Are you sure that you are fitting all the models on the same total data? A first glance looks like you may be including more data in some of the chunk sizes, or be producing an error that update does not know how to deal with.
-- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 From: utkarshsinghal [mailto:utkarsh.sing...@global-analytics.com] Sent: Monday, July 06, 2009 8:58 AM To: Thomas Lumley; Greg Snow Cc: r help Subject: Re: [R] bigglm() results different from glm()+Another question The AIC of the biglm models is highly dependent on the size of chunks selected (example provided below). This I can somehow expect because the model error will increase with the number of chunks. It will be helpful if you can provide your opinion for comparing different models in such cases: * can I compare two models fitted with different chunksizes, or should I always use the same chunk size. * although I am not going to use AIC at all in my model selection, but I think any other model parameters will also vary in the same way. Am I right? * what would be the ideal chunksize? should it be the maximum possible size R and my system's RAM is able to handle? Any comments will be helpful. Example of AIC variation with chunksize: I ran the following code on my data which has 10000 observations and 3 independent variables > chunksize = 500 > fit = biglm(y~x1+x2+x3, data=xx[1:chunksize,]) > for(i in seq(chunksize,10000,chunksize)) fit=update(fit, > data=xx[(i+1):(i+chunksize),]) > AIC(fit) [1] 30647.79 Here are the AIC for other chunksizes: chunksize AIC 500 30647.79 1000 29647.79 2000 27647.79 2500 26647.79 5000 21647.79 10000 11647.79 Regards Utkarsh utkarshsinghal wrote: Thank you Mr. Lumley and Mr. Greg. That was helpful. Regards Utkarsh Thomas Lumley wrote: On Fri, 3 Jul 2009, utkarshsinghal wrote: Hi Sir, Thanks for making package available to us. I am facing few problems if you can give some hints: Problem-1: The model summary and residual deviance matched (in the mail below) but I didn't understand why AIC is still different. AIC(m1) [1] 532965 AIC(m1big_longer) [1] 101442.9 That's because AIC.default uses the unnormalized loglikelihood and AIC.biglm uses the deviance. Only differences in AIC between models are meaningful, not individual values. Problem-2: chunksize argument is there in bigglm but not in biglm, consequently, udate.biglm is there, but not update.bigglm Is my observation correct? If yes, why is this difference? Because update.bigglm is impossible. Fitting a glm requires iteration, which means that it requires multiple passes through the data. Fitting a linear model requires only a single pass. update.biglm can take a fitted or partially fitted biglm and add more data. To do the same thing for a bigglm you would need to start over again from the beginning of the data set. To fit a glm, you need to specify a data source that bigglm() can iterate over. You do this with a function that can be called repeatedly to return the next chunk of data. -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.edu<mailto:tlum...@u.washington.edu> University of Washington, Seattle I don't know why the AIC is different, but remember that there are multiple definitions for AIC (generally differing in the constant added) and it may just be a difference in the constant, or it could be that you have not fit the whole dataset (based on your other question). For an lm model biglm only needs to make a single pass through the data. This was the first function written for the package and the update mechanism was an easy way to write the function (and still works well). The bigglm function came later and the models other than Gaussian require multiple passes through the data so instead of the update mechanism that biglm uses, bigglm requires the data argument to be a function that returns the next chunk of data and can restart to the beginning of the dataset. Also note that the bigglm function usually only does a few passes through the data, usually this is good enough, but in some cases you may need to increase the number of passes. Hope this helps, [[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 and provide commented, minimal, self-contained, reproducible code.
