[R] Bug : Autocorrelation in sample drawn from stats::rnorm (hmh)
hmh
hugomh @end|ng |rom gmx@|r
Fri Oct 5 09:45:10 CEST 2018
Hi,
Thanks William for this fast answer, and sorry for sending the 1st mail
to r-help instead to r-devel.
I noticed that bug while I was simulating many small random walks using
c(0,cumsum(rnorm(10))). Then the negative auto-correlation was inducing
a muchsmaller space visited by the random walks than expected if there
would be no auto-correlation in the samples.
The code I provided and you optimized was only provided to illustrated
and investigate that bug.
It is really worrying that most of the R distributions are affected by
this bug !!!!
What I did should have been one of the first check done for _*each*_
distributions by the developers of these functions !
And if as you suggested this is a "tolerated" _error_ of the algorithm,
I do think this is a bad choice, but any way, this should have been
mentioned in the documentations of the functions !!
cheers,
hugo
On 05/10/2018 01:52, William Bell wrote:
> Hi Hugo,
>
> I've been able to replicate your bug, including for other
> distributions (runif, rexp, rgamma, etc) which shouldn't be surprising
> since they're probably all drawing from the same pseudo-random number
> generator. Interestingly, it does not seem to depend on the choice of
> seed, I am not sure why that is the case.
>
> I'll point out first of all that the R-devel mailing list is perhaps
> better suited for this query, I'm fairly sure we're supposed to direct
> bug reports, etc there.
>
> It is possible this is a known quantity but is tolerated, I could
> think of many reasons why that might be the case, not least of which
> being that as far as I know, the vast majority of Monte Carlo methods
> involve >>40 trials (which seems to be enough for the effect to
> disappear), with the possible exception of procedures for testing the
> power of statistical tests on small samples?
>
> There might be more to be said, but I thought I'd just add what I
> could from playing around with it a little bit.
>
> For anyone who wishes to give it a try, I suggest this implementation
> of the autocorrelation tester which is about 80 times faster:
>
> DistributionAutocorrelation_new <- function(SampleSize) {
> Cor <- replicate(1e5, function() {X <- rnorm(SampleSize)
> return(cor(X[-1], X[-length(X)]))})
> return(Cor)
> }
>
> I have the same Stats package version installed.
>
> - (Thomas) William Bell
> Hons BSc Candidate (Biology and Mathematics)
> BA Candidate (Philosophy)
> McMaster University
>
> # Hi,
> #
> #
> # I just noticed the following bug:
> #
> # When we draw a random sample using the function stats::rnorm, there
> # should be not auto-correlation in the sample. But their is some
> # auto-correlation _when the sample that is drawn is small_.
> #
> # I describe the problem using two functions:
> #
> # DistributionAutocorrelation_Unexpected which as the wrong behavior :
> # _when drawing some small samples using rnorm, there is generally a
> # strong negative auto-correlation in the sample_.
> #
> # and
> #
> # DistributionAutocorrelation_Expected which illustrate the expected
> behavior
> #
> #
> #
> # *Unexpected : *
> #
> # DistributionAutocorrelation_Unexpected = function(SampleSize){
> # Cor = NULL
> # for(repetition in 1:1e5){
> # X = rnorm(SampleSize)
> # Cor[repetition] = cor(X[-1],X[-length(X)])
> # }
> # return(Cor)
> # }
> #
> # par(mfrow=c(3,3))
> # for(SampleSize_ in c(4,5,6,7,8,10,15,20,50)){
> #
> hist(DistributionAutocorrelation_Unexpected(SampleSize_),col='grey',main=paste0('SampleSize=',SampleSize_))
>
> # ; abline(v=0,col=2)
> # }
> #
> # output:
> #
> #
> # *Expected**:*
> #
> # DistributionAutocorrelation_Expected = function(SampleSize){
> # Cor = NULL
> # for(repetition in 1:1e5){
> # X = rnorm(SampleSize)
> # * Cor[repetition] = cor(sample(X[-1]),sample(X[-length(X)]))*
> # }
> # return(Cor)
> # }
> #
> # par(mfrow=c(3,3))
> # for(SampleSize_ in c(4,5,6,7,8,10,15,20,50)){
> #
> hist(DistributionAutocorrelation_Expected(SampleSize_),col='grey',main=paste0('SampleSize=',SampleSize_))
>
> # ; abline(v=0,col=2)
> # }
> #
> #
> #
> #
> # Some more information you might need:
> #
> #
> # packageDescription("stats")
> # Package: stats
> # Version: 3.5.1
> # Priority: base
> # Title: The R Stats Package
> # Author: R Core Team and contributors worldwide
> # Maintainer: R Core Team <R-core using r-project.org>
> # Description: R statistical functions.
> # License: Part of R 3.5.1
> # Imports: utils, grDevices, graphics
> # Suggests: MASS, Matrix, SuppDists, methods, stats4
> # NeedsCompilation: yes
> # Built: R 3.5.1; x86_64-pc-linux-gnu; 2018-07-03 02:12:37 UTC; unix
> #
> # Thanks for correcting that.
> #
> # fill free to ask any further information you would need.
> #
> # cheers,
> #
> # hugo
> #
> #
> # --
> # - no title specified
> #
> # Hugo Mathé-Hubert
> #
> # ATER
> #
> # Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC)
> #
> # UMR 7360 CNRS - Bât IBISE
> #
> # Université de Lorraine - UFR SciFA
> #
> # 8, Rue du Général Delestraint
> #
> # F-57070 METZ
> #
> # +33(0)9 77 21 66 66
> # - - - - - - - - - - - - - - - - - -
> # Les réflexions naissent dans les doutes et meurent dans les
> certitudes.
> # Les doutes sont donc un signe de force et les certitudes un signe de
> # faiblesse. La plupart des gens sont pourtant certains du contraire.
> # - - - - - - - - - - - - - - - - - -
> # Thoughts appear from doubts and die in convictions. Therefore, doubts
> # are an indication of strength and convictions an indication of
> weakness.
> # Yet, most people believe the opposite.
--
- no title specified
Hugo Mathé-Hubert
ATER
Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC)
UMR 7360 CNRS - Bât IBISE
Université de Lorraine - UFR SciFA
8, Rue du Général Delestraint
F-57070 METZ
+33(0)9 77 21 66 66
- - - - - - - - - - - - - - - - - -
Les réflexions naissent dans les doutes et meurent dans les certitudes.
Les doutes sont donc un signe de force et les certitudes un signe de
faiblesse. La plupart des gens sont pourtant certains du contraire.
- - - - - - - - - - - - - - - - - -
Thoughts appear from doubts and die in convictions. Therefore, doubts
are an indication of strength and convictions an indication of weakness.
Yet, most people believe the opposite.
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