R help - Nov 2011 - any updates w.r.t. lapply, sapply, apply retaining classes

Hi All,

    I don't have a "I need help" question, so much as a query into
any
update whether 'R' has made any progress with some of the core functions
retaining classes.  As an example, because it's one of the cases that most
egregiously impacts me & my work and keeps pushing me away from 'R'
and
into other numerical languages (such as NumPy in python), I will use sapply
/ lapply to demonstrate, but this behavior is ubiquitous throughout 'R'.

    Let's say I have a class which is theoretically supported, but not one
of the core "numeric" or "character" classes (and, to some
degree, "factor"
classes).  Many of the basic functions will convert my desired class into
either numeric or character, so that my returned answer is gibberish.

E.g.:

test= as.difftime(c(1, 1, 8, 0.25, 8, 1.25), units= "days")  ## create
a
small array of time differences
class(test)  ## this will return the proper class, "difftime"
class(test[1] ) ## this will also return the proper class, "difftime"
sapply(test, class)  ## this will return *numerics* for all of the classes.
 Ack!!

    In the example I give above, the impact might seem small, but the
implications are *huge*.  This means that I am, in effect, not allowed to
use *any* of the vectoring functions in 'R', which avoid performing
loops
thereby speeding up process time extraordinarily.  Many can sympathize that
'R' is ridiculously slow with "for" loops, compared to other
languages.
 But that's theoretically OK, a good statistician or data analyst should be
able to work comfortably with matrices and vectors.  However, *'R'
cannot
work comfortably* with matrices or vectors, *unless* they are using the
numeric or character classes.  Many of the classes suffer the problem I
just described, although I only used "difftime" in the example. 
Factors
seem a bit more "comfortable", and can be handled most of the time,
but not
as well as numerics, and at times functions working on factors can return
the numerical representation of the factor instead of the original factor.

    Is there any progress in guaranteeing that all core functions either
(a) ideally return exactly the classes, and hierarchy of classes, that they
received (e.g., a list of data frames with difftimes & dates &
characters
would return a list of data frames with difftimes & dates & characters),
or
(b) barring that, the function should at least error out with a clear error
explaining that sapply, for example, cannot vectorize on the class being
used?  Returning incorrect answers is far worse than returning an error,
from a perspective of stability.

    This is, by far, the largest Achilles' heel to 'R'.  Personally,
as my
career advances and I work on more technical things, I am finding that I
have to leave 'R' by the wayside and use other languages for robust
numerical calculations and programming.  This saddens me, because there are
so many wonderful packages developed by the community.  The example above
came up because I am using the "forecast" library to great effect in
predicting how long our product cycle time will be.  However, I spend much
of my time fighting all these class & typing bugs in 'R' (and we
have to
start recognizing that they are bugs, otherwise they may never get
resolved), such that many of the improvements in my productivity due to all
the wonderful computational packages are entirely offset by the time
I spend fighting this issue of poor classes.

                                     Thanks & Regards!
                                              Mike

---
XKCD <http://www.xkcd.com>

	[[alternative HTML version deleted]]

Hi Mike,

This isn't really an answer to your question, but perhaps will serve
to continue discussion.  I think that there are some fundamental
issues when working special classes.  As a thought example, suppose I
wrote a class, "posreal", which inherits from the numeric class.  It
is only valid for positive, real numbers.  I use it in a package, but
do not develop methods for it.  A user comes along and creates a
vector, x that is a posreal.  Then tries: mean(x * -3).  Since I never
bothered to write a special method for mean for my class, R falls back
to the inherited numeric, but gives a value that is clearly not valid
for posreal.  What should happen?  S3 methods do not really have
validation, so in principle, one could write a function like:

f <- function(x) {
  vclass <- class(x)
  res <- mean(x)
  class(res) <- vclass
  return(res)
}

which "retains" the appropriate class, but in name only.  R core
cannot possibly know or imagine all classes that may be written that
inherit from more basic types but with possible special aspects and
requirements.  I think the inherited is considered to be more generic
and that is returned.  It is usually up to the user to ensure that the
function (whose methods were not specific to that special class but
the inherited) is valid for that class and can manually convert it
back:

res <- as.posreal(res)

What about lapply and sapply?  Neither are generic or have methods for
difftime, and so do some unexpected/desirable things.  Again, without
methods defined for a particular class, they cannot know what is
special or appropriate way to handle it, they use defaults which
sometimes work but may give unexpected or undesirable results, but
what else can be done?  (okay, they could just throw an error)  If a
function is naive about a class, it does not seem right to operate on
it using unknown methods and then pretend to be returning the same
type of data.  As it stands, they convert to a data type they know and
return that.

