Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Suharto Anggono Suharto Anggono via R-devel]

Function 'tapply' in R devel r72137 uses
if(!is.null(ans) && is.na(default) && is.atomic(ans)) .

Problems:
- It is possible that user-specified 'default' is not of length 1. If the 
length is zero, the 'if' gives an error.
- It is possible that is.na(default) is TRUE and user-specified 'default' is 
NaN.


On Sat, 4/2/17, Martin Maechler <maech...@stat.math.ethz.ch> wrote:

 Subject: Re: [Rd] RFC: tapply(*, ..., init.value = NA)

 Cc: R-devel@r-project.org
 Date: Saturday, 4 February, 2017, 10:48 PM
 
>>>>> Suharto Anggono Suharto Anggono via R-devel 
>>>>> on Wed, 1 Feb 2017 16:17:06 + writes:

[snip]

> vector(typeof(ans)) (or vector(storage.mode(ans))) has
> length zero and can be used to initialize array.  

Yes,.. unless in the case where ans is NULL.
You have convinced me, that is  nicer.

> Instead of if(missing(default)) , if(identical(default,
> NA)) could be used. The documentation could then say, for
> example: "If default = NA (the default), NA of appropriate
> storage mode (0 for raw) is automatically used."

After some thought (and experiments), I have reverted and no
longer use if(missing). You are right that it is not needed
(and even potentially confusing) here.

Changes are in svn c72106.

Martin Maechler

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Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Martin Maechler]

>>>>> Suharto Anggono Suharto Anggono via R-devel <r-devel@r-project.org>
>>>>> on Wed, 1 Feb 2017 16:17:06 + writes:

> On 'aggregate data.frame', the URL should be
> https://stat.ethz.ch/pipermail/r-help/2016-May/438631.html .

thank you. Yes, using 'drop' makes sense there where the result
is always "linear(ized)" or "one-dimensional".
For tapply() that's only the case for 1D-index.

> vector(typeof(ans)) (or vector(storage.mode(ans))) has
> length zero and can be used to initialize array.  

Yes,.. unless in the case where ans is NULL.
You have convinced me, that is  nicer.

> Instead of if(missing(default)) , if(identical(default,
> NA)) could be used. The documentation could then say, for
> example: "If default = NA (the default), NA of appropriate
> storage mode (0 for raw) is automatically used."

After some thought (and experiments), I have reverted and no
longer use if(missing). You are right that it is not needed
(and even potentially confusing) here.

Changes are in svn c72106.

Martin Maechler


> 
> On Wed, 1/2/17, Martin Maechler
    > <maech...@stat.math.ethz.ch> wrote:

>  Subject: Re: [Rd] RFC: tapply(*, ..., init.value = NA)

>  Cc: R-devel@r-project.org Date: Wednesday, 1 February,
> 2017, 12:14 AM
 
>>>>> Suharto Anggono Suharto Anggono via R-devel 
>>>>> on Tue, 31 Jan 2017 15:43:53 + writes:

>> Function 'aggregate.data.frame' in R has taken a
>> different route. With drop=FALSE, the function is also
>> applied to subset corresponding to combination of
>> grouping variables that doesn't appear in the data
>> (example 2 in
>> https://stat.ethz.ch/pipermail/r-devel/2017-January/073678.html).

> Interesting point (I couldn't easily find 'the example 2'
> though).  However, aggregate.data.frame() is a
> considerably more sophisticated function and one goal was
> to change tapply() as little as possible for compatibility
> (and maintenance!) reasons .

> [snip]

>> With the code using if(missing(default)) , I consider the
>> stated default value of 'default', default = NA ,
>> misleading because the code doesn't use it.

> I know and I also had thought about it and decided to keep
> it in the spirit of "self documentation" because "in
> spirit", the default still *is* NA.

>> Also, tapply(1:3, 1:3, as.raw) is not the same as
>> tapply(1:3, 1:3, as.raw, default = NA) .  The accurate
>> statement is the code in if(missing(default)) , but it
>> involves the local variable 'ans'.

> exactly.  But putting that whole expression in there would
> look confusing to those using str(tapply), args(tapply) or
> similar inspection to quickly get a glimpse of the
> function user "interface".  That's why we typically don't
> do that and rather slightly cheat with the formal default,
> for the above "didactical" purposes.

> If you are puristic about this, then missing() should
> almost never be used when the function argument has a
> formal default.

> I don't have a too strong opinion here, and we do have
> quite a few other cases, where the formal default argument
> is not always used because of if(missing(.))  clauses.

> I think I could be convinced to drop the '= NA' from the
> formal argument list..


>> As far as I know, the result of function 'array' in is
>> not a classed object and the default method of `[<-` will
>> be used in the 'tapply' code portion.

>> As far as I know, the result of 'lapply' is a list
>> without class. So, 'unlist' applied to it uses the
>> default method and the 'unlist' result is a vector or a
>> factor.

> You may be right here ((or not: If a package author makes
> array() into an S3 generic and defines S3method(array, *)
> and she or another make tapply() into a generic with
> methods, are we really sure that this code would not be
> used ??))

> still, the as.raw example did not easily work without a
> warning when using as.vector() .. or similar.

>> With the change, the result of

>> tapply(1:3, 1:3, factor, levels=3:1)

>> is of mode "character". The value is from the internal
>> code, not from the factor levels. It is worse than before
>> the change, where it is really the internal code,
>> integer.

> I agree that this change is not desirable.  One could
> argue that it was quite a

Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Suharto Anggono Suharto Anggono via R-devel]

On 'aggregate data.frame', the URL should be 
https://stat.ethz.ch/pipermail/r-help/2016-May/438631.html .

vector(typeof(ans))
(or  vector(storage.mode(ans)))
has length zero and can be used to initialize array.

Instead of
if(missing(default)) ,
if(identical(default, NA))
could be used. The documentation could then say, for example: "If default = NA 
(the default), NA of appropriate storage mode (0 for raw) is automatically 
used."

On Wed, 1/2/17, Martin Maechler <maech...@stat.math.ethz.ch> wrote:

 Subject: Re: [Rd] RFC: tapply(*, ..., init.value = NA)

 Cc: R-devel@r-project.org
 Date: Wednesday, 1 February, 2017, 12:14 AM
 
>>>>> Suharto Anggono Suharto Anggono via R-devel 
>>>>> on Tue, 31 Jan 2017 15:43:53 + writes:

> Function 'aggregate.data.frame' in R has taken a different route. With 
drop=FALSE, the function is also applied to subset corresponding to combination 
of grouping variables that doesn't appear in the data (example 2 in 
https://stat.ethz.ch/pipermail/r-devel/2017-January/073678.html).

Interesting point (I couldn't easily find 'the example 2' though).
However, aggregate.data.frame() is a considerably more
sophisticated function and one goal was to change tapply() as
little as possible for compatibility (and maintenance!) reasons .

