Re: [Rd] Enhanced version of plot.lm()

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Tue 26 Apr 2005 - 10:13:38 GMT

>>>>> "JMd" == John Maindonald <john.maindonald@anu.edu.au> >>>>> on Tue, 26 Apr 2005 15:44:26 +1000 writes:

    JMd> The web page http://wwwmaths.anu.edu.au/~johnm/r/plot-lm/
    JMd> now includes files:
    JMd> plot.lm.RData: Image for file for plot6.lm, a version of plot.lm in 
    JMd> which
    JMd> David Firth's Cook's distance vs leverage/(1-leverage) plot is plot 6.
    JMd> The tick labels are in units of leverage, and the contour labels are
    JMd> in units of absolute values of the standardized residual.

    JMd> plot6.lm.Rd file: A matching help file

    JMd> Comments will be welcome.

Thank you John!

The *.Rd has the new references and a new example but is not quite complete: the \usage{} has only 4 captions, \arguments{ .. \item{which} ..} only mentions '1:5' --- but never mind.

One of the new examples is

    ## Replace Cook's distance plot by Residual-Leverage plot     plot(lm.SR, which=c(1:3, 5))

and -- conceptually I'd really like to change the default from 'which = 1:4' to the above
'which=c(1:3, 5))'

This would be non-compatible though for all those that have always used the current default 1:4.
OTOH, "MASS" or Peter Dalgaard's book don't mention plot(<lm fit> )
or at least don't show it's result.

What do others think?
How problematic would a change be in the default plots that plot.lm() produces?

    JMd> Another issue, discussed recently on r-help, is that when the model
    JMd> formula is long, the default sub.caption=deparse(x$call) is broken
    JMd> into multiple text elements and overwrites.  
good point!
    JMd>  The only clean and simple way that I can see to handle
    JMd> is to set a default that tests whether the formula is
    JMd> broken into multiple text elements, and if it is then
    JMd> omit it.  Users can then use their own imaginative
    JMd> skills, and such suggestions as have been made on
    JMd> r-help, to construct whatever form of labeling best
    JMd> suits their case, their imaginative skills and their
    JMd> coding skills.

Hmm, yes, but I think we (R programmers) could try a bit harder to provide a reasonable default, e.g., something along  

 cap <- deparse(x$call, width.cutoff = 500)[1]  if((nc <- nchar(cap)) > 53)

     cap <- paste(substr(cap, 1, 50), "....", substr(cap, nc-2, nc))

{untested; some of the details will differ;  and the '53', '50' could depend on par("..") measures}

    JMd> John Maindonald.

    JMd> On 25 Apr 2005, at 8:00 PM, David Firth wrote:

>> From: David Firth <d.firth@warwick.ac.uk>
>> Date: 24 April 2005 10:23:51 PM
>> To: John Maindonald <john.maindonald@anu.edu.au>
>> Cc: r-devel@stat.math.ethz.ch
>> Subject: Re: [Rd] Enhanced version of plot.lm()
>>
>>
>> On 24 Apr 2005, at 05:37, John Maindonald wrote:
>>

    >>> I'd not like to lose the signs of the residuals. Also, as
    >>> plots 1-3 focus on residuals, there is less of a mental
    >>> leap in moving to residuals vs leverage; residuals vs
    >>> leverage/(1-leverage) would also be in the same spirit.

>>
>> Yes, I know what you mean. Mental leaps are a matter of
>> taste...pitfalls, etc, come to mind.
>>
    >>> 
    >>> Maybe, one way or another, both plots (residuals vs
    >>> a function of leverage, and the plot from Hinkley et al)
    >>> should go in.  The easiest way to do this is to add a
    >>> further which=6.  I will do this if the consensus is that
    >>> this is the right way to go.  In any case, I'll add the
    >>> Hinkley et al reference (author of the contribution that
    >>> includes p.74?) to the draft help page.

>>
>> Sorry, I should have given the full reference, which (in BibTeX format
>> from CIS) is
>>
>> @inproceedings{Firt:gene:1991,
>> author = {Firth, D.},
>> title = {Generalized Linear Models},
>> year = {1991},
>> booktitle = {Statistical Theory and Modelling. In Honour of Sir
>> David Cox, FRS},
>> editor = {Hinkley, D. V. and Reid, N. and Snell, E. J.},
>> publisher = {Chapman \& Hall Ltd},
>> pages = {55--82},
>> keywords = {Analysis of deviance; Likelihood}
>> }
>>
>> David
>>
    JMd> John Maindonald             email: john.maindonald@anu.edu.au
    JMd> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
    JMd> Centre for Bioinformation Science, Room 1194,
    JMd> John Dedman Mathematical Sciences Building (Building 27)
    JMd> Australian National University, Canberra ACT 0200.

