From john.maindonald at anu.edu.au  Sun Sep 18 04:28:41 2005
From: john.maindonald at anu.edu.au (John Maindonald)
Date: Sun, 18 Sep 2005 12:28:41 +1000
Subject: [Rd] plot(<lm>): new behavior in R-2.2.0 alpha
In-Reply-To: <17196.13904.78468.758438@deb8.math.ethz.ch>
References: <17190.57225.254938.977464@stat.math.ethz.ch>
	<17194.30238.436418.752419@stat.math.ethz.ch>
	<17196.13904.78468.758438@deb8.math.ethz.ch>
Message-ID: <A6A9F6A1-5E67-4D50-9DF9-DCBD429739C4@anu.edu.au>

Martin -
Thanks for your efforts in initiating and managing this
discussion.

As for the issue of deprecating the plot.lm() pictures in
the published books, surely this will have great benefits
for the authors. It will help them to sell the new editions
of their books that will in due course appear replete with
the new plots!

For 2.2.0, I have nothing more to add to the comments
others have made,  I hope we can in due course agree,
as a minimum, to put some version of John Fox's vif(),
and something akin to Werner Stahl's smooths for up to
20 simulated data sets, into 2.3.0
John Maindonald.

On 18 Sep 2005, at 1:29 AM, Martin Maechler wrote:

>>>>>> "Wst" == Werner Stahel <stahel at stat.math.ethz.ch>
>>>>>>     on Fri, 16 Sep 2005 09:37:02 +0200 writes:
>>>>>>
>
>     Wst> Dear Martin, dear Johns Thanks for including me into
>     Wst> your discussion.
>
>     Wst> I am a strong supporter of "Residuals vs. Hii"
>
>
>>>> One remaining problem I'd like to address is the
>>>> "balanced AOV" situation, ...
>>>>
>
>     Wst> In order to keep the plots consistent, I suggest to
>     Wst> draw a histogram. Other alternatives will or can be
>     Wst> interesting in the general case and therefore are not a
>     Wst> suitable substitute for this plot.
>
> hmm, but all other 3 default plots have
>  (standardized / sqrt) residuals  on the y-axis.
> I'd very much like to keep that for any forth plot.
> So would we want a horizontal histogram?  And do we really want
> a histogram when we've already got the QQ plot?
>
> We need a decent proposal for a 4th plot
> {instead of  R_i vs h_ii  , when  h_ii are constant}
> REAL SOON NOW  since it's feature
> freeze on Monday.
> Of course the current state can be declared a bug and still be
> fixed but that was not the intention...
>
> Also, there are now at least 2 book authors among R-core (and
> more book authors more generally!) in whose books there are
> pictures with the "old-default" 4th plot.
> So I'd like to have convincing reasons for ``deprecating'' all
> the plot.lm() pictures in the published books.
>
> At the moment, I'd still  go for
>
>          R_i  vs i
> or  sqrt|R_i| vs i  -- possibly with type = 'h'
>
> which could be used to "check" an important kind of "temporal"
> auto-correlation.
>
> the latter, because in a 2 x 2 plot arrangement, this gives the
> same y-axis as default plot 3.
>
>     Wst> ........................
>
>     Wst> Back to currently available methods:
>
>     Wst> John Maindonald discusses different contours. I like
>     Wst> the implementation I get currently in R-devel: contours
>     Wst> of Cook's distances, since they are popular and we can
>     Wst> then argue that the plot of D_i vs. i is no more
>     Wst> needed.
>
> what about John's proposal of different contour levels than
> c(0.5, 1)  -- note that these *have* been added as arguments to
> plot.lm() a user could modify.
>
>     Wst> For most plots, I like to see a smoother along with the
>     Wst> points.  I suggest to add the option to include
>     Wst> smoothers, not only as an argument to plot.lm, but even
>     Wst> as an option().  I have heared of the intense
>     Wst> discussions about options().  With Martin, we arrived
>     Wst> at the conclusion that options() should never influence
>     Wst> calculations and results, but is suitable to adjust
>     Wst> outputs (numerical: digits=, graphical: smooth=) to the
>     Wst> user's taste.
>
> {and John Fox agreed, `in general'}
>
> That could be a possibility, for 2.2.0  only applied to
> plot.lm() in any case, where plot.lm() would get a new argument
>
>     add.smooth = getOption("plot.add.smooth")
>
> What do people think about the name?
> it would ``stick with us'' -- so we better choose it well..
>
>
>>>> (4) Are there other diagnostics that ought to be
>>>> included in stats? (perhaps in a function other than
>>>> plot.lm(), which risks being overloaded).  One strong
>>>> claiment is vif() (variance inflation factor),
>>>>
>
>    ...................
>    ...................
>    ...................
>
>
>     Wst> As we focus on plots, my plot method includes the
>     Wst> option (default) to add smooths for 20 simulated
>     Wst> datasets (according to the fitted model).
>
> this and others are really nice.
>
> However not for R 2.2.x in any case.
>
> I agree that one should rather provide `single-plot'
> functions and have plot.lm() just call a few of them; instead of
> having things all part of plot.lm().
> There's the slight advantage that you can guarantee some
> consistence (e.g. in the definition of "standardized residuals")
> and save some computations when have everything in one function,
> but consistency should be possible otherwise as well...
> Anyway this is for 2.3.0 or later.
>
> Martin
>



[Rd] plot(<lm>): new behavior in R-2.2.0 alpha
John Maindonald