[Rd] [External] Re: zapsmall(x) for scalar x
Serguei Sokol
@oko| @end|ng |rom |n@@-tou|ou@e@|r
Mon Dec 18 10:29:02 CET 2023
Le 17/12/2023 à 18:26, Barry Rowlingson a écrit :
> I think what's been missed is that zapsmall works relative to the absolute
> largest value in the vector. Hence if there's only one
> item in the vector, it is the largest, so its not zapped. The function's
> raison d'etre isn't to replace absolutely small values,
> but small values relative to the largest. Hence a vector of similar tiny
> values doesn't get zapped.
>
> Maybe the line in the docs:
>
> " (compared with the maximal absolute value)"
>
> needs to read:
>
> " (compared with the maximal absolute value in the vector)"
I agree that this change in the doc would clarify the situation but
would not resolve proposed corner cases.
I think that an additional argument 'mx' (absolute max value of
reference) would do. Consider:
zapsmall2 <-
function (x, digits = getOption("digits"), mx=max(abs(x), na.rm=TRUE))
{
if (length(digits) == 0L)
stop("invalid 'digits'")
if (all(ina <- is.na(x)))
return(x)
round(x, digits = if (mx > 0) max(0L, digits -
as.numeric(log10(mx))) else digits)
}
then zapsmall2() without explicit 'mx' behaves identically to actual
zapsmall() and for a scalar or a vector of identical value, user can
manually fix the scale of what should be considered as small:
> zapsmall2(y)
[1] 2.220446e-16
> zapsmall2(y, mx=1)
[1] 0
> zapsmall2(c(y, y), mx=1)
[1] 0 0
> zapsmall2(c(y, NA))
[1] 2.220446e-16 NA
> zapsmall2(c(y, NA), mx=1)
[1] 0 NA
Obviously, the name 'zapsmall2' was chosen just for this explanation.
The original name 'zapsmall' could be reused as a full backward
compatibility is preserved.
Best,
Serguei.
>
> Barry
>
>
>
>
>
> On Sun, Dec 17, 2023 at 2:17 PM Duncan Murdoch <murdoch.duncan using gmail.com>
> wrote:
>
>> This email originated outside the University. Check before clicking links
>> or attachments.
>>
>> I'm really confused. Steve's example wasn't a scalar x, it was a
>> vector. Your zapsmall() proposal wouldn't zap it to zero, and I don't
>> see why summary() would if it was using your proposal.
>>
>> Duncan Murdoch
>>
>> On 17/12/2023 8:43 a.m., Gregory R. Warnes wrote:
>>> Isn’t that the correct outcome? The user can change the number of
>> digits if they want to see small values…
>>>
>>> --
>>> Change your thoughts and you change the world.
>>> --Dr. Norman Vincent Peale
>>>
>>>> On Dec 17, 2023, at 12:11 AM, Steve Martin <stevemartin041 using gmail.com>
>> wrote:
>>>> Zapping a vector of small numbers to zero would cause problems when
>>>> printing the results of summary(). For example, if
>>>> zapsmall(c(2.220446e-16, ..., 2.220446e-16)) == c(0, ..., 0) then
>>>> print(summary(2.220446e-16), digits = 7) would print
>>>> Min. 1st Qu. Median Mean 3rd Qu. Max.
>>>> 0 0 0 0 0 0
>>>>
>>>> The same problem can also appear when printing the results of
>>>> summary.glm() with show.residuals = TRUE if there's little dispersion
>>>> in the residuals.
>>>>
>>>> Steve
>>>>
>>>>> On Sat, 16 Dec 2023 at 17:34, Gregory Warnes <greg using warnes.net> wrote:
>>>>>
>>>>> I was quite suprised to discover that applying `zapsmall` to a scalar
>> value has no apparent effect. For example:
>>>>>> y <- 2.220446e-16
>>>>>> zapsmall(y,)
>>>>> [1] 2.2204e-16
>>>>>
>>>>> I was expecting zapsmall(x)` to act like
>>>>>
>>>>>> round(y, digits=getOption('digits'))
>>>>> [1] 0
>>>>>
>>>>> Looking at the current source code, indicates that `zapsmall` is
>> expecting a vector:
>>>>> zapsmall <-
>>>>> function (x, digits = getOption("digits"))
>>>>> {
>>>>> if (length(digits) == 0L)
>>>>> stop("invalid 'digits'")
>>>>> if (all(ina <- is.na(x)))
>>>>> return(x)
>>>>> mx <- max(abs(x[!ina]))
>>>>> round(x, digits = if (mx > 0) max(0L, digits -
>> as.numeric(log10(mx))) else digits)
>>>>> }
>>>>>
>>>>> If `x` is a non-zero scalar, zapsmall will never perform rounding.
>>>>>
>>>>> The man page simply states:
>>>>> zapsmall determines a digits argument dr for calling round(x, digits =
>> dr) such that values close to zero (compared with the maximal absolute
>> value) are ‘zapped’, i.e., replaced by 0.
>>>>> and doesn’t provide any details about how ‘close to zero’ is defined.
>>>>>
>>>>> Perhaps handling the special when `x` is a scalar (or only contains a
>> single non-NA value) would make sense:
>>>>> zapsmall <-
>>>>> function (x, digits = getOption("digits"))
>>>>> {
>>>>> if (length(digits) == 0L)
>>>>> stop("invalid 'digits'")
>>>>> if (all(ina <- is.na(x)))
>>>>> return(x)
>>>>> mx <- max(abs(x[!ina]))
>>>>> round(x, digits = if (mx > 0 && (length(x)-sum(ina))>1 ) max(0L,
>> digits - as.numeric(log10(mx))) else digits)
>>>>> }
>>>>>
>>>>> Yielding:
>>>>>
>>>>>> y <- 2.220446e-16
>>>>>> zapsmall(y)
>>>>> [1] 0
>>>>>
>>>>> Another edge case would be when all of the non-na values are the same:
>>>>>
>>>>>> y <- 2.220446e-16
>>>>>> zapsmall(c(y,y))
>>>>> [1] 2.220446e-16 2.220446e-16
>>>>>
>>>>> Thoughts?
>>>>>
>>>>>
>>>>> Gregory R. Warnes, Ph.D.
>>>>> greg using warnes.net
>>>>> Eternity is a long time, take a friend!
>>>>>
>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
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--
Serguei Sokol
Ingenieur de recherche INRAE
Cellule Mathématiques
TBI, INSA/INRAE UMR 792, INSA/CNRS UMR 5504
135 Avenue de Rangueil
31077 Toulouse Cedex 04
tel: +33 5 61 55 98 49
email: sokol using insa-toulouse.fr
https://www.toulouse-biotechnology-institute.fr/en/plateformes-plateaux/cellule-mathematiques/
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