Re: [Bugs-r-devel] Fw: R2WinBUGS modifications

[Uwe L. <li...@st...>]

Dear Jouni,

after a serious delay due to work-overload, I finally found the time to 
incorporate your changes into R2WinBUGS, most of them unchanged.

So thank you again for your nice code!!!

I replaced bugs.log() by your function bugs.summary() and tried to 
update all the help pages.

The current version is committed to the repository at:
https://sourceforge.net/projects/bugs-r/
If you like, we can give you access as a developer. If not, for the next 
time, please send changes as diffs against the sources on the 
sourceforge address mentioned above.



Dear Dawn, can you quickly test under S-PLUS, please? I think we could 
release this one pretty soon now.

Best wishes,
Uwe




jou...@no... wrote:
> Dear Uwe
> 
> I noticed that Sibylle Sturtz is the maintainer of R2WinBUGS so I sent her 
> the following message. I don't know if you're interested any more but 
> maybe you have some comments?
> 
> best regards
> 
> Jouni Kerman
> 
> 
> -----------
> 
> I've made some improvements and additions to the R2WinBUGS code to make it 
> more flexible. 
> 
> However I would like to make the changes available for everyone. How could 
> I help you best to get them incorporated in the package? 
> 
> ----
> My current code is attached. 
> 
> I have currently 5 rewritten functions for the package. Most are just 
> small modifications and affect only small parts of the functions. I tried 
> not to change too much of the old code just to make it easier to review. 
> 
> In summary the additions and changes are:
> 
> (In function bugs:)
> - Add bugs.seed parameter and the corresponding bugs script entry to 
> specify random seed in WinBUGS
> - Add summary.only parameter (default FALSE) which prevents outputting the 
> coda and only returns the parameter summary
> - Add save.history parameter (default TRUE) which controls whether the 
> trace plots are generated at end
> - Add n.sims parameter (number of simulations to keep). I often specify 
> this and n.iter only. 
> - Fix definition of n.thin which assumes output of 1000 simulations 
> (divide by n.sims instead)
> - If the global option 'R2WinBUGS.bugs.directory' exists, bugs uses it for 
> the R2WinBUGS directory
> - Allow specification of data file that can be named something else than 
> data.txt
> - Allow specification of inits file names
> 
> I have also rewritten the bugs.log routine so it does not crash if DIC is 
> not specified; it also does not make assumptions about the column names. 
> 
> These improvements are all quite useful for us. Especially, bugs.seed is 
> crucial and summary.only helps a lot if one repeats the same analysis many 
> times and only needs some quick summary. 
> 
> If you agree, I would like to have these changes implemented in the next 
> version of R2WinBUGS. 
> 
>  I've tried them out for some time now and there are no known bugs. I have 
> not tried it with openbugs. 
> 
> Best regards, Mit freundlichen Grüssen, Meilleures salutations, 
> Jouni Kerman, Ph.D.
> Novartis Pharma AG
> PH3483, CIS - METHODOLOGY
> CHBS, WSJ-027.3.017
> Phone: +41 61 324 3600
> Fax: +41 61 324 3781
> Email : jou...@no...
> 
>