[snip]

> With the code using
>if(missing(default)) ,
> I consider the stated default value of 'default',
>default = NA ,
> misleading because the code doesn't use it. 

I know and I also had thought about it and decided to keep it 
in the spirit of "self documentation" because  "in spirit", the
default still *is* NA.

> Also,
>  tapply(1:3, 1:3, as.raw)
> is not the same as
>  tapply(1:3, 1:3, as.raw, default = NA) .
> The accurate statement is the code in
> if(missing(default)) ,
> but it involves the local variable 'ans'.

exactly.  But putting that whole expression in there would look
confusing to those using  str(tapply), args(tapply) or similar
inspection to quickly get a glimpse of the function user "interface".
That's why we typically don't do that and rather slightly cheat
with the formal default, for the above "didactical" purposes.

If you are puristic about this, then missing() should almost never
be used when the function argument has a formal default.

I don't have a too strong opinion here, and we do have quite a
few other cases, where the formal default argument is not always
used because of   if(missing(.))  clauses.

I think I could be convinced to drop the '= NA' from the formal
argument list..


> As far as I know, the result of function 'array' in is not a classed 
object and the default method of  `[<-` will be used in the 'tapply' code 
portion.

> As far as I know, the result of 'lapply' is a list without class. So, 
'unlist' applied to it uses the default method and the 'unlist' result is a 
vector or a factor.

You may be right here
  ((or not:  If a package author makes array() into an S3 generic and defines
S3method(array, *) and she or another make tapply() into a
generic with methods,  are we really sure that this code
would not be used ??))

still, the as.raw example did not easily work without a warning
when using as.vector() .. or similar.

> With the change, the result of

> tapply(1:3, 1:3, factor, levels=3:1)

> is of mode "character". The value is from the internal code, not from the 
factor levels. It is worse than before the change, where it is really the 
internal code, integer.

I agree that this change is not desirable.
One could argue that it was quite a "lucky coincidence" that the previous
code returned the internal integer codes though..


[snip]


> To initialize array, a zero-length vector can also be used.

yes, of course; but my  ans[0L][1L]  had the purpose to get the
correct mode specific version of NA .. which works for raw (by
getting '00' because "raw" has *no* NA!).

So it seems I need an additional   !is.factor(ans)  there ...
a bit ugly.


-

[snip]

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Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Martin Maechler]

> Suharto Anggono Suharto Anggono via R-devel 
> on Tue, 31 Jan 2017 15:43:53 + writes:

> Function 'aggregate.data.frame' in R has taken a different route. With 
drop=FALSE, the function is also applied to subset corresponding to combination 
of grouping variables that doesn't appear in the data (example 2 in 
https://stat.ethz.ch/pipermail/r-devel/2017-January/073678.html).

Interesting point (I couldn't easily find 'the example 2' though).
However, aggregate.data.frame() is a considerably more
sophisticated function and one goal was to change tapply() as
little as possible for compatibility (and maintenance!) reasons .

> Because 'default' is used only when simplification happens, putting 'default' 
> after 'simplify' in the argument list may be more logical. 

Yes, from this point of view, you are right; I had thought about
that too; on the other hand, it belongs "closely" to the 'FUN'
and I think that's why I had decided not to change the proposal..

> Anyway, it doesn't affect call to 'tapply' because the argument 'default' 
> must be specified by name.

Exactly.. so we keep the order as is.

> With the code using
>if(missing(default)) ,
> I consider the stated default value of 'default',
>default = NA ,
> misleading because the code doesn't use it. 

I know and I also had thought about it and decided to keep it 
in the spirit of "self documentation" because  "in spirit", the
default still *is* NA.

> Also,
>  tapply(1:3, 1:3, as.raw)
> is not the same as
>  tapply(1:3, 1:3, as.raw, default = NA) .
> The accurate statement is the code in
> if(missing(default)) ,
> but it involves the local variable 'ans'.

exactly.  But putting that whole expression in there would look
confusing to those using  str(tapply), args(tapply) or similar
inspection to quickly get a glimpse of the function user "interface".
That's why we typically don't do that and rather slightly cheat
with the formal default, for the above "didactical" purposes.

If you are puristic about this, then missing() should almost never
be used when the function argument has a formal default.

I don't have a too strong opinion here, and we do have quite a
few other cases, where the formal default argument is not always
used because of   if(missing(.))  clauses.

I think I could be convinced to drop the '= NA' from the formal
argument list..


> As far as I know, the result of function 'array' in is not a classed 
object and the default method of  `[<-` will be used in the 'tapply' code 
portion.

> As far as I know, the result of 'lapply' is a list without class. So, 
'unlist' applied to it uses the default method and the 'unlist' result is a 
vector or a factor.

You may be right here
  ((or not:  If a package author makes array() into an S3 generic and defines
S3method(array, *) and she or another make tapply() into a
generic with methods,  are we really sure that this code
would not be used ??))

still, the as.raw example did not easily work without a warning
when using as.vector() .. or similar.

> With the change, the result of

> tapply(1:3, 1:3, factor, levels=3:1)

> is of mode "character". The value is from the internal code, not from the 
factor levels. It is worse than before the change, where it is really the 
internal code, integer.

I agree that this change is not desirable.
One could argue that it was quite a "lucky coincidence" that the previous
code returned the internal integer codes though..


> In the documentation, the description of argument 'simplify' says: "If 
'TRUE' (the default), then if 'FUN' always returns a scalar, 'tapply' returns 
an array with the mode of the scalar."


> To initialize array, a zero-length vector can also be used.

yes, of course; but my  ans[0L][1L]  had the purpose to get the
correct mode specific version of NA .. which works for raw (by
getting '00' because "raw" has *no* NA!).

So it seems I need an additional   !is.factor(ans)  there ...
a bit ugly.


-

> For 'xtabs', I think that it is better if the result has storage mode 
> "integer" if 'sum' results are of storage mode "integer", as in R 3.3.2. 

you are right, that *is* preferable

>  As 'default' argument for 'tapply', 'xtabs' can use 0L, or use 0L or 0 
> depending on storage mode of the summed quantity.

indeed, that will be an improvement there!

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Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Suharto Anggono Suharto Anggono via R-devel]

Function 'aggregate.data.frame' in R has taken a different route. With 
drop=FALSE, the function is also applied to subset corresponding to combination 
of grouping variables that doesn't appear in the data (example 2 in 
https://stat.ethz.ch/pipermail/r-devel/2017-January/073678.html).

Because 'default' is used only when simplification happens, putting 'default' 
after 'simplify' in the argument list may be more logical. Anyway, it doesn't 
affect call to 'tapply' because the argument 'default' must be specified by 
name.

With the code using
if(missing(default)) ,
I consider the stated default value of 'default',
default = NA ,
misleading because the code doesn't use it. Also,
tapply(1:3, 1:3, as.raw)
is not the same as
tapply(1:3, 1:3, as.raw, default = NA) .
The accurate statement is the code in
if(missing(default)) ,
but it involves the local variable 'ans'.

