[Rd] Proper way to define cbind, rbind for s4 classes in package
Michael Lawrence
lawrence.michael at gene.com
Mon Feb 9 23:38:29 CET 2015
Are you able to create a reproducible example, somehow?
Thanks,
Michael
On Mon, Feb 9, 2015 at 2:28 PM, Mario Annau <mario.annau at gmail.com> wrote:
> Hi Michael,
> I've tested your change in r67699 (using r67773) and the function now
> correctly dispatches to r/cbind2 within the R-session without
> bind_activation(TRUE). However, running unit tests using R CMD check I
> figured out that the same function call delegates to r/cbind.matrix
> (function uses S4 class as first- and matrix as second argument). Is
> this a bug and/or how can I get function dispatch right (to r/cbind2)
> for my test cases?
> best,
> mario
>
>
> Am 02/02/15 um 12:32 schrieb Martin Maechler:
> >>>>>> Michael Lawrence <lawrence.michael at gene.com>
> >>>>>> on Sun, 1 Feb 2015 19:23:06 -0800 writes:
> >
> > > I've implemented the proposed changes in
> > > R-devel. Minimally tested, so please try it. It should
> > > delegate to r/cbind2 when there is at least one S4
> > > argument and S3 dispatch fails (so you'll probably want to
> > > add an S3 method for your class to introduce a conflict,
> > > otherwise it will dispatch to cbind.data.frame if one of
> > > the args is a data.frame). There may no longer be a need
> > > for cBind() and rBind().
> >
> > > Michael
> >
> > This sounds great! Thank you very much, Michael!
> > :-) :-)
> >
> > ... but .... :-( experiments with the Matrix package (and R
> > devel with your change), show a remaining buglet with treating of
> dimnames :
> >
> > > M1 <- Matrix(m1 <- matrix(1:12, 3,4))
> > > cbind(m1, MM = -1)
> > MM
> > [1,] 1 4 7 10 -1
> > [2,] 2 5 8 11 -1
> > [3,] 3 6 9 12 -1
> > > cbind(M1, MM = -1) ## ---- notice the "..."
> > 3 x 5 Matrix of class "dgeMatrix"
> > ...
> > [1,] 1 4 7 10 -1
> > [2,] 2 5 8 11 -1
> > [3,] 3 6 9 12 -1
> > > rbind(R1 = 10:11, m1)
> > [,1] [,2] [,3] [,4]
> > R1 10 11 10 11
> > 1 4 7 10
> > 2 5 8 11
> > 3 6 9 12
> > > rbind(R1 = 10:11, M1) ## --- notice the 'deparse.level'
> > 4 x 4 Matrix of class "dgeMatrix"
> > [,1] [,2] [,3] [,4]
> > deparse.level 10 11 10 11
> > 1 4 7 10
> > 2 5 8 11
> > 3 6 9 12
> > >
> >
> > Also, it seems you are not observing the 'deparse.level'
> > argument at all:
> > Looking at the last three lines of the example in ?cbind,
> >
> > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 0) # middle 2
> rownames
> > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rownames
> (default)
> > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 2) # 4 rownames
> >
> > but using a Matrix matrix 'dd', we see that (row)names
> > construction needs to amended:
> >
> > > (dd <- Matrix(rbind(c(0:1,0,0))))
> > 1 x 4 sparse Matrix of class "dgCMatrix"
> >
> > [1,] . 1 . .
> >
> > > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 0) # middle 2
> rownames
> > 4 x 4 sparse Matrix of class "dgCMatrix"
> >
> > deparse.level 1 2 3 4
> > c 2 2 2 2
> > a++ 10 10 10 10
> > . 1 . .
> > > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rownames
> (default)
> > 4 x 4 sparse Matrix of class "dgCMatrix"
> >
> > deparse.level 1 2 3 4
> > c 2 2 2 2
> > a++ 10 10 10 10
> > . 1 . .
> > > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 2) # 4 rownames
> > 4 x 4 sparse Matrix of class "dgCMatrix"
> >
> > deparse.level 1 2 3 4
> > c 2 2 2 2
> > a++ 10 10 10 10
> > . 1 . .
> > >
> >
> >
> >
> > > On Mon, Jan 26, 2015 at 3:55 AM, Martin Maechler <
> > > maechler at lynne.stat.math.ethz.ch> wrote:
> >
> > >> >>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>>
> > >> on Sat, 24 Jan 2015 06:39:37 -0800 writes:
> > >>
> > >> > On Sat, Jan 24, 2015 at 12:58 AM, Mario Annau >
> > >> <mario.annau at gmail.com> wrote: >> Hi all, this question
> > >> has already been posted on >> stackoverflow, however
> > >> without success, see also
> > >> >>
> > >>
> http://stackoverflow.com/questions/27886535/proper-way-to-use-cbind-rbind-with-s4-classes-in-package
> > >> .
> > >> >>
> > >> >> I have written a package using S4 classes and would
> > >> like >> to use the functions rbind, cbind with these
> > >> defined >> classes.
