Re: [Rd] problem using model.frame()

From: Gavin Simpson <gavin.simpson_at_ucl.ac.uk>
Date: Thu 18 Aug 2005 - 13:22:59 GMT

On Thu, 2005-08-18 at 09:00 -0400, Gabor Grothendieck wrote:
> I think this one is a hard call. Designing software is a
> series of tradeoffs. Its nice to maintain consistency with
> the R base, but in case of extensions (rather than changing
> behavior) as in this case, the argument against the change
> carries less weight.
>
> The main problems with extensions are (1) that one has to
> remember which functions/packages have which extensions if
> one is to use them and (2) they can interfere with other
> future extensions.
>
> On the other hand, if one is using a particular package a
> lot then convenience features like this may be attractive.
> Also, packages are where authors have the freedom to try out
> new ideas and new functionality without being constrained.
>
> Perhaps, if the extension in question is added there could be
> a warning in the help file that this is a convenience feature
> of this particular package and is not generally available
> throughout R.

Thanks again Gabor for another useful contribution to this debate. Also thanks to Martin, Gabor and Jari for their comments, ideas, suggestions and viewpoints.

I still like y1 ~ y2 (both data frames), but during my bike ride to work this morning I considered both sides of the argument and my position has moved towards the R way of doing things - far be it for little old me to go against years of S-formula tradition. So I'll revert the code back to accepting y1 ~ ., data = y2 and leave it to throw an error for the rhs being a data frame case.

Once again, thank you for helping me work through this dilemma.

All the best,

Gav

> On 8/18/05, Gavin Simpson <gavin.simpson@ucl.ac.uk> wrote:
> > On Thu, 2005-08-18 at 07:57 +0300, Jari Oksanen wrote:
> > > On 18 Aug 2005, at 1:49, Gavin Simpson wrote:
> > >
> > > > On Wed, 2005-08-17 at 20:24 +0200, Martin Maechler wrote:
> > > >>>>>>> "GS" == Gavin Simpson <gavin.simpson@ucl.ac.uk>

