R devel - Mar 2007 - Wishlist: Make screeplot() a generic (PR#9541)

Full_Name: Gavin Simpson
Version: 2.5.0
OS: Linux (FC5)
Submission from: (NULL) (128.40.33.76)


Screeplots are a common plot-type used to interpret the results of various
ordination methods and other techniques. A number of packages include ordination
techniques not included in a standard R installation. screeplot() works for
princomp and prcomp objects, but not for these other techniques as it was not
designed to do so. The current situation means, for example, that I have called
a function Screeplot() in one of my packages, but it would be easier for users
if they only had to remember to use screeplot() to generate a screeplot.

I would like to request that screeplot be made generic and methods for prcomp
and princomp added to R devel. This way, package authors can provide screeplot
methods for their functions as appropriate.

I have taken a look at the sources for R devel (from the SVN repository) in file
princomp-add.R and prcomp.R and it looks a relatively simple change to make
screeplot generic.

I would be happy to provide patches and documentation if R Core were interested
in making this change - I haven't done this yet as I don't want to spend
time
doing something that might not be acceptable to R core in general.

Many thanks,

G

Dear List

Having not received any comments for or against my proposal to make
screeplot() a generic function, I found some time to make the relevant
changes to the svn trunk repository (revision 40848).

Please find attached a patch against the R svn trunk sources including
changes to the relevant help files and NAMESPACE. This builds and passes
make check-devel out of the box on my FC4 machine.

I took the option of making the default method for screeplot the
existing function and the plot methods for princomp and prcomp both call
screeplot.default directly. This, I hope, preserves the current
behaviour and should be backwards compatible with
code/packages/examples/docs that use these functions.

One alternative would be to have explicit methods for classes "prcomp"
and "princomp" that extract the relevant variances and pass on to
screeplot.default for plotting. If this is preferred I can provide a
patch for this scenario for consideration?

All the best,

Gav

On Fri, 2007-03-02 at 17:53 +0100, gavin.simpson at ucl.ac.uk
wrote:
> Full_Name: Gavin Simpson
> Version: 2.5.0
> OS: Linux (FC5)
> Submission from: (NULL) (128.40.33.76)
> 
> 
> Screeplots are a common plot-type used to interpret the results of various
> ordination methods and other techniques. A number of packages include
ordination
> techniques not included in a standard R installation. screeplot() works for
> princomp and prcomp objects, but not for these other techniques as it was
not
> designed to do so. The current situation means, for example, that I have
called
> a function Screeplot() in one of my packages, but it would be easier for
users
> if they only had to remember to use screeplot() to generate a screeplot.
> 
> I would like to request that screeplot be made generic and methods for
prcomp
> and princomp added to R devel. This way, package authors can provide
screeplot
> methods for their functions as appropriate.
> 
> I have taken a look at the sources for R devel (from the SVN repository) in
file
> princomp-add.R and prcomp.R and it looks a relatively simple change to make
> screeplot generic.
> 
> I would be happy to provide patches and documentation if R Core were
interested
> in making this change - I haven't done this yet as I don't want to
spend time
> doing something that might not be acceptable to R core in general.
> 
> Many thanks,
> 
> G
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Gavin Simpson                     [t] +44 (0)20 7679 0522
ECRC                              [f] +44 (0)20 7679 0565
UCL Department of Geography
Pearson Building                  [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street
London, UK                        [w] http://www.ucl.ac.uk/~ucfagls/
WC1E 6BT                          [w] http://www.freshwaters.org.uk/
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>>>>> "GS" == Gavin Simpson <gavin.simpson at
ucl.ac.uk>
>>>>>     on Sat, 17 Mar 2007 13:02:29 +0000 writes:
    GS> Dear List
    GS> Having not received any comments for or against my proposal to make
    GS> screeplot() a generic function, I found some time to make the
relevant
    GS> changes to the svn trunk repository (revision 40848).

    GS> Please find attached a patch against the R svn trunk sources
including
    GS> changes to the relevant help files and NAMESPACE. This builds and
passes
    GS> make check-devel out of the box on my FC4 machine.

also for me;
thank you Gavin!

    GS> I took the option of making the default method for screeplot the
    GS> existing function and the plot methods for princomp and prcomp both
call
    GS> screeplot.default directly. This, I hope, preserves the current
    GS> behaviour and should be backwards compatible with
    GS> code/packages/examples/docs that use these functions.

[[it is still a matter of taste if  screeplot.default should be
  called explicitly, but since this is in the same namespace, it
  works nicely and slightly more efficiently]]

I have committed your patches (+ a NEWS entry) as is, to be
there early enough before beta stage.



    GS> One alternative would be to have explicit methods for classes
"prcomp"
    GS> and "princomp" that extract the relevant variances and pass
on to
    GS> screeplot.default for plotting. If this is preferred I can provide a
    GS> patch for this scenario for consideration?

I'd prefer it in general, but not in this case where the plot.*
method for these already use screeplot();  still another matter
of taste.

Thanks for your contribution.

Martin