Thanks for the advice. I found the function : summary(mcmc(x)), from the
coda package.


2010/6/4 Gavin Simpson <gavin.simpson@ucl.ac.uk>

> On Thu, 2010-06-03 at 23:44 +0200, Jimmy Söderly wrote:
> > Thanks for your help.
> >
> > Does it have something to do with the mcmc package, the coda package, or
> the
> > lattice package ?
>
> Is there something stopping you checking this for yourself? You have the
> code *you* are running, after all, and we don't.
>
> The coda package contains a great many functions and as you have yet to
> show us any code or your Sweave file, that would involve me looking
> through the entirety of those packages to find out.
>
> coda mentions glm() in the spectrum0() function. Are you using that?
>
> I doubt it will be lattice - it is primarily a graphics package.
>
> mcmc doesn't appear to have any obvious calls to glm().
>
> Why don't you Tangle your Sweave file to extract the code, then step
> through your code until it issues the warnings. Then you'll know exactly
> where the code is failing to converge. I mentioned this in my earlier
> reply. I'm afraid I'll be unable to provide further enlightenment unless
> you can work out what code is causing the error.
>
> HTH
>
> G
>
> >
> > Jimmy
> >
> > 2010/6/3 Gavin Simpson <gavin.simpson@ucl.ac.uk>
> >
>  > > On Wed, 2010-06-02 at 20:29 +0200, Jimmy Sderly wrote:
> > > > Dear R users,
> > > >
> > > > After running Sweave, this is what I get :
> > > >
> > > > Warning messages:
> > > > 1: glm.fit: algorithm did not converge
> > > > 2: glm.fit: algorithm did not converge
> > > > There is no glm.fit function in my code.
> > >
> > > glm calls glm.fit did you call glm() or any code that might use glm()
> > > (or glm.fit()). glm.fit() is the function that does the actual model
> > > fitting etc, with glm() being a convenience wrapper providing the
> > > formula interface etc.
> > >
> > > > Where does it come from ? From Sweave ? From system.time ?
> > >
> > > Your call to glm() or any function that calls glm(). This is nothing to
> > > sweave or system.time.
> > >
> > > Your model fitting has failed to converge. There may be many reasons
> why
> > > glm.fit is failing to converge for the model your are fitting.
> > >
> > > Either extract the R code or tangle the sweave file to do the
> > > extraction, and then step through the code to see where the warning is
> > > being generated. Then figure out why glm.fit is not converging (you
> > > might need to up the number of iterations or provide better starting
> > > values or rethink the type of model you are trying to fit).
> > >
> > > HTH
> > >
> > > G
> > >
> > > --
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> > >  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
> > >  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
> > >  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk<http://gavin.simpsonatnospamucl.ac.uk/>
> <http://gavin.simpsonatnospamucl.ac.uk/>
> > >  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
> > >  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
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> > >
> > >
> >
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>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk<http://gavin.simpsonatnospamucl.ac.uk/>
>  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
>  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
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>
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