From suharto_anggono at yahoo.com  Sat Nov 26 18:14:01 2016
From: suharto_anggono at yahoo.com (Suharto Anggono Suharto Anggono)
Date: Sat, 26 Nov 2016 17:14:01 +0000 (UTC)
Subject: [Rd] ifelse() woes ... can we agree on a ifelse2() ?
References: <1188177957.798916.1480180441229.ref@mail.yahoo.com>
Message-ID: <1188177957.798916.1480180441229@mail.yahoo.com>

Just stating, in 'ifelse', 'test' is not recycled. As I said in "R-intro: length of 'ifelse' result" (https://stat.ethz.ch/pipermail/r-devel/2016-September/073136.html), ifelse(condition, a, b) returns a vector of the length of 'condition', even if 'a' or 'b' is longer.

On current 'ifelse' code in R:
* The part
ans[nas] <- NA
could be omitted because NA's are already in place.
If the part is removed, variable 'nas' is no longer used.
* The any(*) part actually checks the thing that is used as the index vector. The index vector could be stored and then repeatedly used, like the following.
? ? if (any(sel <- test & ok))
??? ans[sel] <- rep(yes, length.out = length(ans))[sel]
* If 'test' is a factor, doing
storage.mode(test) <- "logical"
is not appropriate, but is.atomic(test) returns TRUE. Maybe use
if(!is.object(test))
instead of
if(is.atomic(test)) .

On ifelse-checks.R:
* In function 'chkIfelse', if the fourth function argument names is not "NA.", the argument name is changed, but the function body still uses the old name. That makes error in chkIfelse(ifelseHW) .
A fix:
? ? ? ? if(names(formals(FUN))[[4]] != "NA.") {
? ? ? ? ? ? body(FUN) <- do.call(substitute, list(body(FUN),
? ? ? ? ? ? ? ? setNames(list(quote(NA.)), names(formals(FUN))[[4]])))
? ? ? ? ? ? names(formals(FUN))[[4]] <- "NA."
? ? ? ? }
After fixing, chkIfelse(ifelseHW) just fails at identical(iflt, as.POSIXlt(ifct)) .
'iflt' has NA as 'tzone' and 'isdst' components.
* Because function 'chkIfelse' continues checking after failure,
as.POSIXlt(ifct)
may give error. The error happens, for example, in chkIfelse(ifelseR) . Maybe place it inside try(...).
* If 'lt' is a "POSIXlt" object, (lt-100) is a "POSIXct" object.
So,
FUN(c(TRUE, FALSE, NA, TRUE), lt, lt-100)
is an example of mixed class.
* The part of function 'chkIfelse' in
for(i in seq_len(nFact))
uses 'NA.' function argument. That makes error when 'chkIfelse' is applied to function without fourth argument.
The part should be wrapped in
if(has.4th) .
* Function 'ifelseJH' has fourth argument, but the argument is not for value if NA. So, instead of
chkIfelse(ifelseJH) ,
maybe call
chkIfelse(function(test, yes, no) ifelseJH(test, yes, no)) .

A concrete version of 'ifelse2' that starts the result from 'yes':
function(test, yes, no, NA. = NA) {
? ? if(!is.logical(test))
? ? ? ? test <- if(isS4(test)) methods::as(test, "logical") else as.logical(test)
? ? n <- length(test)
? ? ans <- rep(yes, length.out = n)
? ? ans[!test & !is.na(test)] <- rep(no, length.out = n)[!test & !is.na(test)]
? ? ans[is.na(test)] <- rep(NA., length.out = n)[is.na(test)]
? ? ans
}

It requires 'rep' method that is compatible with subsetting. It also works with "POSIXlt" in R 2.7.2, when 'length' gives 9, and gives an appropriate result if time zones are the same.
For coercion of 'test', there is no need of keeping attributes. So, it doesn't do
storage.mode(test) <- "logical"
and goes directly to 'as.logical'.
It relies on subassignment for silent coercions of
logical < integer < double < complex .
Unlike 'ifelse', it never skips any subassignment. So, phenomenon as in "example of different return modes" in ?ifelse doesn't happen.