As far as I know, the result of function 'array' in is not a classed object and 
the default method of  `[<-` will be used in the 'tapply' code portion.

As far as I know, the result of 'lapply' is a list without class. So, 'unlist' 
applied to it uses the default method and the 'unlist' result is a vector or a 
factor.

With the change, the result of
tapply(1:3, 1:3, factor, levels=3:1)
is of mode "character". The value is from the internal code, not from the 
factor levels. It is worse than before the change, where it is really the 
internal code, integer.
In the documentation, the description of argument 'simplify' says: "If 'TRUE' 
(the default), then if 'FUN' always returns a scalar, 'tapply' returns an array 
with the mode of the scalar."

To initialize array, a zero-length vector can also be used.

For 'xtabs', I think that it is better if the result has storage mode "integer" 
if 'sum' results are of storage mode "integer", as in R 3.3.2. As 'default' 
argument for 'tapply', 'xtabs' can use 0L, or use 0L or 0 depending on storage 
mode of the summed quantity.


> Henrik Bengtsson 
> on Fri, 27 Jan 2017 09:46:15 -0800 writes:

> On Fri, Jan 27, 2017 at 12:34 AM, Martin Maechler
>  wrote:
>> 
>> > On Jan 26, 2017 07:50, "William Dunlap via R-devel"
>>  > wrote:
>> 
>> > It would be cool if the default for tapply's init.value
>> could be > FUN(X[0]), so it would be 0 for FUN=sum or
>> FUN=length, TRUE for > FUN=all, -Inf for FUN=max, etc.
>> But that would take time and would > break code for which
>> FUN did not work on length-0 objects.
>> 
>> > Bill Dunlap > TIBCO Software > wdunlap tibco.com
>> 
>> I had the same idea (after my first post), so I agree
>> that would be nice. One could argue it would take time
>> only if the user is too lazy to specify the value, and we
>> could use tryCatch(FUN(X[0]), error = NA) to safeguard
>> against those functions that fail for 0 length arg.
>> 
>> But I think the main reason for _not_ setting such a
>> default is back-compatibility.  In my proposal, the new
>> argument would not be any change by default and so all
>> current uses of tapply() would remain unchanged.
>> 
>>> Henrik Bengtsson  on
>>> Thu, 26 Jan 2017 07:57:08 -0800 writes:
>> 
>> > On a related note, the storage mode should try to match
>> ans[[1]] (or > unlist:ed and) when allocating 'ansmat' to
>> avoid coercion and hence a full > copy.
>> 
>> Yes, related indeed; and would fall "in line" with Bill's
>> idea.  OTOH, it could be implemented independently, by
>> something like
>> 
>> if(missing(init.value)) init.value <- if(length(ans))
>> as.vector(NA, mode=storage.mode(ans[[1]])) else NA

> I would probably do something like:

>   ans <- unlist(ans, recursive = FALSE, use.names = FALSE)
>   if (length(ans)) storage.mode(init.value) <- storage.mode(ans[[1]])
>   ansmat <- array(init.value, dim = extent, dimnames = namelist)

> instead.  That completely avoids having to use missing() and the value
> of 'init.value' will be coerced later if not done upfront.  use.names
> = FALSE speeds up unlist().

Thank you, Henrik.
That's a good idea to do the unlist() first, and with 'use.names=FALSE'.
I'll copy that.

On the other hand, "brutally" modifying  'init.value' (now called 'default')
even when the user has specified it is not acceptable I think.
You are right that it would be coerced anyway subsequently, but
the coercion will happen in whatever method of  `[<-` will be
appropriate.
Good S3 and S4 programmers will write such methods for their classes.

For that reason, I'm even more conservative now, only fiddle in
case of an atomic 'ans' and make use of the corresponding '['
method rather than as.vector(.) ... because that will fulfill
the following new regression test {not fulfilled in current R}:

identical(tapply(1:3, 1:3, as.raw),
  array(as.raw(1:3), 3L, dimnames=list(1:3)))

Also, I've done a few more things -- treating if(.) 

Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Martin Maechler]

> Henrik Bengtsson 
> on Fri, 27 Jan 2017 09:46:15 -0800 writes:

> On Fri, Jan 27, 2017 at 12:34 AM, Martin Maechler
>  wrote:
>> 
>> > On Jan 26, 2017 07:50, "William Dunlap via R-devel"
>>  > wrote:
>> 
>> > It would be cool if the default for tapply's init.value
>> could be > FUN(X[0]), so it would be 0 for FUN=sum or
>> FUN=length, TRUE for > FUN=all, -Inf for FUN=max, etc.
>> But that would take time and would > break code for which
>> FUN did not work on length-0 objects.
>> 
>> > Bill Dunlap > TIBCO Software > wdunlap tibco.com
>> 
>> I had the same idea (after my first post), so I agree
>> that would be nice. One could argue it would take time
>> only if the user is too lazy to specify the value, and we
>> could use tryCatch(FUN(X[0]), error = NA) to safeguard
>> against those functions that fail for 0 length arg.
>> 
>> But I think the main reason for _not_ setting such a
>> default is back-compatibility.  In my proposal, the new
>> argument would not be any change by default and so all
>> current uses of tapply() would remain unchanged.
>> 
>>> Henrik Bengtsson  on
>>> Thu, 26 Jan 2017 07:57:08 -0800 writes:
>> 
>> > On a related note, the storage mode should try to match
>> ans[[1]] (or > unlist:ed and) when allocating 'ansmat' to
>> avoid coercion and hence a full > copy.
>> 
>> Yes, related indeed; and would fall "in line" with Bill's
>> idea.  OTOH, it could be implemented independently, by
>> something like
>> 
>> if(missing(init.value)) init.value <- if(length(ans))
>> as.vector(NA, mode=storage.mode(ans[[1]])) else NA

> I would probably do something like:

>   ans <- unlist(ans, recursive = FALSE, use.names = FALSE)
>   if (length(ans)) storage.mode(init.value) <- storage.mode(ans[[1]])
>   ansmat <- array(init.value, dim = extent, dimnames = namelist)

> instead.  That completely avoids having to use missing() and the value
> of 'init.value' will be coerced later if not done upfront.  use.names
> = FALSE speeds up unlist().

Thank you, Henrik.
That's a good idea to do the unlist() first, and with 'use.names=FALSE'.
I'll copy that.

On the other hand, "brutally" modifying  'init.value' (now called 'default')
even when the user has specified it is not acceptable I think.
You are right that it would be coerced anyway subsequently, but
the coercion will happen in whatever method of  `[<-` will be
appropriate.
Good S3 and S4 programmers will write such methods for their classes.