> > > >>>>>>> on Tue, 16 Aug 2005 18:44:23 +0100 writes:
> > > >>
> > > >> GS> On Tue, 2005-08-16 at 12:35 -0400, Gabor Grothendieck
> > > >> GS> wrote:
> > > >>>> On 8/16/05, Gavin Simpson <gavin.simpson@ucl.ac.uk>
> > > >>>> wrote: > On Tue, 2005-08-16 at 11:25 -0400, Gabor
> > > >>>> Grothendieck wrote: > > It can handle data frames like
> > > >>>> this:
> > > >>>>>>
> > > >>>>>> model.frame(y1) > > or > > model.frame(~., y1)
> > > >>>>>
> > > >>>>> Thanks Gabor,
> > > >>>>>
> > > >>>>> Yes, I know that works, but I want the function
> > > >>>> coca.formula to accept a > formula like this y2 ~ y1,
> > > >>>> with both y1 and y2 being data frames. It is
> > > >>>>
> > > >>>> The expressions I gave work generally (i.e. lm, glm,
> > > >>>> ...), not just in model.matrix, so would it be ok if the
> > > >>>> user just does this?
> > > >>>>
> > > >>>> yourfunction(y2 ~., y1)
> > > >>
> > > >> GS> Thanks again Gabor for your comments,
> > > >>
> > > >> GS> I'd prefer the y1 ~ y2 as data frames - as this is the
> > > >> GS> most natural way of doing things. I'd like to have (y2
> > > >> GS> ~., y1) as well, and (y2 ~ spp1 + spp2 + spp3, y1) also
> > > >> GS> work - silently without any trouble.
> > > >>
> > > >> I'm sorry, Gavin, I tend to disagree quite a bit.
> > > >>
> > > >> The formula notation has quite a history in the S language, and
> > > >> AFAIK never was the idea to use data.frames as formula
> > > >> components, but rather as "environments" in which formula
> > > >> components are looked up --- exactly as Gabor has explained.
> > > >
> > > > Hi Martin, thanks for your comments,
> > > >
> > > > But then one could have a matrix of variables on the rhs of the formula
> > > > and it would work - whether this is a documented feature or un-intended
> > > > side-effect of matrices being stored as vectors with dims, I don't
> > > > know.
> > > >
> > > > And whilst the formula may have a long history, a number of packages
> > > > have extended the interface to implement a specific feature, which
> > > > don't
> > > > work with standard functions like lm, glm and friends. I don't see how
> > > > what I wanted to achieve is greatly different to that or using a
> > > > matrix.
> > > >
> > > >> To break with such a deeply rooted principle,
> > > >> you should have very very good reasons, because you're breaking
> > > >> the concepts on which all other uses of formulae are based.
> > > >> And this would potentially lead to much confusion of your users,
> > > >> at least in the way they should learn to think about what
> > > >> formulae mean.
> > > >
> > > > In the end I managed to treat y1 ~ y2 (both data frames) as a special
> > > > case, which allows the existing formula notation to work as well, so I
> > > > can use y1 ~ y2, y1 ~ ., data = y2, or y1 ~ var + var2, data = y2. This
> > > > is what I wanted all along, to extend my interface (not do anything to
> > > > R's formulae), but to also work in the traditional sense.
> > > >
> > > > The model I am writing code for really is modelling the relationship
> > > > between two matrices of data. In one version of the method, there is
> > > > real equivalence between both sides of the formula so it would seem odd
> > > > to treat the two sides of the formula differently. At least to me ;-)
> > >
> > > It seems that I may be responsible for one of these extensions (lhs as
> > > a data.frame in cca and rda in vegan package). There the response (lhs)
> > > is multivariate or a multispecies community, and you must take that as
> > > a whole without manipulation (and if you tried using VGAM you see there
> > > really is painful to define lhs with, say, 127 elements).
> >
> > Hi Jari,
> >
> > Thanks for reminding me about this - I'd forgotten about not normally
> > being able to have a data.frame on the lhs of the formula either - I'm
> > surprised no-one pulled me up on that one before, either ;-)
> >
> > I guess what I'm proposing is really pushing the formula representation
> > too far for some people. I'm coming round to the y1 ~ ., data = y2 way
> > of doing things - still prefer y1 ~ y2 though ;-)
> >
> > Also, both y1 and y2 are community matrices (i.e. both have many, many
> > species, aka variables for the non-community ecologists reading this).
> > I'm not sure that it makes sense to treat the two sides differently. In
> > the predictive co-correspondence mode (the default), multivariate pls is
> > used to regress one matrix on another, with the number of pls components
> > being chosen by cross-validation or a permutation test.
> >
> > > However, in
> > > general you shouldn't use models where you use all the 'explanatory'
> > > variables (rhs) that yo happen to have by accident. So much bad science
> > > has been created with that approach even in your field, Gav.
> >
> > Well, I agree with you there...
> >
> > > The whole
> > > idea of formula is the ability to choose from candidate variables. That
> > > is: to build a model. Therefore you have one-sided formulae in prcomp()
> > > and princomp(): you can say prcomp(~ x1 + log(x2) +x4, data) or
> > > prcomp(~ . - x3, data). I think you should try to keep it so. Do
> > > instead like Gabor suggested: you could have a function coca.default or
> > > coca.matrix with interface:
> > >
> > > coca.matrix(matx, maty, matz) -- or you can name this as coca.default.
> > >
> > > and coca.formula which essentially parses your formula and returns a
> > > list of matrices you need:
> > >
> > > coca.formula <- function(formula, data)
> > > {
> > > matricesout <- parsemyformula(formula, data)
> > > coca(matricesout$matx, matricesout$maty, matricesoutz)
> > > }
> > > Then you need the generic: coca <- function(...) UseMethod("coca") and
> > > it's done (but fails in R CMD check unless you add "..." in all
> > > specific functions...). The real work is always done in coca.matrix (or
> > > coca.default), and the others just chew your data into suitable form
> > > for your workhorse.
> > >
> > > If then somebody thinks that they need all possible variables as
> > > 'explanatory' variables (or perhaps constraints in your case), they
> > > just call the function as
> > >
> > > coca(matx, maty, matz)
> >
> > My functions are already generic with coca.default and coca.formula. The
> > issue with matrices/data.frames was only a problem in the formula
> > interface.
> >
> > > And if you have coca.data.frame they don't need 'quacking' with extra
> > > steps:
> > >
> > > coca.data.frame <- function(dfx, dfy dfz) coca(as.matrix(dfx),
> > > as.matrix(dfy), as.matrix(dfz)).
> > >
> > > This you call as coca(dfx, dfy, dfz) and there you go.
> > >
> > > The essential feature in formula is the ability to define the model.
> > > Don't give it away.
> >
> > I think the point I'm trying to make is that I don't think what I'm
> > trying to do is any different than doing lm(y ~ x, data), (where y, x
> > are vectors) - it is just that my x and y happen to be multivariate. I
> > think it is easier to think of each community as a single entity in this
> > regard - the relationship *is* between community 1 and community 2, not
> > parts of community 2, or some parsimonious model of community 2 - but
> > that might just be semantics - unlike your cca/rda functions which
> > really are a (weighted) multivariate multiple regression. Happy to be
> > convinced otherwise though.
> >
> > Also, it is worth re-iterating that I haven't broken the traditional way
> > of working with formulae with my function - you can still do y1 ~ .,
> > data = y2, or y1 ~ spp1 + spp2 + spp3, data = y2, for maximum
> > flexibility. All I wanted (and worked out how) to do was treat the rhs
> > in a special way if it were a data frame, just like Jari treats a
> > data.frame on the lhs of formulae in package vegan as a special case.
> >
> > Thanks everyone for your ideas and comments - lots of food for thought.
> > I wavering between both camps on this - still time to be convinced and
> > change it before I finish the package.
> >
> > All the best,
> >
> > G
> >
> > >
> > > cheers, jazza
> > > --
> > > Jari Oksanen, Oulu, Finland
> > >
> > --
> > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
> > Gavin Simpson [T] +44 (0)20 7679 5522
> > ENSIS Research Fellow [F] +44 (0)20 7679 7565
> > ENSIS Ltd. & ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk
> > UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/
> > 26 Bedford Way [W] http://www.ucl.ac.uk/~ucfagls/
> > London. WC1H 0AP.
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> >
> > ______________________________________________
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> >

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Gavin Simpson                     [T] +44 (0)20 7679 5522
ENSIS Research Fellow             [F] +44 (0)20 7679 7565
ENSIS Ltd. & ECRC                 [E] gavin.simpsonATNOSPAMucl.ac.uk
UCL Department of Geography       [W] http://www.ucl.ac.uk/~ucfagls/cv/
26 Bedford Way                    [W] http://www.ucl.ac.uk/~ucfagls/
London.  WC1H 0AP.
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Received on Fri Aug 19 20:36:26 2005

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