Another version, for keeping attributes as pointed out by Duncan Murdoch:
function(test, yes, no, NA. = NA) {
? ? if(!is.logical(test))
? ? ? ? test <- if(isS4(test)) methods::as(test, "logical") else as.logical(test)
? ? n <- length(test)
? ? n.yes <- length(yes); n.no <- length(no)
? ? if (n.yes != n) {
? ? ? ? if (n.no == n) {? # swap yes <-> no
? ? ? ? ? ? test <- !test
? ? ? ? ? ? ans <- yes; yes <- no; no <- ans
? ? ? ? ? ? n.no <- n.yes
? ? ? ? } else yes <- yes[rep_len(seq_len(n.yes), n)]
? ? }
? ? ans <- yes
? ? if (n.no == 1L)
? ? ? ? ans[!test] <- no
? ? else
? ? ? ? ans[!test & !is.na(test)] <- no[
? ? ? ? ? ? if (n.no == n) !test & !is.na(test)
? ? ? ? ? ? else rep_len(seq_len(n.no), n)[!test & !is.na(test)]]
? ? stopifnot(length(NA.) == 1L)
? ? ans[is.na(test)] <- NA.
? ? ans
}

Note argument evaluation order: 'test', 'yes', 'no', 'NA.'.
First, it chooses the first of 'yes' and 'no' that has the same length as the result. If none of 'yes' and 'no' matches the length of the result, it chooses recycled (or truncated) 'yes'.
It uses 'rep' on the index and subsetting as a substitute for 'rep' on the value.
It requires 'length' method that is compatible with subsetting.
Additionally, it uses the same idea as dplyr::if_else, or more precisely the helper function 'replace_with'. It doesn't use 'rep' if the length of 'no' is 1 or is the same as the length of the result. For subassignment with value of length 1, recycling happens by itself and NA in index is OK.
It limits 'NA.' to be of length 1, considering 'NA.' just as a label for NA.

Cases where the last version above or 'ifelse2 or 'ifelseHW' in ifelse-def.R gives inappropriate answers:
- 'yes' and 'no' are "difftime" objects with different "units" attribute
- 'yes' and 'no' are "POSIXlt" objects with different time zone
Example: 'yes' in "UTC" and 'no' in "EST5EDT". The reverse, 'yes' in "EST5EDT" and 'no' in "UTC" gives error.

For the cases, c(yes, no) helps. Function 'ifelseJH' in ifelse-def.R gives a right answer for "POSIXlt" case.
---------------------
Martin et al.,




On Tue, Nov 22, 2016 at 2:12 AM, Martin Maechler <maechler at stat.math.ethz.ch
> wrote:

>
> Note that my premise was really to get *away* from inheriting
> too much from 'test'.
> Hence, I have *not* been talking about replacing ifelse() but
> rather of providing a new? ifelse2()
>
>? ? ? ? [ or if_else()? if Hadley was willing to ditch the dplyr one
>? ? ? ? ? ? ? ? ? ? ? ? in favor of a base one]
>
>? ???> Specifically, based on an unrelated discussion with Henrik Bengtsson
> on
>? ???> Twitter, I wonder if preserving the recycling behavior test is
> longer than
>? ???> yes, no, but making the case where
>
>? ???> length( test ) < max(length( yes ), length( no ))
>
>? ???> would simplify usage for userRs in a useful way.
>

That was a copyediting bug on my part, it seems I hit send with my message
only half-edited/proofread. Apologies.

 That should have said that making the case where test is the one that will
be recycled (because it is shorter than either yes or no) an error. My
claim is that the fact that test itself can be recycled, rather than just
yes or no, is confusing to many R users. If we are writing an ifelse2 we
might want to drop that feature and just throw an error in that case.
(Users could still use the original ifelse if they understand and
specifically want that behavior).

Does that make more sense?



