[Rd] plot functions, formula interfaces and NAs

Prof Brian Ripley ripley at stats.ox.ac.uk
Mon May 3 15:30:00 CEST 2004

As we have seen from PR#6846, we don't document much what happens to NAs
in plot functions.  The formula interfaces do seem to be a bit of a mess,
as they call model.frame and so some (but only some) of them pick up the
options() setting of na.action.  This means that for example

pairs(~ x +y + z)  and pairs(cbind(x, y, z))

may well treat NAs differently, depending on the value of 

However, the formula methods for plot, lines and points do ignore
getOption("na.action") and use na.action=NULL (or equivalently, na.pass).

I believe no function should be using getOption("na.action") without a 
means to override it, and thus the formula methods of

boxplot, mosaicplot and  pairs

should get an na.action argument.  Further, since in all cases the 
non-formula methods do handle missing values, I think the default should 
be na.pass.  That is a change in behaviour, but the existing behaviour is 

The proposal is to document this for 1.9.1 and change it for 2.0.0.

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

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