    JMd> ______________________________________________
    JMd> R-devel@stat.math.ethz.ch mailing list     JMd> https://stat.ethz.ch/mailman/listinfo/r-devel

>>>>> "JMd" == John Maindonald <john.maindonald@anu.edu.au> >>>>> on Tue, 26 Apr 2005 15:44:26 +1000 writes:

    JMd> The web page
    JMd> http://wwwmaths.anu.edu.au/~johnm/r/plot-lm/ now
    JMd> includes files: plot.lm.RData: Image for file for
    JMd> plot6.lm, a version of plot.lm in which David Firth's
    JMd> Cook's distance vs leverage/(1-leverage) plot is plot
    JMd> 6.  The tick labels are in units of leverage, and the
    JMd> contour labels are in units of absolute values of the
    JMd> standardized residual.

    JMd> plot6.lm.Rd file: A matching help file

    JMd> Comments will be welcome.

    JMd> Another issue, discussed recently on r-help, is that
    JMd> when the model formula is long, the default
    JMd> sub.caption=deparse(x$call) is broken into multiple
    JMd> text elements and overwrites.  The only clean and
    JMd> simple way that I can see to handle is to set a default
    JMd> that tests whether the formula is broken into multiple
    JMd> text elements, and if it is then omit it.  Users can
    JMd> then use their own imaginative skills, and such
    JMd> suggestions as have been made on r-help, to construct
    JMd> whatever form of labeling best suits their case, their
    JMd> imaginative skills and their coding skills.

    JMd> John Maindonald.

    JMd> On 25 Apr 2005, at 8:00 PM, David Firth wrote:

>> From: David Firth <d.firth@warwick.ac.uk> Date: 24 April
>> 2005 10:23:51 PM To: John Maindonald
>> <john.maindonald@anu.edu.au> Cc:
>> r-devel@stat.math.ethz.ch Subject: Re: [Rd] Enhanced
>> version of plot.lm()
>>
>>
>> On 24 Apr 2005, at 05:37, John Maindonald wrote:
>>

    >>> I'd not like to lose the signs of the residuals. Also,
    >>> as plots 1-3 focus on residuals, there is less of a
    >>> mental leap in moving to residuals vs leverage;
    >>> residuals vs leverage/(1-leverage) would also be in the
    >>> same spirit.

>> Yes, I know what you mean. Mental leaps are a matter of
>> taste...pitfalls, etc, come to mind.
>>
    >>>  Maybe, one way or another, both plots (residuals vs a
    >>> function of leverage, and the plot from Hinkley et al)
    >>> should go in.  The easiest way to do this is to add a
    >>> further which=6.  I will do this if the consensus is
    >>> that this is the right way to go.  In any case, I'll add
    >>> the Hinkley et al reference (author of the contribution
    >>> that includes p.74?) to the draft help page.

>> Sorry, I should have given the full reference, which (in
>> BibTeX format from CIS) is
>>
>> @inproceedings{Firt:gene:1991, author = {Firth, D.},
>> title = {Generalized Linear Models}, year = {1991},
>> booktitle = {Statistical Theory and Modelling. In Honour
>> of Sir David Cox, FRS}, editor = {Hinkley, D. V. and
>> Reid, N. and Snell, E. J.}, publisher = {Chapman \& Hall
>> Ltd}, pages = {55--82}, keywords = {Analysis of deviance;
>> Likelihood} }
>>
>> David
>>
    JMd> John Maindonald email: john.maindonald@anu.edu.au phone
    JMd> : +61 2 (6125)3473 fax : +61 2(6125)5549 Centre for
    JMd> Bioinformation Science, Room 1194, John Dedman
    JMd> Mathematical Sciences Building (Building 27) Australian
    JMd> National University, Canberra ACT 0200.

    JMd> ______________________________________________
    JMd> R-devel@stat.math.ethz.ch mailing list     JMd> https://stat.ethz.ch/mailman/listinfo/r-devel

R-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Tue Apr 26 20:32:22 2005

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