>
>? ???> Also, If we combine a stricter contract that the output will always
> be of
>? ???> length with the suggestion of a specified output class
>
>
Here, again, I was talking about the restriction that the output be
guaranteed to be the length of test, regardless of the length of yes and
no. That, combined with a specific, guaranteed output class would make a
much narrower/more restricted but also (I argue) much easier to understand
function. Particularly for beginning and intermediate users.

I do hear what you're saying about silent conversion, though, so what I'm
describing might be a third function (ifelse3 for lack of a better name for
now), as you pointed out.


> that was not my intent here.... but would be another interesting
> extension. However, I would like to keep? R-semantic silent coercions
> such as
>? ? ? ? ???logical < integer < double < complex
>
> and your pseudo code below would not work so easily I think.
>
>? ???> the pseudo code could be
>
> (I'm changing assignment '=' to? '<-' ...? [please!] )
>
>? ???> ifelse2 <- function(test, yes, no, outclass) {
>? ???>???lenout? <- length(test)
>? ???>???out <- as( rep(yes, length.out <- lenout), outclass)
>? ???>???out[!test] <- as(rep(no, length.out = lenout)[!test], outclass)
>? ???>???# handle NA stuff
>? ???>???out
>? ???> }
>
>
>? ???> NAs could be tricky if outclass were allowed to be completely
> general, but
>? ???> doable, I think? Another approach? if we ARE fast-passing while
> leaving
>? ???> ifelse intact is that maybe NA's in test just aren't allowed in
> ifelse2.
>? ???> I'm not saying we should definitely do that, but it's possible and
> would
>? ???> make things faster.
>
>? ???> Finally, In terms of efficiency, with the stuff that Luke and I are
> working
>? ???> on, the NA detection could be virtually free in certain cases, which
> could
>? ???> give a nice boost for long vectors? that don't have any NAs (and
> 'know'
>? ???> that they don't).
>
> That *is* indeed a very promising prospect!
> Thank you in advance!
>
>? ???> Best,
>? ???> ~G
>
> I still am bit disappointed by the fact that it seems nobody has
> taken a good look at my ifelse2() proposal.
>

I plan to look at it soon. Thanks again for all your work.

