From ripley at stats.ox.ac.uk  Fri Aug  1 23:45:25 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 1 Aug 2008 22:45:25 +0100 (BST)
Subject: [Rd] data.matrix (was sapply(Date, is.numeric))
In-Reply-To: <18577.29753.76571.661140@stat.math.ethz.ch>
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	<alpine.LFD.1.10.0807301248250.24325@auk.stats.ox.ac.uk>
	<18576.26736.142076.965510@stat.math.ethz.ch>
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	<18577.29753.76571.661140@stat.math.ethz.ch>
Message-ID: <alpine.LFD.1.10.0808012244100.30451@gannet.stats.ox.ac.uk>

I've committed a more liberal version to R-devel.  (It even handles S4 
classes with an as() method.)

On Thu, 31 Jul 2008, Martin Maechler wrote:

>>>>>> "PBR" == Prof Brian Ripley <ripley at stats.ox.ac.uk>
>>>>>>     on Thu, 31 Jul 2008 08:36:22 +0100 (BST) writes:
>
>    PBR> I've now committed fixes in R-patched and R-devel.
>    PBR> There is one consequence: data.matrix() was testing for numeric columns by
>    PBR> unlist(lapply(x, is.numeric)) and so incorrectly treating Date and POSIXct
>    PBR> columns as numeric (which we had decided they were not).  This affects
>    PBR> package gvlma.
>
>    PBR> data.matrix() is now working as documented, but as we have an exception
>    PBR> for factors, do we also want exceptions for Date and POSIXct?
>
> Yes, that's a good idea, and much in the spirit of
> data.matrix()
> as I have understood it.
>
> Note the following from  help(data.matrix)
>
> where I think the 'Title' and 'Description' are more liberal
> (rightly so) than 'Details' :
>
> >> Convert a Data Frame to a Numeric Matrix
> >>
> >> Description:
> >>
> >>      Return the matrix obtained by converting all the variables in a
> >>      data frame to numeric mode and then binding them together as the
> >>      columns of a matrix.  Factors and ordered factors are replaced by
> >>      their internal codes.
>
>     [...........]
>
> >> Details:
> >>
> >>      Supplying a data frame with columns which are not numeric, factor
> >>      or logical is an error.  A warning is given if any non-factor
> >>      column has a class, as then information can be lost.
>
>
> Do we really have good reasons to give an error if a column is
> not numeric (nor of the "exception class")?
>
> Couldn't we just   lapply(., as.numeric)
> and if that doesn't give errors
> just "be happy" ?
>
> Martin
>
>
>    PBR> On Wed, 30 Jul 2008, Martin Maechler wrote:
>
>    >>>>>>> "BDR" == Prof Brian Ripley <ripley at stats.ox.ac.uk>
>    >>>>>>> on Wed, 30 Jul 2008 13:29:38 +0100 (BST) writes:
>    >>
>    BDR> On Wed, 30 Jul 2008, Martin Maechler wrote:
>    >> >>>>>>> "RobMcG" == McGehee, Robert <Robert.McGehee at geodecapital.com>
>    >> >>>>>>> on Tue, 29 Jul 2008 15:40:37 -0400 writes:
>    >> >>
>    RobMcG> FYI,
>    RobMcG> I've tried posting the below message twice to the bug tracking system,
>    >> >>
>    >> >> [....... r-bugs problems discussed in a separate thread ....]
>    >> >>
>    >> >>
>    >> >>
>    RobMcG> R-developers,
>    RobMcG> The results below are inconsistent. From the documentation for
>    RobMcG> is.numeric, I expect FALSE in both cases.
>    >> >>
>    >> >> >> x <- data.frame(dt=Sys.Date())
>    >> >> >> is.numeric(x$dt)
>    RobMcG> [1] FALSE
>    >> >> >> sapply(x, is.numeric)
>    RobMcG> dt
>    RobMcG> TRUE
>    >> >>
>    RobMcG> ## Yet, sapply seems aware of the Date class
>    >> >> >> sapply(x, class)
>    RobMcG> dt
>    RobMcG> "Date"
>    >> >>
>    >> >> Yes, thanks a lot, Robert, for the report.
>    >> >>
>    >> >> That *is* a bug somewhere in the .Internal(lapply(...)) C code,
>    >> >> when S3 dispatch of primitive functions should happen.
>    >>
>    BDR> The bug is in do_is, which uses CHAR(PRINTNAME(CAR(call))), and when
>    BDR> called from lapply that gives "FUN" not "is.numeric".  The root cause is
>    BDR> the following comment
>    >>
>    BDR> FUN = CADR(args);  /* must be unevaluated for use in e.g. bquote */
>    >>
>    BDR> and hence that the function in the *call* passed to do_is can be
>    BDR> unevaluated.
>    >>
>    >> aah!  I see.
>    >>
>    >> >> Here's an R scriptlet exposing a 2nd example
>    >> >>
>    >> >> ### lapply(list, FUN)
>    >> >> ### ------------------ seems to sometimes fail for
>    >> >> ### .Primitive S3-generic functions
>    >> >>
>    >> >> (ds <- seq(from=Sys.Date(), by=1, length=4))
>    >> >> ##[1] "2008-07-30" "2008-07-31" "2008-08-01" "2008-08-02"
>    >> >> ll <- list(d=ds)
>    >> >> lapply(list(d=ds), round)
>    >> >> ## -> Error in lapply(list(d = ds), round) : dispatch error
>    >>
>    >>
>    BDR> And that's a separate issue, in DispatchGroup which states that arguments
>    BDR> have been evaluated (true) but the 'call' from lapply gives the
>    BDR> unevaluated arguments and so there is a mismatch.
>    >>
>    >> yes, I too found that this was a separate issue, the latter
>    >> one being new since version 2.7.0
>    >>
>    BDR> I'm testing fixes for both.
>    >>
>    >> Excellent!
>    >> Martin
>    >>
>    >>
>    >> >> ## or -- related to bug report by Robert McGehee on R-devel, on 2008-07-29:
>    >> >> sapply(list(d=ds), is.numeric)
>    >> >> ## TRUE
>    >> >>
>    >> >> ## in spite of
>    >> >> is.numeric(`[[`(ll,1)) ## FALSE , because of
>    >> >> is.numeric.date
>    >> >>
>    >> >> ## or
>    >> >> round(`[[`(ll,1))
>    >> >> ## [1] "2008-07-30" "2008-07-31" "2008-08-01" "2008-08-02"
>    >> >>
>    >> >> ##-----------------------------
>    >> >>
>    >> >> But I'm currently too much tied up with other duties,
>    >> >> to find and test bug-fix.
>    >> >>
>    >> >> Martin Maechler, ETH Zurich and R-Core Team
>    >>
>    >> ______________________________________________
>    >> R-devel at r-project.org mailing list
>    >> https://stat.ethz.ch/mailman/listinfo/r-devel
>    >>
>
>    PBR> --
>    PBR> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>    PBR> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>    PBR> University of Oxford,             Tel:  +44 1865 272861 (self)
>    PBR> 1 South Parks Road,                     +44 1865 272866 (PA)
>    PBR> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>

-- 
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



[Rd] data.matrix (was sapply(Date, is.numeric))
Prof Brian Ripley