Is a list an atomic object? (or is there an issue with the help page of ?tapply ?)

Yes, exactly.

So my point is that this:

  "X: a vector-like object that supports subsetting with `[`, typically
     an atomic vector."

is incorrect, or at least a bit opaque, without further emphasizing
that FUN must accept the result of "[".

With atomic vectors, the error
that you produced was obvious, but with lists, I believe not so.

I Appreciate the desire for brevity, but I think clarity should be the
primary goal. Maybe it *is* just me, but I think a few extra words of
explanation here would not go amiss.

But, anyway, thanks for the clarification.

Cheers,
Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Feb 14, 2017 at 6:04 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:

Right. More precisely the function passed thru the FUN argument must
work on the subsets of X generated internally by tapply(). You can
actually see these subsets by passing the identity function:

  X <- letters[1:10]
  INDEX <- c(rep(1,5),rep(2,5))
  tapply(X, INDEX, FUN=identity)
  # $`1`
  # [1] "a" "b" "c" "d" "e"
  #
  # $`2`
  # [1] "f" "g" "h" "i" "j"

Doing this shows you how tapply() splits the vector-like object X into
a list of subsets. If you replace the identity function with a function
that cannot be applied to these subsets, then you get an error:

  tapply(X, INDEX, FUN=sum)
  # Error in FUN(X[[i]], ...) : invalid 'type' (character) of argument

As you can see, here we get an error even though X is an atomic vector.

H.



On 02/14/2017 05:41 PM, Richard M. Heiberger wrote:

The problem with Bert's second example is that sum doesn't work on a list.
The tapply worked correctly.

unlist(l[1:5])

[1] 1 2 3 4 5

sum(l[1:5])

Error in sum(l[1:5]) : invalid 'type' (list) of argument



On Tue, Feb 14, 2017 at 8:28 PM, Bert Gunter <bgunter.4567 at gmail.com>
wrote:

Herv?:

Kindly explain this, then:

l <- as.list(1:10)
is.atomic(l) # FALSE

[1] FALSE

index <- c(rep(1,5),rep(2,5))


tapply(l,index,unlist)

$`1`
[1] 1 2 3 4 5

$`2`
[1]  6  7  8  9 10

## But

tapply(l,index, sum)

Error in FUN(X[[i]], ...) : invalid 'type' (list) of argument

Cheers,
Bert
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Feb 14, 2017 at 5:10 PM, Herv? Pag?s <hpages at fredhutch.org>
wrote:

Hi,

tapply() will work on any object 'X' that has a length and supports
single-bracket subsetting. These objects are sometimes called
"vector-like" objects. Atomic vectors, lists, S4 objects with a "length"
and "[" method, etc... are examples of "vector-like" objects.

So instead of saying

  X: an atomic object, typically a vector.

I think it would be more accurate if the man page was saying something
like

  X: a vector-like object that supports subsetting with `[`, typically
     an atomic vector.

H.

On 02/04/2017 04:17 AM, Tal Galili wrote:

In the help page of ?tapply it says that the first argument (X) is "an
atomic object, typically a vector."

However, tapply seems to be able to handle list objects. For example:

###################

l <- as.list(1:10)
is.atomic(l) # FALSE
index <- c(rep(1,5),rep(2,5))
tapply(l,index,unlist)

tapply(l,index,unlist)

$`1`
[1] 1 2 3 4 5

$`2`
[1]  6  7  8  9 10


###################

Hence, does it mean a list an atomic object? (which I thought it
wasn't)
or
is the help for tapply needs updating?
(or some third option I'm missing?)

Thanks.





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--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319