For that reason, I'm even more conservative now, only fiddle in
case of an atomic 'ans' and make use of the corresponding '['
method rather than as.vector(.) ... because that will fulfill
the following new regression test {not fulfilled in current R}:

identical(tapply(1:3, 1:3, as.raw),
  array(as.raw(1:3), 3L, dimnames=list(1:3)))

Also, I've done a few more things -- treating if(.) . else . as a
function call, etc  and now committed as  rev 72040  to
R-devel... really wanting to get this out.

We can bet if there will be ripples in (visible) package space,
I give it relatively high chance for no ripples (and much higher
chance for problems with the more aggressive proposal..)

Thank you again, for your "thinking along" and constructive
suggestions.

Martin

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Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Henrik Bengtsson]

On Fri, Jan 27, 2017 at 12:34 AM, Martin Maechler
 wrote:
>
> > On Jan 26, 2017 07:50, "William Dunlap via R-devel" 
> 
> > wrote:
>
> > It would be cool if the default for tapply's init.value could be
> > FUN(X[0]), so it would be 0 for FUN=sum or FUN=length, TRUE for
> > FUN=all, -Inf for FUN=max, etc.  But that would take time and would
> > break code for which FUN did not work on length-0 objects.
>
> > Bill Dunlap
> > TIBCO Software
> > wdunlap tibco.com
>
> I had the same idea (after my first post), so I agree that would
> be nice. One could argue it would take time only if the user is too lazy
> to specify the value,  and we could use
>tryCatch(FUN(X[0]), error = NA)
> to safeguard against those functions that fail for 0 length arg.
>
> But I think the main reason for _not_ setting such a default is
> back-compatibility.  In my proposal, the new argument would not
> be any change by default and so all current uses of tapply()
> would remain unchanged.
>
>> Henrik Bengtsson 
>> on Thu, 26 Jan 2017 07:57:08 -0800 writes:
>
> > On a related note, the storage mode should try to match ans[[1]] (or
> > unlist:ed and) when allocating 'ansmat' to avoid coercion and hence a 
> full
> > copy.
>
> Yes, related indeed; and would fall "in line" with Bill's idea.
> OTOH, it could be implemented independently,
> by something like
>
>if(missing(init.value))
>  init.value <-
>if(length(ans)) as.vector(NA, mode=storage.mode(ans[[1]]))
>else NA

I would probably do something like:

  ans <- unlist(ans, recursive = FALSE, use.names = FALSE)
  if (length(ans)) storage.mode(init.value) <- storage.mode(ans[[1]])
  ansmat <- array(init.value, dim = extent, dimnames = namelist)

instead.  That completely avoids having to use missing() and the value
of 'init.value' will be coerced later if not done upfront.  use.names
= FALSE speeds up unlist().

/Henrik

>
> .
>
> A colleague proposed to use the shorter argument name 'default'
> instead of 'init.value'  which indeed maybe more natural and
> still not too often used as "non-first" argument in  FUN(.).
>
> Thank you for the constructive feedback!
> Martin
>
> > On Thu, Jan 26, 2017 at 2:42 AM, Martin Maechler
> >  wrote:
> >> Last week, we've talked here about "xtabs(), factors and NAs",
> -> https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html
> >>
> >> In the mean time, I've spent several hours on the issue
> >> and also committed changes to R-devel "in two iterations".
> >>
> >> In the case there is a *Left* hand side part to xtabs() formula,
> >> see the help page example using 'esoph',
> >> it uses  tapply(...,  FUN = sum)   and
> >> I now think there is a missing feature in tapply() there, which
> >> I am proposing to change.
> >>
> >> Look at a small example:
> >>
> >>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]),
> > N=3)[-c(1,5), ]; xtabs(~., D2)
> >> , , N = 3
> >>
> >> L
> >> n   A B C D E F
> >> 1 1 2 0 0 0 0
> >> 2 0 0 1 2 0 0
> >> 3 0 0 0 0 2 2
> >>
> >>> DN <- D2; DN[1,"N"] <- NA; DN
> >> n L  N
> >> 2  1 A NA
> >> 3  1 B  3
> >> 4  1 B  3
> >> 6  2 C  3
> >> 7  2 D  3
> >> 8  2 D  3
> >> 9  3 E  3
> >> 10 3 E  3
> >> 11 3 F  3
> >> 12 3 F  3
> >>> with(DN, tapply(N, list(n,L), FUN=sum))
> >> A  B  C  D  E  F
> >> 1 NA  6 NA NA NA NA
> >> 2 NA NA  3  6 NA NA
> >> 3 NA NA NA NA  6  6
> >>>
> >>
> >> and as you can see, the resulting matrix has NAs, all the same
> >> NA_real_, but semantically of two different kinds:
> >>
> >> 1) at ["1", "A"], the  NA  comes from the NA in 'N'
> >> 2) all other NAs come from the fact that there is no such factor
> > combination
> >> *and* from the fact that tapply() uses
> >>
> >> array(dim = .., dimnames = ...)
> >>
> >> i.e., initializes the array with NAs  (see definition of 'array').
> >>
> >> My proposition is the following patch to  tapply(), adding a new
> >> option 'init.value':
> >>
> >> 
> > -
> >>
> >> -tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
> >> +tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, 
> simplify
> > = TRUE)
> >> {
> >> FUN <- if (!is.null(FUN)) match.fun(FUN)
> >> if (!is.list(INDEX)) INDEX <- list(INDEX)
> >> @@ -44,7 +44,7 @@
> >> index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
> >> ans <- lapply(X = ans[index], FUN = FUN, ...)
> >> if (simplify && all(lengths(ans) == 1L)) {
> >> -   ansmat <- array(dim = extent, dimnames = namelist)
> >> 

Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Martin Maechler]

> Suharto Anggono Suharto Anggono via R-devel 
> on Fri, 27 Jan 2017 16:36:59 + writes:

> The "no factor combination" case is distinguishable by 'tapply' with 
simplify=FALSE.
>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]), N=3)
>> D2 <- D2[-c(1,5), ]
>> DN <- D2; DN[1,"N"] <- NA
>> with(DN, tapply(N, list(n,L), FUN=sum, simplify=FALSE))
> ABCDEF
> 1 NA   6NULL NULL NULL NULL
> 2 NULL NULL 36NULL NULL
> 3 NULL NULL NULL NULL 66

Yes, I know that simplify=FALSE  behaves differently, it returns
a list with dim & dimnames, sometimes also called a "list - matrix"
... and it *can* be used instead, but to be useful needs to be
post processed and that overall is somewhat inefficient and ugly.


> There is an old related discussion starting on 
https://stat.ethz.ch/pipermail/r-devel/2007-November/047338.html .

Thank you, indeed, for finding that. There Andrew Robinson did
raise the same issue, but his proposed solution was not much
back compatible and I think was primarily dismissed because of that.

Martin

> --
> Last week, we've talked here about "xtabs(), factors and NAs",
-> https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html

> In the mean time, I've spent several hours on the issue
> and also committed changes to R-devel "in two iterations".

