From gavin.simpson at ucl.ac.uk  Mon Jul 16 16:21:44 2007
From: gavin.simpson at ucl.ac.uk (Gavin Simpson)
Date: Mon, 16 Jul 2007 15:21:44 +0100
Subject: [Rd] formula(CO2)
In-Reply-To: <XFMail.070716145756.ted.harding@nessie.mcc.ac.uk>
References: <XFMail.070716145756.ted.harding@nessie.mcc.ac.uk>
Message-ID: <1184595704.32447.66.camel@gsimpson.geog.ucl.ac.uk>

On Mon, 2007-07-16 at 14:57 +0100, ted.harding at nessie.mcc.ac.uk wrote:
> On 16-Jul-07 13:28:50, Gabor Grothendieck wrote:
> > The formula attribute of the builtin CO2 dataset seems a bit strange:
> > 
> >> formula(CO2)
> > Plant ~ Type + Treatment + conc + uptake
> > 
> > What is one supposed to do with that?  Certainly its not suitable
> > for input to lm and none of the examples in ?CO2 use the above.
> 
> I think one is supposed to ignore it! (Or maybe be inspired to
> write a mail to the list ... ).
> 
> I couldn't find anything that looked like the above formula from
> str(CO2). But I did spot that the order of terms in the formula:
> Plant, Type, treatment, conc, uptake, is the same as the order
> of the "columns" in the dataframe.

CO2 is a groupedData object not a data.frame per se.

> class(CO2)
[1] "nfnGroupedData" "nfGroupedData"  "groupedData"    "data.frame"

What Gabor saw was the result of formula.data.frame being applied to
CO2, which, as you surmise Ted, is being produced from the columns of
CO2.

> formula(CO2)
Plant ~ Type + Treatment + conc + uptake
> stats:::formula.data.frame(CO2)
Plant ~ Type + Treatment + conc + uptake

But if we load nlme, we see that now (via a groupedData method for
formula) a more useful formula is displayed.

> require(nlme)
Loading required package: nlme
[1] TRUE
> formula(CO2)
uptake ~ conc | Plant

as this can then be directly used in lme

> lme(CO2)
Linear mixed-effects model fit by REML
  Data: CO2
  Log-restricted-likelihood: -283.1447
  Fixed: uptake ~ conc
(Intercept)        conc
19.50028981  0.01773059
<snip />

But like Gabor, I'm struggling to see where this [formula(data.frame)]
might be used (useful)?

G
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[Rd] formula(CO2)
Gavin Simpson