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. > > ______________________________________________ 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.