> In the case there is a *Left* hand side part to xtabs() formula,
> see the help page example using 'esoph',
> it uses  tapply(...,  FUN = sum)   and
> I now think there is a missing feature in tapply() there, which
> I am proposing to change. 

> Look at a small example:

>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]), 
N=3)[-c(1,5), ]; xtabs(~., D2)
> , , N = 3

> L
> n   A B C D E F
> 1 1 2 0 0 0 0
> 2 0 0 1 2 0 0
> 3 0 0 0 0 2 2

>> DN <- D2; DN[1,"N"] <- NA; DN
> n L  N
> 2  1 A NA
> 3  1 B  3
> 4  1 B  3
> 6  2 C  3
> 7  2 D  3
> 8  2 D  3
> 9  3 E  3
> 10 3 E  3
> 11 3 F  3
> 12 3 F  3
>> with(DN, tapply(N, list(n,L), FUN=sum))
> A  B  C  D  E  F
> 1 NA  6 NA NA NA NA
> 2 NA NA  3  6 NA NA
> 3 NA NA NA NA  6  6
>> 

> and as you can see, the resulting matrix has NAs, all the same
> NA_real_, but semantically of two different kinds:

> 1) at ["1", "A"], the  NA  comes from the NA in 'N'
> 2) all other NAs come from the fact that there is no such factor 
combination
> *and* from the fact that tapply() uses

> array(dim = .., dimnames = ...)

> i.e., initializes the array with NAs  (see definition of 'array').

> My proposition is the following patch to  tapply(), adding a new
> option 'init.value':

> 
-
 
> -tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
> +tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify 
= TRUE)
> {
> FUN <- if (!is.null(FUN)) match.fun(FUN)
> if (!is.list(INDEX)) INDEX <- list(INDEX)
> @@ -44,7 +44,7 @@
> index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
> ans <- lapply(X = ans[index], FUN = FUN, ...)
> if (simplify && all(lengths(ans) == 1L)) {
> - ansmat <- array(dim = extent, dimnames = namelist)
> + ansmat <- array(init.value, dim = extent, dimnames = namelist)
> ans <- unlist(ans, recursive = FALSE)
> } else {
> ansmat <- array(vector("list", prod(extent)),

> 
-

> With that, I can set the initial value to '0' instead of array's
> default of NA :

>> with(DN, tapply(N, list(n,L), FUN=sum, init.value=0))
> A B C D E F
> 1 NA 6 0 0 0 0
> 2  0 0 3 6 0 0
> 3  0 0 0 0 6 6
>> 

> which now has 0 counts and NA  as is desirable to be used inside
> xtabs().

> All fine... and would not be worth a posting to R-devel,
> except for this:

> The change will not be 100% back compatible -- by necessity: any new 
argument for
> tapply() will make that argument name not available to be
> specified (via '...') for 'FUN'.  The new function would be

>> str(tapply)
> function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = TRUE)  

> where the '...' are passed FUN(),  and with the new signature,
> 'init.value' then won't be passed to FUN  "anymore" (compared to
> R <= 3.3.x).

> For that reason, we could use   'INIT.VALUE' instead (possibly decreasing
> the probability the arg name is used in other functions).


> Opinions?

> Thank you in advance,
> Martin

> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Suharto Anggono Suharto Anggono via R-devel]

The "no factor combination" case is distinguishable by 'tapply' with 
simplify=FALSE.

> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]), N=3)
> D2 <- D2[-c(1,5), ]
> DN <- D2; DN[1,"N"] <- NA
> with(DN, tapply(N, list(n,L), FUN=sum, simplify=FALSE))
  ABCDEF
1 NA   6NULL NULL NULL NULL
2 NULL NULL 36NULL NULL
3 NULL NULL NULL NULL 66


There is an old related discussion starting on 
https://stat.ethz.ch/pipermail/r-devel/2007-November/047338.html .

--
Last week, we've talked here about "xtabs(), factors and NAs",
 ->  https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html

In the mean time, I've spent several hours on the issue
and also committed changes to R-devel "in two iterations".

In the case there is a *Left* hand side part to xtabs() formula,
see the help page example using 'esoph',
it uses  tapply(...,  FUN = sum)   and
I now think there is a missing feature in tapply() there, which
I am proposing to change. 

Look at a small example:

> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]), N=3)[-c(1,5), 
> ]; xtabs(~., D2)
, , N = 3

   L
n   A B C D E F
  1 1 2 0 0 0 0
  2 0 0 1 2 0 0
  3 0 0 0 0 2 2

> DN <- D2; DN[1,"N"] <- NA; DN
   n L  N
2  1 A NA
3  1 B  3
4  1 B  3
6  2 C  3
7  2 D  3
8  2 D  3
9  3 E  3
10 3 E  3
11 3 F  3
12 3 F  3
> with(DN, tapply(N, list(n,L), FUN=sum))
   A  B  C  D  E  F
1 NA  6 NA NA NA NA
2 NA NA  3  6 NA NA
3 NA NA NA NA  6  6
>  

and as you can see, the resulting matrix has NAs, all the same
NA_real_, but semantically of two different kinds:

1) at ["1", "A"], the  NA  comes from the NA in 'N'
2) all other NAs come from the fact that there is no such factor combination
   *and* from the fact that tapply() uses

   array(dim = .., dimnames = ...)

i.e., initializes the array with NAs  (see definition of 'array').

My proposition is the following patch to  tapply(), adding a new
option 'init.value':

-
 
-tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
+tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = 
TRUE)
 {
 FUN <- if (!is.null(FUN)) match.fun(FUN)
 if (!is.list(INDEX)) INDEX <- list(INDEX)
@@ -44,7 +44,7 @@
 index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
 ans <- lapply(X = ans[index], FUN = FUN, ...)
 if (simplify && all(lengths(ans) == 1L)) {
-   ansmat <- array(dim = extent, dimnames = namelist)
+   ansmat <- array(init.value, dim = extent, dimnames = namelist)
ans <- unlist(ans, recursive = FALSE)
 } else {
ansmat <- array(vector("list", prod(extent)),

-

With that, I can set the initial value to '0' instead of array's
default of NA :

> with(DN, tapply(N, list(n,L), FUN=sum, init.value=0))
   A B C D E F
1 NA 6 0 0 0 0
2  0 0 3 6 0 0
3  0 0 0 0 6 6
> 

which now has 0 counts and NA  as is desirable to be used inside
xtabs().

All fine... and would not be worth a posting to R-devel,
except for this:

The change will not be 100% back compatible -- by necessity: any new argument 
for
tapply() will make that argument name not available to be
specified (via '...') for 'FUN'.  The new function would be

> str(tapply)
function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = TRUE)  

where the '...' are passed FUN(),  and with the new signature,
'init.value' then won't be passed to FUN  "anymore" (compared to
R <= 3.3.x).