> > >> >>
> > >> >> Since it does not seem to be possible to define rbind
> > >> and >> cbind directly as S4 methods (see ?cBind) I
> > >> defined >> rbind2 and cbind2 instead:
> > >> >>
> > >>
> > >> > This needs some clarification. It certainly is possible
> > >> to > define cbind and rbind methods. The BiocGenerics
> > >> package > defines generics for those and many methods are
> > >> defined by > e.g. S4Vectors, IRanges, etc. The issue is
> > >> that dispatch > on "..." is singular, i.e., you can only
> > >> specify one class > that all args in "..." must share
> > >> (potentially through > inheritance).
> > >>
> > >> > Thus, trying to combine objects from a > different
> > >> hierarchy (or non-S4 objects) will not > work.
> > >>
> > >> Yes, indeed, that's the drawback
> > >>
> > >> I've been there almost surely before everyone else, with
> > >> the Matrix package... and I have been the author of
> > >> cbind2(), rbind2(), and of course, of cBind(), and
> > >> rBind().
> > >>
> > >> At the time when I introduced these, the above
> > >> possibility of writing S4 methods for '...' where not
> > >> yet part of R.
> > >>
> > >> > This has not been a huge problem for us in >
> > >> practice. For example, we have a DataFrame object that >
> > >> mimics data.frame. To cbind a data.frame with a
> > >> DataFrame, > the user can just call the DataFrame() >
> > >> constructor. rbind() between different data structures is
> > >> > much less common.
> > >>
> > >> well... yes and no. Think of using the Matrix package,
> > >> maybe with another package that defines another
> > >> generalized matrix class... It would be nice if things
> > >> worked automatically / perfectly there.
> > >>
> > >> > The cBind and rBind functions in Matrix (and the
> > >> r/cbind > that get installed by bind_activation, the code
> > >> is shared) > work by recursing, dropping the first
> > >> argument until two > are left, and then combining with
> > >> r/cbind2(). The Biobase > package uses a similar strategy
> > >> to mimic c() via its > non-standard combine()
> > >> generic. The nice thing about the > combine() approach is
> > >> the user entry point and the generic > are the same,
> > >> instead of having methods on rbind2() and > the user
> > >> calling rBind().
> > >>
> > >> > I would argue that bind_activation(TRUE) should be >
> > >> discouraged,
> > >>
> > >> Yes, you are right Michael; it should be discouraged at
> > >> least to be run in a *package*. One could think of its
> > >> use by an explicit user call.
> > >>
> > >> > because it replaces the native rbind and > cbind with
> > >> recursive variants that are going to cause > problems,
> > >> performance and otherwise. This is why it is >
> > >> hidden. Perhaps a reasonable compromise would be for the
> > >> > native cbind and rbind to check whether any arguments
> > >> are > S4 and if so, resort to recursion. Recursion does
> > >> seem to > be a clean way to implement "type promotion",
> > >> i.e., to > answer the question "which type should the
> > >> result be when > faced with mixed-type args?".
> > >>
> > >> Exactly. That has been my idea at the time .. ((yes,
> > >> I'm also the author of the bind_activation()
> > >> "(mis)functionality".))
> > >>
> > >> > Hopefully others have better ideas.
> > >>
> > >> that would be great.
> > >>
> > >> And even if not, it would be great if we could implement
> > >> your idea > Perhaps a reasonable compromise would be for
> > >> the > native cbind and rbind to check whether any
> > >> arguments are > S4 and if so, resort to recursion.
> > >>
> > >> without a noticable performance penalty in the case of no
> > >> S4 arguments.
> > >>
> > >> Martin
> > >>
> > >>
> > >> > Michael
> > >>
> > >> >> setMethod("rbind2", signature(x="ClassA", y = "ANY"),
> > >> >> function(x, y) { # Do stuff ... })
> > >> >>
> > >> >> setMethod("cbind2", signature(x="ClassA", y = "ANY"),
> > >> >> function(x, y) { # Do stuff ... })
> > >> >>
> > >> >> >From ?cbind2 I learned that these functions need to
> > >> be >> activated using methods:::bind_activation to
> > >> replace >> rbind and cbind from base.
> > >> >>
> > >> >> I included the call in the package file R/zzz.R using
> > >> the >> .onLoad function:
> > >> >>
> > >> >> .onLoad <- function(...) { # Bind activation of
> > >> cbind(2) >> and rbind(2) for S4 classes >>
> > >> methods:::bind_activation(TRUE) } This works as >>
> > >> expected. However, running R CMD check I am now getting
> > >> >> the following NOTE since I am using an unexported >>
> > >> function in methods:
> > >> >>
> > >> >> * checking dependencies in R code ... NOTE Unexported
> > >> >> object imported by a ':::' call: >>
> > >> 'methods:::bind_activation' See the note in ?`:::` about
> > >> >> the use of this operator. How can I get rid of the
> > >> NOTE >> and what is the proper way to define the methods
> > >> cbind >> and rbind for S4 classes in a package?
> > >> >>
> > >> >> Best, mario
> > >> >>
> > >> >> ______________________________________________ >>
> > >> R-devel at r-project.org mailing list >>
> > >> https://stat.ethz.ch/mailman/listinfo/r-devel
> > >>
> > >> > ______________________________________________ >
> > >> R-devel at r-project.org mailing list >
> > >> https://stat.ethz.ch/mailman/listinfo/r-devel
> > >>
> >
>
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