This is strange and does not happen for me.
Anyway, if it is a problem at all, then I doubt it is in R2WinBUGS:
R2WinBUGS asks WinBUGS to write the coda files and afterwards calls the
following function
read.bugs <- function(codafiles, ...){
if(!is.R() && !require("coda"))
stop("package 'coda' is required to use this
function")
mcmc.list(lapply(codafiles, read.coda,
index.file = file.path(dirname(codafiles[1]),
"codaIndex.txt"),
...))
}
that keeps the order from the codaIndex file and just calls other
functions such as read.coda and mcmc.list() from the coda package.
Anyway, if the problem persists for you, you may want to send me an
example that is reproducible, i.e. including data, model files and what
you function calls in R were ....
Best,
Uwe Ligges
On 12.11.2010 20:55, Barth B. Riley wrote:> Dear list
>
> I am calling the functiton bugs() provided by R2WinBugs to performs an IRT
analysis. The function returns a set of estimated parameters over n
replications/iterations. For each replication, two sets of person measures
(theta1 and theta2) and two sets of item difficulty parameters (diff1 and diff2)
are returned. The code used to obtain these estimates is as follows:
>
> sim<-
bugs(data,init,model.file="drift.bugs",parameters=c("theta1","theta2","diff1","diff2"),n.chains=n.chains,n.iter=n.reps,n.burnin=1000,bin=1,n.thin=1,digits=3,
codaPkg=T)
> sim.list<- read.bugs(sim)
>
> However, when I read the coda files using read.bugs the order of the
columns in the parameter matrix are as follows:
>
> [1] "deviance" "diff1[1]"
"diff1[10]" "diff1[100]" "diff1[11]"
"diff1[12]" "diff1[13]"
> [8] "diff1[14]" "diff1[15]"
"diff1[16]" "diff1[17]" "diff1[18]"
"diff1[19]" "diff1[2]"
> ...
> ...
> ..............................................................
"diff2[10]" "diff2[100]" "diff2[11]"
> [106] "diff2[12]" "diff2[13]"
"diff2[14]" "diff2[15]" "diff2[16]"
"diff2[17]" "diff2[18]"
> [113] "diff2[19]" "diff2[2]"
"diff2[20]" "diff2[21]" "diff2[22]"
"diff2[23]" "diff2[24]"
> ...
> ...
>
.............................................................................
"theta1[1]" "theta1[10]"
> [204] "theta1[100]" "theta1[101]"
"theta1[102]" "theta1[103]" "theta1[104]"
"theta1[105]" "theta1[106]"
> [211] "theta1[107]" "theta1[108]"
"theta1[109]" "theta1[11]" "theta1[110]"
"theta1[111]" "theta1[112]"
>
> The columns, in other words, are not in numerical order according to the
index of the item difficulty or person measure parameter. Rather they appear to
be in text-sorted order (e.g., 1, 10, 100...). Any ideas as to what might be
going on?
>
>
> Thanks
>
> Barth
>
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