For that reason, we could use   'INIT.VALUE' instead (possibly decreasing
the probability the arg name is used in other functions).


Opinions?

Thank you in advance,
Martin

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Gabor Grothendieck]

If xtabs is enhanced then as.data.frame.table may also need to be
modified so that it continues to be usable as an inverse, at least to
the degree feasible.


On Thu, Jan 26, 2017 at 5:42 AM, Martin Maechler
 wrote:
> Last week, we've talked here about "xtabs(), factors and NAs",
>  ->  https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html
>
> In the mean time, I've spent several hours on the issue
> and also committed changes to R-devel "in two iterations".
>
> In the case there is a *Left* hand side part to xtabs() formula,
> see the help page example using 'esoph',
> it uses  tapply(...,  FUN = sum)   and
> I now think there is a missing feature in tapply() there, which
> I am proposing to change.
>
> Look at a small example:
>
>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]), 
>> N=3)[-c(1,5), ]; xtabs(~., D2)
> , , N = 3
>
>L
> n   A B C D E F
>   1 1 2 0 0 0 0
>   2 0 0 1 2 0 0
>   3 0 0 0 0 2 2
>
>> DN <- D2; DN[1,"N"] <- NA; DN
>n L  N
> 2  1 A NA
> 3  1 B  3
> 4  1 B  3
> 6  2 C  3
> 7  2 D  3
> 8  2 D  3
> 9  3 E  3
> 10 3 E  3
> 11 3 F  3
> 12 3 F  3
>> with(DN, tapply(N, list(n,L), FUN=sum))
>A  B  C  D  E  F
> 1 NA  6 NA NA NA NA
> 2 NA NA  3  6 NA NA
> 3 NA NA NA NA  6  6
>>
>
> and as you can see, the resulting matrix has NAs, all the same
> NA_real_, but semantically of two different kinds:
>
> 1) at ["1", "A"], the  NA  comes from the NA in 'N'
> 2) all other NAs come from the fact that there is no such factor combination
>*and* from the fact that tapply() uses
>
>array(dim = .., dimnames = ...)
>
> i.e., initializes the array with NAs  (see definition of 'array').
>
> My proposition is the following patch to  tapply(), adding a new
> option 'init.value':
>
> -
>
> -tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
> +tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = 
> TRUE)
>  {
>  FUN <- if (!is.null(FUN)) match.fun(FUN)
>  if (!is.list(INDEX)) INDEX <- list(INDEX)
> @@ -44,7 +44,7 @@
>  index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
>  ans <- lapply(X = ans[index], FUN = FUN, ...)
>  if (simplify && all(lengths(ans) == 1L)) {
> -   ansmat <- array(dim = extent, dimnames = namelist)
> +   ansmat <- array(init.value, dim = extent, dimnames = namelist)
> ans <- unlist(ans, recursive = FALSE)
>  } else {
> ansmat <- array(vector("list", prod(extent)),
>
> -
>
> With that, I can set the initial value to '0' instead of array's
> default of NA :
>
>> with(DN, tapply(N, list(n,L), FUN=sum, init.value=0))
>A B C D E F
> 1 NA 6 0 0 0 0
> 2  0 0 3 6 0 0
> 3  0 0 0 0 6 6
>>
>
> which now has 0 counts and NA  as is desirable to be used inside
> xtabs().
>
> All fine... and would not be worth a posting to R-devel,
> except for this:
>
> The change will not be 100% back compatible -- by necessity: any new argument 
> for
> tapply() will make that argument name not available to be
> specified (via '...') for 'FUN'.  The new function would be
>
>> str(tapply)
> function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = TRUE)
>
> where the '...' are passed FUN(),  and with the new signature,
> 'init.value' then won't be passed to FUN  "anymore" (compared to
> R <= 3.3.x).
>
> For that reason, we could use   'INIT.VALUE' instead (possibly decreasing
> the probability the arg name is used in other functions).
>
>
> Opinions?
>
> Thank you in advance,
> Martin
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

__
R-devel@r-project.org mailing list
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Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Martin Maechler]

> On Jan 26, 2017 07:50, "William Dunlap via R-devel" 

> wrote:

> It would be cool if the default for tapply's init.value could be
> FUN(X[0]), so it would be 0 for FUN=sum or FUN=length, TRUE for
> FUN=all, -Inf for FUN=max, etc.  But that would take time and would
> break code for which FUN did not work on length-0 objects.

> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com

I had the same idea (after my first post), so I agree that would
be nice. One could argue it would take time only if the user is too lazy
to specify the value,  and we could use 
   tryCatch(FUN(X[0]), error = NA)
to safeguard against those functions that fail for 0 length arg.

But I think the main reason for _not_ setting such a default is
back-compatibility.  In my proposal, the new argument would not
be any change by default and so all current uses of tapply()
would remain unchanged.

> Henrik Bengtsson 
> on Thu, 26 Jan 2017 07:57:08 -0800 writes:

> On a related note, the storage mode should try to match ans[[1]] (or
> unlist:ed and) when allocating 'ansmat' to avoid coercion and hence a full
> copy.

Yes, related indeed; and would fall "in line" with Bill's idea.
OTOH, it could be implemented independently,
by something like

   if(missing(init.value))
 init.value <-
   if(length(ans)) as.vector(NA, mode=storage.mode(ans[[1]]))
   else NA

.

A colleague proposed to use the shorter argument name 'default'
instead of 'init.value'  which indeed maybe more natural and
still not too often used as "non-first" argument in  FUN(.).