Now, you mention that for loops are slow in R, and this is true to a
degree.  However, the *apply functions are basically just internal
loops, so they do not really save you (they are certainly not
vectorized!), though they are more elegant than explicit loops IMO.
One way to use them while retaining class would be like:

sapply(seq_along(test), function(i) class(test[i]))

this is less efficient then sapply(test, class), but the overhead
drops considerably as the function does nontrivial calculations.
Finally, I find the (relatively) new compiler package really shines at
making functions that are just wrappers for for loops more efficient.
Take a look at the examples from:

require(compiler)
?cmpfun

I am not familiar with numPy so I do not know how it handles new
classes, but with some tweaks to my workflow, I do not find myself
running into problems with how R handles them.  I definitely
appreciate your position because I have been there...as I became more
familiar with R, classes, and methods, I find I work in a way that
avoids passing objects to functions that do not know how to handle
them properly.

Cheers,

Josh


On Thu, Nov 3, 2011 at 11:08 AM, Mike Williamson <this.is.mvw at
gmail.com> wrote:
> Hi All,
>
> ? ?I don't have a "I need help" question, so much as a query
into any
> update whether 'R' has made any progress with some of the core
functions
> retaining classes. ?As an example, because it's one of the cases that
most
> egregiously impacts me & my work and keeps pushing me away from
'R' and
> into other numerical languages (such as NumPy in python), I will use sapply
> / lapply to demonstrate, but this behavior is ubiquitous throughout
'R'.
>
> ? ?Let's say I have a class which is theoretically supported, but not
one
> of the core "numeric" or "character" classes (and, to
some degree, "factor"
> classes). ?Many of the basic functions will convert my desired class into
> either numeric or character, so that my returned answer is gibberish.
>
> E.g.:
>
> test= as.difftime(c(1, 1, 8, 0.25, 8, 1.25), units= "days") ?##
create a
> small array of time differences
> class(test) ?## this will return the proper class, "difftime"
> class(test[1] ) ## this will also return the proper class,
"difftime"
> sapply(test, class) ?## this will return *numerics* for all of the classes.
> ?Ack!!
>
> ? ?In the example I give above, the impact might seem small, but the
> implications are *huge*. ?This means that I am, in effect, not allowed to
> use *any* of the vectoring functions in 'R', which avoid performing
loops
> thereby speeding up process time extraordinarily. ?Many can sympathize that
> 'R' is ridiculously slow with "for" loops, compared to
other languages.
> ?But that's theoretically OK, a good statistician or data analyst
should be
> able to work comfortably with matrices and vectors. ?However, *'R'
cannot
> work comfortably* with matrices or vectors, *unless* they are using the
> numeric or character classes. ?Many of the classes suffer the problem I
> just described, although I only used "difftime" in the example.
?Factors
> seem a bit more "comfortable", and can be handled most of the
time, but not
> as well as numerics, and at times functions working on factors can return
> the numerical representation of the factor instead of the original factor.
>
> ? ?Is there any progress in guaranteeing that all core functions either
> (a) ideally return exactly the classes, and hierarchy of classes, that they
> received (e.g., a list of data frames with difftimes & dates &
characters
> would return a list of data frames with difftimes & dates &
characters), or
> (b) barring that, the function should at least error out with a clear error
> explaining that sapply, for example, cannot vectorize on the class being
> used? ?Returning incorrect answers is far worse than returning an error,
> from a perspective of stability.
>
> ? ?This is, by far, the largest Achilles' heel to 'R'.
?Personally, as my
> career advances and I work on more technical things, I am finding that I
> have to leave 'R' by the wayside and use other languages for robust
> numerical calculations and programming. ?This saddens me, because there are
> so many wonderful packages developed by the community. ?The example above
> came up because I am using the "forecast" library to great effect
in
> predicting how long our product cycle time will be. ?However, I spend much
> of my time fighting all these class & typing bugs in 'R' (and
we have to
> start recognizing that they are bugs, otherwise they may never get
> resolved), such that many of the improvements in my productivity due to all
> the wonderful computational packages are entirely offset by the time
> I spend fighting this issue of poor classes.
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Thanks & Regards!
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Mike
>
> ---
> XKCD <http://www.xkcd.com>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/

> ? ?In the example I give above, the impact might seem small, but the
> implications are *huge*. ?This means that I am, in effect, not allowed to
> use *any* of the vectoring functions in 'R', which avoid performing
loops
> thereby speeding up process time extraordinarily. ?Many can sympathize that
> 'R' is ridiculously slow with "for" loops, compared to
other languages.
> ?But that's theoretically OK, a good statistician or data analyst
should be
> able to work comfortably with matrices and vectors.
Two comments:

* sapply is generally only _slightly_ faster than a for loop

* it's almost always better to use vapply instead of sapply.

But I agree that simplify2array should be a generic so that you can
write custom methods to support new classes.

Hadley


-- 
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/