[Rd] Enhanced version of plot.lm()
Martin Maechler
maechler at stat.math.ethz.ch
Tue Apr 26 12:13:38 CEST 2005
>>>>> "JMd" == John Maindonald <john.maindonald at 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 at warwick.ac.uk>
>> Date: 24 April 2005 10:23:51 PM
>> To: John Maindonald <john.maindonald at anu.edu.au>
>> Cc: r-devel at 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 at 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 at stat.math.ethz.ch mailing list
JMd> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>> "JMd" == John Maindonald <john.maindonald at 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 at warwick.ac.uk> Date: 24 April
>> 2005 10:23:51 PM To: John Maindonald
>> <john.maindonald at anu.edu.au> Cc:
>> r-devel at 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 at 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 at stat.math.ethz.ch mailing list
JMd> https://stat.ethz.ch/mailman/listinfo/r-devel
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