Thank you for the constructive feedback!
Martin

> On Thu, Jan 26, 2017 at 2:42 AM, Martin Maechler
>  wrote:
>> Last week, we've talked here about "xtabs(), factors and NAs",
-> https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html
>> 
>> In the mean time, I've spent several hours on the issue
>> and also committed changes to R-devel "in two iterations".
>> 
>> In the case there is a *Left* hand side part to xtabs() formula,
>> see the help page example using 'esoph',
>> it uses  tapply(...,  FUN = sum)   and
>> I now think there is a missing feature in tapply() there, which
>> I am proposing to change.
>> 
>> Look at a small example:
>> 
>>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]),
> N=3)[-c(1,5), ]; xtabs(~., D2)
>> , , N = 3
>> 
>> L
>> n   A B C D E F
>> 1 1 2 0 0 0 0
>> 2 0 0 1 2 0 0
>> 3 0 0 0 0 2 2
>> 
>>> DN <- D2; DN[1,"N"] <- NA; DN
>> n L  N
>> 2  1 A NA
>> 3  1 B  3
>> 4  1 B  3
>> 6  2 C  3
>> 7  2 D  3
>> 8  2 D  3
>> 9  3 E  3
>> 10 3 E  3
>> 11 3 F  3
>> 12 3 F  3
>>> with(DN, tapply(N, list(n,L), FUN=sum))
>> A  B  C  D  E  F
>> 1 NA  6 NA NA NA NA
>> 2 NA NA  3  6 NA NA
>> 3 NA NA NA NA  6  6
>>> 
>> 
>> and as you can see, the resulting matrix has NAs, all the same
>> NA_real_, but semantically of two different kinds:
>> 
>> 1) at ["1", "A"], the  NA  comes from the NA in 'N'
>> 2) all other NAs come from the fact that there is no such factor
> combination
>> *and* from the fact that tapply() uses
>> 
>> array(dim = .., dimnames = ...)
>> 
>> i.e., initializes the array with NAs  (see definition of 'array').
>> 
>> My proposition is the following patch to  tapply(), adding a new
>> option 'init.value':
>> 
>> 
> -
>> 
>> -tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
>> +tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify
> = TRUE)
>> {
>> FUN <- if (!is.null(FUN)) match.fun(FUN)
>> if (!is.list(INDEX)) INDEX <- list(INDEX)
>> @@ -44,7 +44,7 @@
>> index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
>> ans <- lapply(X = ans[index], FUN = FUN, ...)
>> if (simplify && all(lengths(ans) == 1L)) {
>> -   ansmat <- array(dim = extent, dimnames = namelist)
>> +   ansmat <- array(init.value, dim = extent, dimnames = namelist)
>> ans <- unlist(ans, recursive = FALSE)
>> } else {
>> ansmat <- array(vector("list", prod(extent)),
>> 
>> 
> -
>> 
>> With that, I can set the initial value to '0' instead of array's
>> default of NA :
>> 
>>> with(DN, tapply(N, list(n,L), FUN=sum, init.value=0))
>> A B C D E F
>> 1 NA 6 0 0 0 0
>> 2  0 0 3 6 0 0
>> 3  0 0 0 0 6 6
>>> 
>> 
>> which now has 0 counts and NA  as is desirable to be used inside
>> xtabs().
>> 
>> All fine... and would not be worth a posting to R-devel,

Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[Henrik Bengtsson]

On a related note, the storage mode should try to match ans[[1]] (or
unlist:ed and) when allocating 'ansmat' to avoid coercion and hence a full
copy.

Henrik


On Jan 26, 2017 07:50, "William Dunlap via R-devel" 
wrote:

It would be cool if the default for tapply's init.value could be
FUN(X[0]), so it would be 0 for FUN=sum or FUN=length, TRUE for
FUN=all, -Inf for FUN=max, etc.  But that would take time and would
break code for which FUN did not work on length-0 objects.
Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Thu, Jan 26, 2017 at 2:42 AM, Martin Maechler
 wrote:
> Last week, we've talked here about "xtabs(), factors and NAs",
>  ->  https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html
>
> In the mean time, I've spent several hours on the issue
> and also committed changes to R-devel "in two iterations".
>
> In the case there is a *Left* hand side part to xtabs() formula,
> see the help page example using 'esoph',
> it uses  tapply(...,  FUN = sum)   and
> I now think there is a missing feature in tapply() there, which
> I am proposing to change.
>
> Look at a small example:
>
>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]),
N=3)[-c(1,5), ]; xtabs(~., D2)
> , , N = 3
>
>L
> n   A B C D E F
>   1 1 2 0 0 0 0
>   2 0 0 1 2 0 0
>   3 0 0 0 0 2 2
>
>> DN <- D2; DN[1,"N"] <- NA; DN
>n L  N
> 2  1 A NA
> 3  1 B  3
> 4  1 B  3
> 6  2 C  3
> 7  2 D  3
> 8  2 D  3
> 9  3 E  3
> 10 3 E  3
> 11 3 F  3
> 12 3 F  3
>> with(DN, tapply(N, list(n,L), FUN=sum))
>A  B  C  D  E  F
> 1 NA  6 NA NA NA NA
> 2 NA NA  3  6 NA NA
> 3 NA NA NA NA  6  6
>>
>
> and as you can see, the resulting matrix has NAs, all the same
> NA_real_, but semantically of two different kinds:
>
> 1) at ["1", "A"], the  NA  comes from the NA in 'N'
> 2) all other NAs come from the fact that there is no such factor
combination
>*and* from the fact that tapply() uses
>
>array(dim = .., dimnames = ...)
>
> i.e., initializes the array with NAs  (see definition of 'array').
>
> My proposition is the following patch to  tapply(), adding a new
> option 'init.value':
>
> 
-
>
> -tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
> +tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify
= TRUE)
>  {
>  FUN <- if (!is.null(FUN)) match.fun(FUN)
>  if (!is.list(INDEX)) INDEX <- list(INDEX)
> @@ -44,7 +44,7 @@
>  index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
>  ans <- lapply(X = ans[index], FUN = FUN, ...)
>  if (simplify && all(lengths(ans) == 1L)) {
> -   ansmat <- array(dim = extent, dimnames = namelist)
> +   ansmat <- array(init.value, dim = extent, dimnames = namelist)
> ans <- unlist(ans, recursive = FALSE)
>  } else {
> ansmat <- array(vector("list", prod(extent)),
>
> 
-
>
> With that, I can set the initial value to '0' instead of array's
> default of NA :
>
>> with(DN, tapply(N, list(n,L), FUN=sum, init.value=0))
>A B C D E F
> 1 NA 6 0 0 0 0
> 2  0 0 3 6 0 0
> 3  0 0 0 0 6 6
>>
>
> which now has 0 counts and NA  as is desirable to be used inside
> xtabs().
>
> All fine... and would not be worth a posting to R-devel,
> except for this:
>
> The change will not be 100% back compatible -- by necessity: any new
argument for
> tapply() will make that argument name not available to be
> specified (via '...') for 'FUN'.  The new function would be
>
>> str(tapply)
> function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = TRUE)
>
> where the '...' are passed FUN(),  and with the new signature,
> 'init.value' then won't be passed to FUN  "anymore" (compared to
> R <= 3.3.x).
>
> For that reason, we could use   'INIT.VALUE' instead (possibly decreasing
> the probability the arg name is used in other functions).
>
>
> Opinions?
>
> Thank you in advance,
> Martin
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: [Rd] RFC: tapply(*, ..., init.value = NA)

[William Dunlap via R-devel]

