Inline. 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 4:19 PM, Gene Leynes <gleyne...@gmail.com> wrote: > 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. Study the tutorials. You still don't appear to get it. Of course there is a boxcox.default. ?methods methods(boxcox) It is not exported from MASS so must be accessed via ":::" ?"::" -- Bert > > Did you mistakenly say "boxplot" instead of "boxcox" when referring to the > default method that does the "heavy lifting"? Yes. Thanks. > > 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. >> > >> > > > ______________________________________________ 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.
