On Tue, Feb 19, 2013 at 7:18 AM, Uwe Ligges <ligges@statistik.tu-dortmund.de
> wrote:

>
>
> On 18.02.2013 05:24, Jia Liu wrote:
>
>> Hi all,
>>
>> I used both OpenBugs and R function bugs{R2WinBUGS} to run a linear mixed
>> effects model based on the same data set and initial values. I got the
>> same
>> summary statistics but different posterior samples. However, if I order
>> these two sets of samples, one is generated from OpenBugs and the other is
>> generated from R, they turn to be the same. And the samples from R do not
>> have any autocorrelation. I do not know why and how this R function
>> destroy
>> the orders of posterior samples. Have anyone ever met this situation
>> before? Any idea is appreciated.
>>
>
> Not sure what you are looking at, since there is no reproducible example
> nor any code in your message.
>

Sorry for the inconvenience, I should have posted a sample code with it.


> However, I guess you came across a specific design decision by Andrew
> Gelman, who wrote some code of R2WinBUGS before it was turned into an R
> package. That feature is documented on the ?bugs help page:
>
> "for convenience, the n.keep*n.chains simulations in sims.matrix and
> sims.list (but NOT sims.array) have been randomly permuted".
>
> It is exactly what I asked. I noticed that the posterior sample have been
randomly permuted. But I am curious the reason for doing that. So if the
autocorrelation is of my interest, I should use sims.array, not sims.list.

Thanks,

Jia



> Best,
> Uwe Ligges
>
>
>
>
>
>
>
>> Thanks,
>>
>> Jia
>>
>>
>>  sessionInfo()R version 2.15.1 (2012-06-22)
>>>
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>> States.1252
>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] R2WinBUGS_2.1-18 BRugs_0.8-0      coda_0.15-2      lattice_0.20-6
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.15.1  tools_2.15.1
>>
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>>
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>>
>>

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