It would be cool if the default for tapply's init.value could be
FUN(X[0]), so it would be 0 for FUN=sum or FUN=length, TRUE for
FUN=all, -Inf for FUN=max, etc.  But that would take time and would
break code for which FUN did not work on length-0 objects.
Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Thu, Jan 26, 2017 at 2:42 AM, Martin Maechler
 wrote:
> Last week, we've talked here about "xtabs(), factors and NAs",
>  ->  https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html
>
> In the mean time, I've spent several hours on the issue
> and also committed changes to R-devel "in two iterations".
>
> In the case there is a *Left* hand side part to xtabs() formula,
> see the help page example using 'esoph',
> it uses  tapply(...,  FUN = sum)   and
> I now think there is a missing feature in tapply() there, which
> I am proposing to change.
>
> Look at a small example:
>
>> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]), 
>> N=3)[-c(1,5), ]; xtabs(~., D2)
> , , N = 3
>
>L
> n   A B C D E F
>   1 1 2 0 0 0 0
>   2 0 0 1 2 0 0
>   3 0 0 0 0 2 2
>
>> DN <- D2; DN[1,"N"] <- NA; DN
>n L  N
> 2  1 A NA
> 3  1 B  3
> 4  1 B  3
> 6  2 C  3
> 7  2 D  3
> 8  2 D  3
> 9  3 E  3
> 10 3 E  3
> 11 3 F  3
> 12 3 F  3
>> with(DN, tapply(N, list(n,L), FUN=sum))
>A  B  C  D  E  F
> 1 NA  6 NA NA NA NA
> 2 NA NA  3  6 NA NA
> 3 NA NA NA NA  6  6
>>
>
> and as you can see, the resulting matrix has NAs, all the same
> NA_real_, but semantically of two different kinds:
>
> 1) at ["1", "A"], the  NA  comes from the NA in 'N'
> 2) all other NAs come from the fact that there is no such factor combination
>*and* from the fact that tapply() uses
>
>array(dim = .., dimnames = ...)
>
> i.e., initializes the array with NAs  (see definition of 'array').
>
> My proposition is the following patch to  tapply(), adding a new
> option 'init.value':
>
> -
>
> -tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
> +tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = 
> TRUE)
>  {
>  FUN <- if (!is.null(FUN)) match.fun(FUN)
>  if (!is.list(INDEX)) INDEX <- list(INDEX)
> @@ -44,7 +44,7 @@
>  index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
>  ans <- lapply(X = ans[index], FUN = FUN, ...)
>  if (simplify && all(lengths(ans) == 1L)) {
> -   ansmat <- array(dim = extent, dimnames = namelist)
> +   ansmat <- array(init.value, dim = extent, dimnames = namelist)
> ans <- unlist(ans, recursive = FALSE)
>  } else {
> ansmat <- array(vector("list", prod(extent)),
>
> -
>
> With that, I can set the initial value to '0' instead of array's
> default of NA :
>
>> with(DN, tapply(N, list(n,L), FUN=sum, init.value=0))
>A B C D E F
> 1 NA 6 0 0 0 0
> 2  0 0 3 6 0 0
> 3  0 0 0 0 6 6
>>
>
> which now has 0 counts and NA  as is desirable to be used inside
> xtabs().
>
> All fine... and would not be worth a posting to R-devel,
> except for this:
>
> The change will not be 100% back compatible -- by necessity: any new argument 
> for
> tapply() will make that argument name not available to be
> specified (via '...') for 'FUN'.  The new function would be
>
>> str(tapply)
> function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = TRUE)
>
> where the '...' are passed FUN(),  and with the new signature,
> 'init.value' then won't be passed to FUN  "anymore" (compared to
> R <= 3.3.x).
>
> For that reason, we could use   'INIT.VALUE' instead (possibly decreasing
> the probability the arg name is used in other functions).
>
>
> Opinions?
>
> Thank you in advance,
> Martin
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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[Rd] RFC: tapply(*, ..., init.value = NA)

[Martin Maechler]

Last week, we've talked here about "xtabs(), factors and NAs",
 ->  https://stat.ethz.ch/pipermail/r-devel/2017-January/073621.html

In the mean time, I've spent several hours on the issue
and also committed changes to R-devel "in two iterations".

In the case there is a *Left* hand side part to xtabs() formula,
see the help page example using 'esoph',
it uses  tapply(...,  FUN = sum)   and
I now think there is a missing feature in tapply() there, which
I am proposing to change. 

Look at a small example:

> D2 <- data.frame(n = gl(3,4), L = gl(6,2, labels=LETTERS[1:6]), N=3)[-c(1,5), 
> ]; xtabs(~., D2)
, , N = 3

   L
n   A B C D E F
  1 1 2 0 0 0 0
  2 0 0 1 2 0 0
  3 0 0 0 0 2 2

> DN <- D2; DN[1,"N"] <- NA; DN
   n L  N
2  1 A NA
3  1 B  3
4  1 B  3
6  2 C  3
7  2 D  3
8  2 D  3
9  3 E  3
10 3 E  3
11 3 F  3
12 3 F  3
> with(DN, tapply(N, list(n,L), FUN=sum))
   A  B  C  D  E  F
1 NA  6 NA NA NA NA
2 NA NA  3  6 NA NA
3 NA NA NA NA  6  6
>  

and as you can see, the resulting matrix has NAs, all the same
NA_real_, but semantically of two different kinds:

1) at ["1", "A"], the  NA  comes from the NA in 'N'
2) all other NAs come from the fact that there is no such factor combination
   *and* from the fact that tapply() uses

   array(dim = .., dimnames = ...)

i.e., initializes the array with NAs  (see definition of 'array').

My proposition is the following patch to  tapply(), adding a new
option 'init.value':

-
 
-tapply <- function (X, INDEX, FUN = NULL, ..., simplify = TRUE)
+tapply <- function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = 
TRUE)
 {
 FUN <- if (!is.null(FUN)) match.fun(FUN)
 if (!is.list(INDEX)) INDEX <- list(INDEX)
@@ -44,7 +44,7 @@
 index <- as.logical(lengths(ans))  # equivalently, lengths(ans) > 0L
 ans <- lapply(X = ans[index], FUN = FUN, ...)
 if (simplify && all(lengths(ans) == 1L)) {
-   ansmat <- array(dim = extent, dimnames = namelist)
+   ansmat <- array(init.value, dim = extent, dimnames = namelist)
ans <- unlist(ans, recursive = FALSE)
 } else {
ansmat <- array(vector("list", prod(extent)),

-

With that, I can set the initial value to '0' instead of array's
default of NA :

> with(DN, tapply(N, list(n,L), FUN=sum, init.value=0))
   A B C D E F
1 NA 6 0 0 0 0
2  0 0 3 6 0 0
3  0 0 0 0 6 6
> 

which now has 0 counts and NA  as is desirable to be used inside
xtabs().

All fine... and would not be worth a posting to R-devel,
except for this:

The change will not be 100% back compatible -- by necessity: any new argument 
for
tapply() will make that argument name not available to be
specified (via '...') for 'FUN'.  The new function would be

> str(tapply)
function (X, INDEX, FUN = NULL, ..., init.value = NA, simplify = TRUE)  

where the '...' are passed FUN(),  and with the new signature,
'init.value' then won't be passed to FUN  "anymore" (compared to
R <= 3.3.x).

For that reason, we could use   'INIT.VALUE' instead (possibly decreasing
the probability the arg name is used in other functions).


Opinions?

Thank you in advance,
Martin

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