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

[Dawn W. <dwo...@in...>]

I have checked that the latest changes work in S-PLUS 8.0.  There was =
only
one problem, which has now been resolved.  The new bugs.seed argument =
works,
which is great!  Thanks for the helpful changes!

Dawn



-----Original Message-----
From: bug...@li...
[mailto:bug...@li...] On Behalf Of Uwe =
Ligges
Sent: Sunday, January 06, 2008 1:25 PM
To: jou...@no...
Cc: bug...@li...
Subject: Re: [Bugs-r-devel] Fw: R2WinBUGS modifications

Dear Jouni,

after a serious delay due to work-overload, I finally found the time to=20
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=20
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=20
sourceforge address mentioned above.



Dear Dawn, can you quickly test under S-PLUS, please? I think we could=20
release this one pretty soon now.

Best wishes,
Uwe




jou...@no... wrote:
> Dear Uwe
>=20
> I noticed that Sibylle Sturtz is the maintainer of R2WinBUGS so I sent =
her=20
> the following message. I don't know if you're interested any more but=20
> maybe you have some comments?
>=20
> best regards
>=20
> Jouni Kerman
>=20
>=20
> -----------
>=20
> I've made some improvements and additions to the R2WinBUGS code to =
make it=20
> more flexible.=20
>=20
> However I would like to make the changes available for everyone. How =
could=20
> I help you best to get them incorporated in the package?=20
>=20
> ----
> My current code is attached.=20
>=20
> I have currently 5 rewritten functions for the package. Most are just=20
> small modifications and affect only small parts of the functions. I =
tried=20
> not to change too much of the old code just to make it easier to =
review.=20
>=20
> In summary the additions and changes are:
>=20
> (In function bugs:)
> - Add bugs.seed parameter and the corresponding bugs script entry to=20
> specify random seed in WinBUGS
> - Add summary.only parameter (default FALSE) which prevents outputting =
the=20
> 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=20
> this and n.iter only.=20
> - Fix definition of n.thin which assumes output of 1000 simulations=20
> (divide by n.sims instead)
> - If the global option 'R2WinBUGS.bugs.directory' exists, bugs uses it =
for=20
> the R2WinBUGS directory
> - Allow specification of data file that can be named something else =
than=20
> data.txt
> - Allow specification of inits file names
>=20
> I have also rewritten the bugs.log routine so it does not crash if DIC =
is=20
> not specified; it also does not make assumptions about the column =
names.=20
>=20
> These improvements are all quite useful for us. Especially, bugs.seed =
is=20
> crucial and summary.only helps a lot if one repeats the same analysis =
many=20
> times and only needs some quick summary.=20
>=20
> If you agree, I would like to have these changes implemented in the =
next=20
> version of R2WinBUGS.=20
>=20
>  I've tried them out for some time now and there are no known bugs. I =
have=20
> not tried it with openbugs.=20
>=20
> Best regards, Mit freundlichen Gr=FCssen, Meilleures salutations,=20
> 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...
>=20
>=20

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