~G


>
> I really would like an alternative to ifelse() in *addition* to
> the current ifelse(), but hopefully in the future being used in
> quite a few places instead of ifelse()
> efficiency but for changed semantics, namely working for considerably
> more "vector like" classes of? 'yes' and 'no'? than the current
> ifelse().
>
> As I said, the current proposal works for objects of class
>? ? "Date", "POSIXct", "POSIXlt", "factor",? "mpfr" (pkg 'Rmpfr')
> and hopefully for "sparseVector" (in a next version of the 'Matrix' pkg).
>
> Martin
>
>? ???> On Tue, Nov 15, 2016 at 3:58 AM, Martin Maechler <
> maechler at stat.math.ethz.ch
>? ???>> wrote:
>
>? ???>> Finally getting back to this :
>? ???>>
>? ???>> >>>>> Hadley Wickham <h.wickham at gmail.com>
>? ???>> >>>>>? ???on Mon, 15 Aug 2016 07:51:35 -0500 writes:
>? ???>>
>? ???>> > On Fri, Aug 12, 2016 at 11:31 AM, Hadley Wickham
>? ???>> > <h.wickham at gmail.com> wrote:
>? ???>> >>> >> One possibility would also be to consider a
>? ???>> >>> "numbers-only" or >> rather "same type"-only {e.g.,
>? ???>> >>> would also work for characters} >> version.
>? ???>> >>>
>? ???>> >>> > I don't know what you mean by these.
>? ???>> >>>
>? ???>> >>> In the mean time, Bob Rudis mentioned dplyr::if_else(),
>? ???>> >>> which is very relevant, thank you Bob!
>? ???>> >>>
>? ???>> >>> As I have found, that actually works in such a "same
>? ???>> >>> type"-only way: It does not try to coerce, but gives an
>? ???>> >>> error when the classes differ, even in this somewhat
>? ???>> >>> debatable case :
>? ???>> >>>
>? ???>> >>> > dplyr::if_else(c(TRUE, FALSE), 2:3, 0+10:11) Error:
>? ???>> >>> `false` has type 'double' not 'integer'
>? ???>> >>> >
>? ???>> >>>
>? ???>> >>> As documented, if_else() is clearly stricter than
>? ???>> >>> ifelse() and e.g., also does no recycling (but of
>? ???>> >>> length() 1).
>? ???>> >>
>? ???>> >> I agree that if_else() is currently too strict - it's
>? ???>> >> particularly annoying if you want to replace some values
>? ???>> >> with a missing:
>? ???>> >>
>? ???>> >> x <- sample(10) if_else(x > 5, NA, x) # Error: `false`
>? ???>> >> has type 'integer' not 'logical'
>? ???>> >>
>? ???>> >> But I would like to make sure that this remains an error:
>? ???>> >>
>? ???>> >> if_else(x > 5, x, "BLAH")
>? ???>> >>
>? ???>> >> Because that seems more likely to be a user error (but
>? ???>> >> reasonable people might certainly believe that it should
>? ???>> >> just work)
>? ???>> >>
>? ???>> >> dplyr is more accommodating in other places (i.e. in
>? ???>> >> bind_rows(), collapse() and the joins) but it's
>? ???>> >> surprisingly hard to get all the details right. For
>? ???>> >> example, what should the result of this call be?
>? ???>> >>
>? ???>> >> if_else(c(TRUE, FALSE), factor(c("a", "b")),
>? ???>> >> factor(c("c", "b"))
>? ???>> >>
>? ???>> >> Strictly speaking I think you could argue it's an error,
>? ???>> >> but that's not very user-friendly. Should it be a factor
>? ???>> >> with the union of the levels? Should it be a character
>? ???>> >> vector + warning? Should the behaviour change if one set
>? ???>> >> of levels is a subset of the other set?
>? ???>> >>
>? ???>> >> There are similar issues for POSIXct (if the time zones
>? ???>> >> are different, which should win?), and difftimes
>? ???>> >> (similarly for units).? Ideally you'd like the behaviour
>? ???>> >> to be extensible for new S3 classes, which suggests it
>? ???>> >> should be a generic (and for the most general case, it
>? ???>> >> would need to dispatch on both arguments).
>? ???>>
>? ???>> > One possible principle would be to use c() -
>? ???>> > i.e. construct out as
>? ???>>
>? ???>> > out <- c(yes[0], no[0]
>? ???>> > length(out) <- max(length(yes), length(no))
>? ???>>
>? ???>> yes; this would require that a? `length<-` method works for the
>? ???>> class of the result.
>? ???>>
>? ???>> Duncan Murdoch mentioned a version of this, in his very
>? ???>> first reply:
>? ???>>
>? ???>> ans <- c(yes, no)[seq_along(test)]
>? ???>> ans <- ans[seq_along(test)]
>? ???>>
>? ???>> which is less efficient for atomic vectors, but requires
