In searching for NextMethod on http://www.rseek.org/ I found some helpful tutorials on S3 and S4 methods.
Between your answer and the tutorials, I think I'm starting to understand. The NextMethod is just a dispatcher type of thing that doesn't do anything directly. I think you're saying that when lm is called on a boxcox object then this part of the code handles it (maybe I have it backwards though). So, can you tell from this what the "next method" would be? I tried doing "debug(boxcox.default)" but there is no boxcox.default. Did you mistakenly say "boxplot" instead of "boxcox" when referring to the default method that does the "heavy lifting"? I just want to see the code that calculates the log likelihood values of y in boxcox. Thank you On Fri, Feb 14, 2014 at 4:33 PM, Bert Gunter <gunter.ber...@gene.com> wrote: > Well, since this is really a question about understanding how S3 > methods work, and this is not the place for a tutorial, I think what > you need to do is search out a tutorial that you understand. > > But very briefly, it does what it says. The "object" argument is > supplied to the boxcox generic; lm() takes this (presumably a formula) > as an argument and replaces the object argument with the fit, which is > of "lm" class . NextMethod() then would call the next method, > boxcox.lm on "object" . boxcox.lm does something similar, calling > boxplot.default on the (possibly fixed up) fit, as that is the "next" > method after boxplot.lm on "object." boxplot.default is where all the > work is done. > > *** If this is wrong in any way, I would appreciate being corrected.*** > > Others may have useful tutorials that provide greater detail. > > Cheers, > Bert > > Bert Gunter > Genentech Nonclinical Biostatistics > (650) 467-7374 > > "Data is not information. Information is not knowledge. And knowledge > is certainly not wisdom." > H. Gilbert Welch > > > > > On Fri, Feb 14, 2014 at 2:00 PM, Gene Leynes <gleyne...@gmail.com> wrote: > > Yes I read the help on NextMethod. In fact, since people frequently > respond > > with "did you read the help" I mentioned that I had read the help in my > > original post. I'm very grateful for the time and effort that people put > > into answering questions, so I always try to answer the question myself > > first usually for more than one day. > > > > I didn't find anything in ?NextMethod that helped me understand how > > NextMethod works here: > >>> m <- length(lambda) > >>> object <- lm(object, y = TRUE, qr = TRUE, ...) > >>> result <- NextMethod() > > > > This part seemed like the the most likely part: > >> > >> NextMethod invokes the next method (determined by the class vector, > either > >> of the object supplied to the generic, or of the first argument to the > >> function containing NextMethod if a method was invoked directly). > >> NormallyNextMethod is used with only one argument, generic, but if > further > >> arguments are supplied these modify the call to the next method. > > > > > > But, since NextMethod is called with no arguments, what "class vector" > > determines the "next method"? If this is invoking the "next" method, > then > > was the "previous" method? How can it be called with no arguments? > > > > Maybe my problem is that I don't understand the S3 and S4 classes and I > > should really read something else, because this help doesn't seem to > stand > > on it's own. I've been using R for a long time and this help left me > > scratching my head. > > > > I don't actually care about NextMethod, I was just trying to figure out > how > > the boxcox function is calculating the y part of the return values. > Since I > > couldn't figure it out from ?boxcox I tried to dig into the code, but I > was > > stymied by the code. Does the lm function compute the boxcox > transformation? > > > > > > On Thu, Feb 13, 2014 at 4:59 PM, Bert Gunter <gunter.ber...@gene.com> > wrote: > >> > >> Have you tried: > >> > >> ?NextMethod > >> > >> ? > >> > >> -- Bert > >> > >> Bert Gunter > >> Genentech Nonclinical Biostatistics > >> (650) 467-7374 > >> > >> "Data is not information. Information is not knowledge. And knowledge > >> is certainly not wisdom." > >> H. Gilbert Welch > >> > >> > >> > >> > >> On Thu, Feb 13, 2014 at 2:17 PM, Gene Leynes <gleyne...@gmail.com> > wrote: > >> > I was trying to understand the boxcox function in MASS to get a better > >> > understanding of where and how the log-Likelihood values are > calculated. > >> > > >> > By using "debug(boxcox)" I found this code while running the examples: > >> > > >> >> m <- length(lambda) > >> >> object <- lm(object, y = TRUE, qr = TRUE, ...) > >> >> result <- NextMethod() > >> > > >> > > >> > Can someone tell me how this is optimizing the values for Lambda? I'm > >> > assuming that it has something to do with the qr decomposition that > >> > happens > >> > in lm? > >> > > >> > > >> > Thank you, > >> > > >> > Gene > >> > > >> > > >> > > >> > > >> > Notes and disclaimers: > >> > > >> > - Yes, I read the help for NextMethod and boxcox. > >> > - I don't think my OS / R / MASS versions are relevant but if you > >> > must > >> > know I happen to be on Windows 8 right now and using R version > 3.0.2 > >> > (2013-09-25) -- "Frisbee Sailing", Platform: x86_64-w64-mingw32/x64 > >> > (64-bit). MASS version is 7.3-29. > >> > > >> > [[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. > > > > > [[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.
