[R] NextMethod in boxcox

[Bert Gunter]

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 <gleynes+r at 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.berton at 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 <gleynes+r at 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 at 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.
>
>