 2.00000E+00, 5.00000E+00,
5.00000E+00, 1.00000E+00, 4.00000E+00, 4.00000E+00, 1.00000E+00,
3.00000E+00, 1.00000E+00, 2.00000E+00, 4.00000E+00, 5.00000E+00,
3.00000E+00, 2.00000E+00, 1.00000E+00, 5.00000E+00, 6.00000E+00,
3.00000E+00, 1.00000E+00, 2.00000E+00, 4.00000E+00, 8.00000E+00,
2.00000E+00, 7.00000E+00, 4.00000E+00, 2.00000E+00, 1.00000E+00,
6.00000E+00, 7.00000E+00, 3.00000E+00, 2.00000E+00, 1.00000E+00,
6.00000E+00, 3.00000E+00, 2.00000E+00, 7.00000E+00, 3.00000E+00,
2.00000E+00, 3.00000E+00, 3.00000E+00, 7.00000E+00, 1.00000E+00,
3.00000E+00, 5.00000E+00, 5.00000E+00, 5.00000E+00, 6.00000E+00,
4.00000E+00, 6.00000E+00, 2.00000E+00, 2.00000E+00, 1.00000E+00,
4.00000E+00, 1.00000E+00, 8.00000E+00, 4.00000E+00, 5.00000E+00,
1.00000E+00, 4.00000E+00, 6.00000E+00, 2.00000E+00, 1.00000E+00,
3.00000E+00, 3.00000E+00, 1.00000E+00, 4.00000E+00, 2.00000E+00,
1.00000E+00, 2.00000E+00, 1.00000E+00, 3.00000E+00, 7.00000E+00,
8.00000E+00, 2.00000E+00, 2.00000E+00, 3.00000E+00, 2.00000E+00,
6.00000E+00, 1.00000E+00, 2.00000E+00, 4.00000E+00, 5.00000E+00,
4.00000E+00, 3.00000E+00, 3.00000E+00, 6.00000E+00, 2.00000E+00,
1.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00, 5.00000E+00,
1.00000E+00, 4.00000E+00, 4.00000E+00, 6.00000E+00, 3.00000E+00,
2.00000E+00, 5.00000E+00, 7.00000E+00, 5.00000E+00, 4.00000E+00,
3.00000E+00, 1.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00,
2.00000E+00, 3.00000E+00, 5.00000E+00, 1.00000E+00, 5.00000E+00,
1.00000E+00, 6.00000E+00, 6.00000E+00, 2.00000E+00, 2.00000E+00,
3.00000E+00, 3.00000E+00, 1.00000E+00, 3.00000E+00, 3.00000E+00,
4.00000E+00, 7.00000E+00, 5.00000E+00, 1.00000E+00, 1.00000E+00,
2.00000E+00, 1.00000E+00, 4.00000E+00, 4.00000E+00, 4.00000E+00,
2.00000E+00, 8.00000E+00, 7.00000E+00, 3.00000E+00, 5.00000E+00,
1.00000E+00, 6.00000E+00, 1.00000E+00, 2.00000E+00, 4.00000E+00,
1.00000E+00, 5.00000E+00, 3.00000E+00, 1.00000E+00, 4.00000E+00,
6.00000E+00, 3.00000E+00, 4.00000E+00, 7.00000E+00, 6.00000E+00,
1.00000E+00, 1.00000E+00, 8.00000E+00, 7.00000E+00, 6.00000E+00,
1.00000E+00, 4.00000E+00, 3.00000E+00, 2.00000E+00, 1.00000E+00,
2.00000E+00, 4.00000E+00, 1.00000E+00, 2.00000E+00, 2.00000E+00,
2.00000E+00, 1.00000E+00, 3.00000E+00, 2.00000E+00, 3.00000E+00,
4.00000E+00, 5.00000E+00, 5.00000E+00, 3.00000E+00, 5.00000E+00,
2.00000E+00, 6.00000E+00, 1.00000E+00, 5.00000E+00, 4.00000E+00,
4.00000E+00, 3.00000E+00, 5.00000E+00, 4.00000E+00, 1.00000E+00,
1.00000E+00, 2.00000E+00, 7.00000E+00, 4.00000E+00, 2.00000E+00,
5.00000E+00, 2.00000E+00, 6.00000E+00, 1.00000E+00, 6.00000E+00,
2.00000E+00, 3.00000E+00, 2.00000E+00, 3.00000E+00, 3.00000E+00,
4.00000E+00, 1.00000E+00, 1.00000E+00, 2.00000E+00, 3.00000E+00,
3.00000E+00, 7.00000E+00, 1.00000E+00, 2.00000E+00, 1.00000E+00,
5.00000E+00, 8.00000E+00, 4.00000E+00, 1.00000E+00, 8.00000E+00,
1.00000E+00, 5.00000E+00, 6.00000E+00, 3.00000E+00, 5.00000E+00,
4.00000E+00, 1.00000E+00, 3.00000E+00, 2.00000E+00, 5.00000E+00,
4.00000E+00, 3.00000E+00, 6.00000E+00, 1.00000E+00, 1.00000E+00,
7.00000E+00, 4.00000E+00, 2.00000E+00, 2.00000E+00, 4.00000E+00,
2.00000E+00, 1.00000E+00, 2.00000E+00, 5.00000E+00, 2.00000E+00,
3.00000E+00, 7.00000E+00, 2.00000E+00, 1.00000E+00, 1.00000E+00,
3.00000E+00, 6.00000E+00, 3.00000E+00), .Dim=c(3, 144)), S=3.00000E+00,
Q=1.44000E+02, N=9.00000E+00)
##################################################################
Which is my data from files g.txt and q.txt - I go looking for a missing
collection operator c but cannot find it anywhere, if anyone has a clue what
I could do to get past this point, I would be so grateful!
Best,
N
--
View this message in context:
http://r.789695.n4.nabble.com/R2WinBUGS-expected-collection-operator-c-error-tp4688032.html
Sent from the R help mailing list archive at Nabble.com.
______________________________________________
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.
