Thanks for the advice. I found the function : summary(mcmc(x)), from the coda package.
2010/6/4 Gavin Simpson <gavin.simp...@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.simp...@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 > > > > > > -- > > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > > 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 > > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > > > > > > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html> > > and provide commented, minimal, self-contained, reproducible code. > > -- > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > 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 > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > [[alternative HTML version deleted]]
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