[R] *not* using attach() *but* in one case ....

[Duncan Murdoch]

On 19/05/2011 10:34 AM, Liaw, Andy wrote:
> From: Prof Brian Ripley
> >
> >  Hmm, load() does have an 'envir' argument.  So you could simply use
> >  that and with() (which is pretty much what attach() does internally).
> >
> >  If people really wanted a lazy approach, with() could be extended to
> >  allow file names (as attach does).
>
> I'm not sure if laziness like this should be encouraged.
>
> If I may bring up another "black hole":  IMHO the formula interface
> allows too much flexibility (perhaps to allow some laziness?) that
> beginners and even non-beginners fall into its various traps a bit too
> often, and sometimes not even aware of it.  It would be great if there's
> a way to (optionally?) limit the scope of where a formula looks for
> variables.

I think there is:  put the variables in an environment that doesn't have 
parents covering everything visible, and use that as the environment of 
the formula.

For example, you could follow

x <- 1:10
y <- rnorm(10)
z <- rnorm(10)
f <- y ~ x + z

with

e <- new.env(parent=baseenv())
e$x <- x
e$y <- y
environment(f) <- e

and you'll get a failure with

lm(f)

because it can't find z.  Obviously this could be wrapped in a 
friendlier function if you really wanted it.

Duncan Murdoch



>
> Just my $0.02...
>
> Andy
>
> >  On Thu, 19 May 2011, Martin Maechler wrote:
> >
> >  >  [modified 'Subject' on purpose;
> >  >  Good mail readers will still thread correctly, using the
> >  'References'
> >  >  and 'In-Reply-To' headers, however, unfortunately,
> >  >  in my limited experience, good mail readers seem to
> >  disappear more and more ..
> >  >  ]
> >  >
> >  >>>>>>  Peter Ehlers<ehlers at ucalgary.ca>
> >  >>>>>>      on Tue, 17 May 2011 06:08:30 -0700 writes:
> >  >
> >  >     >  On 2011-05-17 02:22, Timothy Bates wrote:
> >  >     >>  Dear Bryony: the suggestion was not to change the name of
> >  >     >>  the data object, but to explicitly tell glm.nb what
> >  >     >>  dataset it should look in to find the variables you
> >  >     >>  mention in the formula.
> >  >     >>
> >  >     >>  so the salient difference is:
> >  >     >>
> >  >     >>  m1<- glm.nb(Cells ~ Cryogel*Day, data = side)
> >  >     >>
> >  >     >>  instead of
> >  >     >>
> >  >     >>  attach(side) m1<- glm.nb(Cells ~ Cryogel*Day)
> >  >     >>
> >  >     >>  This works for other functions also, but not uniformly as
> >  >     >>  yet (how I wish it did and I could say hist(x, data=side)
> >  >     >>  Instead of hist(side$x)
> >  >     >>
> >  >     >>  this inconsistency encourages the need for attach()
> >  >
> >  >     >  Only if the user hasn't yet been introduced to the with()
> >  >     >  function, which is linked to on the ?attach page.
> >  >
> >  >     >  Note also this sentence from the ?attach page:
> >  >     >  ".... attach can lead to confusion."
> >  >
> >  >     >  I can't remember the last time I needed attach().
> >  >     >  Peter Ehlers
> >  >
> >  >  Well, then you don't know  *THE ONE* case where modern users of
> >  >  R should use attach() ... as I have been teaching for a while,
> >  >  but seem not have got enought students listening ;-) ...
> >  >
> >  >   ---  Use it instead of load()  {for save()d R objects} ---
> >  >
> >  >  The advantage of attach() over load() there is that loaded
> >  >  objects (and there maye be a bunch!), are put into a separate
> >  >  place in the search path and will not accidentally overwrite
> >  >  objects in the global "workspace".
> >  >
> >  >  Of course, there are still quite a few situations {e.g. in
> >  >  typical BATCH use of R for simulations, or Sweaving, etc} where
> >  >  load() is good enough, and the extras of using attach() are not
> >  >  worth it.
> >  >
> >  >  But the unconditional  "do not use attach()"
> >  >  is not quite ok,
> >  >  at least not when you talk to non-beginners.
> >  >
> >  >  Martin Maechler, ETH Zurich
> >
> >  -- 
> >  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
> >
> >  ______________________________________________
> >  R-help at r-project.org mailing list
> >  https://stat.ethz.ch/mailman/listinfo/r-help
> >  PLEASE do read the posting guide
> >  http://www.R-project.org/posting-guide.html
> >  and provide commented, minimal, self-contained, reproducible code.
> >
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