R help - Aug 2003 - Cook-distance-type plot (vertical bars)

Hi,

Figure 13 of Emmanuel Paradis's "R for Beginners" was produced by
termplot
working on an aov object. The lower right-hand plot is labelled "Cook's
distance plot", and I'd really like to produce a similar type of
figure,
but in a totally different context. (I'm not even sure what this kind of 
figure is called, perhaps an "impulse plot", where instead of a point
at
(x,y), there's a vertical bar running from the x-axis up to where the point 
would be).

Can anyone give me pointers on where to look for more info. I've had a look 
in the places I could think of (plot.lm.R, termplot.R, plot.R, aov.R), and 
couldn't find anything. Maybe I overlooked it?

Thanks

-Frank Gibbons

PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons

On Thu, 28 Aug 2003, Frank Gibbons wrote:
> Hi,
> 
> Figure 13 of Emmanuel Paradis's "R for Beginners" was
produced by termplot
> working on an aov object. The lower right-hand plot is labelled
"Cook's
> distance plot", and I'd really like to produce a similar type of
figure,
> but in a totally different context. (I'm not even sure what this kind
of
> figure is called, perhaps an "impulse plot", where instead of a
point at
> (x,y), there's a vertical bar running from the x-axis up to where the
point
> would be).
Often called an `index plot'.  It's done by plot(type="h").  R
seems to
think that is `histogram-like', but the notation comes from S which calls
it `high-density lines'.  I've never found either intuitive notation.
> Can anyone give me pointers on where to look for more info. I've had a
look
> in the places I could think of (plot.lm.R, termplot.R, plot.R, aov.R), and 
> couldn't find anything. Maybe I overlooked it?
I suspect it was done by plot.lm(which=4), which does an index plot of 
Cook's distance.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

On Thu, 28 Aug 2003, Frank Gibbons wrote:
> Hi,
>
> Figure 13 of Emmanuel Paradis's "R for Beginners" was
produced by termplot
> working on an aov object.
No, it was produced by plot() working on a aov object, as its caption
indicates.  The termplot() is Figure 14.
>		 The lower right-hand plot is labelled "Cook's
> distance plot", and I'd really like to produce a similar type of
figure,
> but in a totally different context. (I'm not even sure what this kind
of
> figure is called, perhaps an "impulse plot", where instead of a
point at
> (x,y), there's a vertical bar running from the x-axis up to where the
point
> would be).
It's called a high-density plot, and you get it by specifying
type="h" in
a plot() command.  It's mentioned on page 31 of `R for beginners'

It is in the code for plot.lm, where you say you also looked: the cook's
distance plot is created with
    plot(cook, type = "h", ylim = c(0, ymx), main = main,
         xlab = "Obs. number", ylab = "Cook's distance",
...)


	-thomas

Thanks to all who responded, and so promptly too: it works exactly as you 
describe.
> >
> > Figure 13 of Emmanuel Paradis's "R for Beginners" was
produced by termplot
> > working on an aov object.
>
>No, it was produced by plot() working on a aov object, as its caption
>indicates.  The termplot() is Figure 14.
Thomas Lumley is quite right, it's produced by plot() (not termplot()), and 
it is mentioned on p31 of "R for beginners". My mistake.

In the interest of self education, is there a more comprehensive source for 
plot-types that I should read? Ideally, this would be something with lots 
of figures, so that I could browse the figures to find what I want to do, 
and then look up how to do it. "R for Beginners" goes some way along
this
path, but perhaps there's something more comprehensive?

Thanks again,

-Frank

PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons

I'm (relatively) new to R myself, and recently found 
the documentation by Dr. William Cleveland et al at

http://cm.bell-labs.com/cm/ms/departments/sia/project/trellis/
http://cm.bell-labs.com/cm/ms/departments/sia/project/trellis/software.writi
ng.html

It has been helpful, and covers S/Splus trellis graphics.  In R, the
equivalent is known as "lattice" graphics, and the syntax is
virtually identical.  Earlier today, Dr. Peter Dunn posted a 
notice to the R listserv announcing a workshop in Australia being
led by Dr. John Maindonald... in that announcement, you will find

"...John Maindonald, the author of the forthcoming book 'Data Analysis 
and Graphics Using R: An Example-Based Approach' (with John Braun)..."

so apparently there is a forthcoming book detailing the graphical
capabilities of R.  I'm eagerly awaiting the opportunity to buy it
and digest its contents!  Until then, I think the links to the 
.ps and .pdf files above should serve well.


Best wishes,
  david paul


P.S. - You should keep in mind that there are two classes of 
graphical functions in S/Splus/R: "regular" functions and
"trellis/lattice" functions.  They operate very differently.
After using a few of each, I must say that I am very impressed
with the power and flexibility of the trellis/lattice 
plotting functions.



-----Original Message-----
From: Frank Gibbons [mailto:fgibbons at hms.harvard.edu] 
Sent: Thursday, August 28, 2003 1:53 PM
To: R users
Subject: Re: [R] Cook-distance-type plot (vertical bars)


Thanks to all who responded, and so promptly too: it works exactly as you 
describe.
> >
> > Figure 13 of Emmanuel Paradis's "R for Beginners" was
produced by
> > termplot working on an aov object.
>
>No, it was produced by plot() working on a aov object, as its caption 
>indicates.  The termplot() is Figure 14.
Thomas Lumley is quite right, it's produced by plot() (not termplot()), and 
it is mentioned on p31 of "R for beginners". My mistake.

In the interest of self education, is there a more comprehensive source for 
plot-types that I should read? Ideally, this would be something with lots 
of figures, so that I could browse the figures to find what I want to do, 
and then look up how to do it. "R for Beginners" goes some way along
this
path, but perhaps there's something more comprehensive?

Thanks again,

-Frank

PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555       Fax: 
617-432-3557       http://llama.med.harvard.edu/~fgibbons

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