[R] problem (and solution) to rle on vector with NA values

[Cormac Long]

D'oh! Completely missed that. Definately a case or RTFMS (RTFM, Stupid).

My apologies for the spam.

Sincerely (with additional grovelling)
Cormac.

On 23 June 2011 15:59, Nick Sabbe <nick.sabbe at ugent.be> wrote:
> Hello Cormac.
>
> Not having thoroughly checked whether your code actually works, the behavior
> of rle you describe is the one documented (check the details of ?rle) and
> makes sense as the missingness could have different reasons.
> As such, changing this type of behavior would probably break a lot of
> existing code that is built on top of rle.
>
> There are other peculiarities and disputabilities about some base R
> functions (the order of the arguments for sample trips me every time), but
> unless the argument is really strong or a downright bug, I doubt people will
> be willing to change this. Perhaps making the new behavior optional (through
> a new parameter na.action or similar, with the default the original
> behavior) is an option?
>
> Feel free to run your own version of rle in any case. I suggest you rename
> it, though, as it may cause problems for some packages.
>
>
> Nick Sabbe
> --
> ping: nick.sabbe at ugent.be
> link: http://biomath.ugent.be
> wink: A1.056, Coupure Links 653, 9000 Gent
> ring: 09/264.59.36
>
> -- Do Not Disapprove
>
>
>
>
>> -----Original Message-----
>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
>> project.org] On Behalf Of Cormac Long
>> Sent: donderdag 23 juni 2011 15:44
>> To: r-help at r-project.org
>> Subject: [R] problem (and solution) to rle on vector with NA values
>>
>> Hello there R-help,
>>
>> I'm not sure if this should be posted here - so apologies if this is
>> the case.
>> I've found a problem while using rle and am proposing a solution to the
>> issue.
>>
>> Description:
>> I ran into a niggle with rle today when working with vectors with NA
>> values
>> (using R 2.31.0 on Windows 7 x64). It transpires that a run of NA
>> values
>> is not encoded in the same way as a run of other values. See the
>> following
>> example as an illustration:
>>
>> Example:
>> The example
>>         rv<-c(1,1,NA,NA,3,3,3);rle(rv)
>> Returns
>>         Run Length Encoding
>>           lengths: int [1:4] 2 1 1 3
>>           values : num [1:4] 1 NA NA 3
>> not
>>         Run Length Encoding
>>           lengths: int [1:3] 2 2 3
>>           values : num [1:3] 1 NA 3
>> as I expected. This caused my code to fail later (unsurprising).
>>
>> Analysis:
>> The problem stems from the test
>>          y <- x[-1L] != x[-n]
>> in line 7 of the rle function body. In this test, NA values return
>> logical NA
>> values, not TRUE/FALSE (again, unsurprising).
>>
>> Resolution:
>> I modified the rle function code as included below. As far as I tested,
>> this
>> modification appears safe. The convoluted construction of naMaskVal
>> should guarantee that the NA masking value is always different from
>> any value in the vector and should be safe regardless of the input
>> vector
>> form (a raw vector is not handled since the NA values do not apply
>> here).
>>
>> rle<-function (x)
>> {
>>     if (!is.vector(x) && !is.list(x))
>>         stop("'x' must be an atomic vector")
>>     n <- length(x)
>>     if (n == 0L)
>>         return(structure(list(lengths = integer(), values = x),
>>             class = "rle"))
>>
>>     #### BEGIN NEW SECTION PART 1 ####
>>     naRepFlag<-F
>>     if(any(is.na(x))){
>>         naRepFlag<-T
>>         IS_LOGIC<-ifelse(typeof(x)=="logical",T,F)
>>
>>         if(typeof(x)=="logical"){
>>             x<-as.integer(x)
>>             naMaskVal<-2
>>         }else if(typeof(x)=="character"){
>>             naMaskVal<-
>> paste(sample(c(letters,LETTERS,0:9),32,replace=T),collapse="")
>>         }else{
>>             naMaskVal<-max(0,abs(x[!is.infinite(x)]),na.rm=T)+1
>>         }
>>
>>         x[which(is.na(x))]<-naMaskVal
>>     }
>>     #### END NEW SECTION PART 1 ####
>>
>>     y <- x[-1L] != x[-n]
>>     i <- c(which(y), n)
>>
>>     #### BEGIN NEW SECTION PART 2 ####
>>     if(naRepFlag)
>>         x[which(x==naMaskVal)]<-NA
>>
>>     if(IS_LOGIC)
>>         x<-as.logical(x)
>>     #### END NEW SECTION PART 2 ####
>>
>>     structure(list(lengths = diff(c(0L, i)), values = x[i]),
>>         class = "rle")
>> }
>>
>> Conclusion:
>> I think that the proposed code modification is an improvement on the
>> existing
>> implementation of rle. Is it impertinent to suggest this R-modification
>> to the
>> gurus at R?
>>
>> Best wishes (in flame-war trepidation),
>> Dr. Cormac Long.
>>
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>
>