NextMethod in boxcox

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]]

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]]

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.berton at 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 <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]]

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 <gleynes+r at 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.berton at 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 <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]]

How can I see the code for boxcox.default?

library(MASS)
boxcox.default

Error: object 'boxcox.default' not found

	[[alternative HTML version deleted]]