>? ???>> less from the class: it "only" needs `c` and `[` to work
>? ???>>
>? ???>> and a mixture of your two proposals would be possible too:
>? ???>>
>? ???>> ans <- c(yes[0], no[0])
>? ???>> ans <- ans[seq_along(test)]
>? ???>>
>? ???>> which does *not* work for my "mpfr" numbers (CRAN package 'Rmpfr'),
>? ???>> but that's a buglet in the? c.mpfr() implementation of my Rmpfr
>? ???>> package... (which has already been fixed in the development version
> on
>? ???>> R-forge,
>? ???>> https://r-forge.r-project.org/R/?group_id=386)
>? ???>>
>? ???>> > But of course that wouldn't help with factor responses.
>? ???>>
>? ???>> Yes.? However, a version of Duncan's suggestion -- of treating
> 'yes' first
>? ???>> -- does help in that case.
>? ???>>
>? ???>> For once, mainly as "feasability experiment",
>? ???>> I have created a github gist to make my current ifelse2() proposal
>? ???>> available
>? ???>> for commenting, cloning, pullrequesting, etc:
>? ???>>
>? ???>> Consisting of 2 files
>? ???>> - ifelse-def.R :? Functions definitions only, basically all the
> current
>? ???>> proposals, called? ifelse*()
>? ???>> - ifelse-checks.R : A simplistic checking function
>? ???>> and examples calling it, notably demonstrating that my
>? ???>> ifelse2()? does work with
>? ???>> "Date", <dateTime> (i.e. "POSIXct" and "POSIXlt"), factors,
>? ???>> and "mpfr" (the arbitrary-precision numbers in my package "Rmpfr")
>? ???>>
>? ???>> Also if you are not on github, you can quickly get to the ifelse2()
>? ???>> definition :
>? ???>>
>? ???>> https://gist.github.com/mmaechler/9cfc3219c4b89649313bfe6853d878
>? ???>> 94#file-ifelse-def-r-L168
>? ???>>
>? ???>> > Also, if you're considering an improved ifelse(), I'd
>? ???>> > strongly urge you to consider adding an `na` argument,
>? ???>>
>? ???>> I now did (called it 'NA.').
>? ???>>
>? ???>> > so that you can use ifelse() to transform all three
>? ???>> > possible values in a logical vector.
>? ???>>
>? ???>> > Hadley
>? ???>> > -- http://hadley.nz
>? ???>>
>? ???>> For those who really hate GH (and don't want or cannot easily
> follow the
>? ???>> above URL), here's my current definition:
>? ???>>
>? ???>>
>? ???>> ##' Martin Maechler, 14. Nov 2016 --- taking into account Duncan M.
> and
>? ???>> Hadley's
>? ???>> ##' ideas in the R-devel thread starting at (my mom's 86th
> birthday):
>? ???>> ##' https://stat.ethz.ch/pipermail/r-devel/2016-August/072970.html
>? ???>> ifelse2 <- function (test, yes, no, NA. = NA) {
>? ???>> if(!is.logical(test)) {
>? ???>> if(is.atomic(test))
>? ???>> storage.mode(test) <- "logical"
>? ???>> else ## typically a "class"; storage.mode<-() typically fails
>? ???>> test <- if(isS4(test)) methods::as(test, "logical") else
>? ???>> as.logical(test)
>? ???>> }
>? ???>>
>? ???>> ## No longer optimize the? "if (a) x else y"? cases:
>? ???>> ## Only "non-good" R users use ifelse(.) instead of if(.) in these
>? ???>> cases.
>? ???>>
>? ???>> ans <-
>? ???>> tryCatch(rep(if(is.object(yes) && identical(class(yes), class(no)))
>? ???>> ## as c(o) or o[0] may not work for the class
>? ???>> yes else c(yes[0], no[0]), length.out =
>? ???>> length(test)),
>? ???>> error = function(e) { ## try asymmetric, yes-leaning
>? ???>> r <- yes
>? ???>> r[!test] <- no[!test]
>? ???>> r
>? ???>> })
>? ???>> ok <- !(nas <- is.na(test))
>? ???>> if (any(test[ok]))
>? ???>> ans[test & ok] <- rep(yes, length.out = length(ans))[test & ok]
>? ???>> if (any(!test[ok]))
>? ???>> ans[!test & ok] <- rep(no, length.out = length(ans))[!test & ok]
>? ???>> ans[nas] <- NA. # possibly coerced to class(ans)
>? ???>> ans
>? ???>> }
>? ???>>
>? ???>> ______________________________________________
>? ???>> R-devel at r-project.org mailing list
>? ???>> https://stat.ethz.ch/mailman/listinfo/r-devel
>? ???>>
>
>
>
>? ???> --
>? ???> Gabriel Becker, PhD
>? ???> Associate Scientist (Bioinformatics)
>? ???> Genentech Research
>
>? ???> [[alternative HTML version deleted]]
>
>


-- 
Gabriel Becker, PhD
Associate Scientist (Bioinformatics)
Genentech Research

??? [[alternative HTML version deleted]]



[Rd] ifelse() woes ... can we agree on a ifelse2() ?
Suharto Anggono Suharto Anggono