R help - Oct 2008 - possible bug in function 'var' in R 2.7.2?

Dear R-Help,

 

I have used R2.6.0 until I recently installed also R2.7.2 (see details below)

 

In R 2.6.0, the following script using the function 'var' (cor(stats)):

 

x.test <- c(NA, NA, NA, NA)

var(x.test, na.rm=T)        

 

gives the output: 

 

NA

 

In R2.7.2 the output of the same script generates an error message and stops R:

 

 'Error in var(x.test, na.rm = T) : no complete element pairs'

 

R2.7.2 can handle it if there is just one non-NA value in the list but not if
they are all NA.

 

I prefer the output of 2.6.0. Is this a bug in 2.7.2 or is it a deliberate
change compare to previous versions? Or is there a way to make R2.7.2 give NA as
output?

 

Thank you for any helo/comments!

 

Best regards,

 

Klaus

 

Details on R versions installed and platform:

Platform: Windows XP Prof, English, ver. 5.1

R2.6.0:

"LC_COLLATE=Danish_Denmark.1252;LC_CTYPE=Danish_Denmark.1252;LC_MONETARY=Danish_Denmark.1252;LC_NUMERIC=C;LC_TIME=Danish_Denmark.1252"

R2.7.2:

"LC_COLLATE=Danish_Denmark.1252;LC_CTYPE=Danish_Denmark.1252;LC_MONETARY=Danish_Denmark.1252;LC_NUMERIC=C;LC_TIME=Danish_Denmark.1252"

 

Klaus Steenberg Larsen
Scientist
Phone direct +45 4677 4157
klaus.steenberg.larsen@risoe.dk
 

Biosystems Division
Risø National Lab. for sustainable Energy
Risø DTU
Building 309, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4100
Fax +45 4677 4160
www.risoe.dk 
>From 1 January 2007, Risø National Laboratory, the Danish Institute for Food
and Veterinary Research,
the Danish Institute for Fisheries Research, the Danish National Space Center
and
the Danish Transport Research Institute have been merged with
the Technical University of Denmark (DTU) with DTU as the continuing unit.













 


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<klaus.steenberg.larsen <at> risoe.dk> writes:
> 
> Dear R-Help,
> 
> I have used R2.6.0 until I recently installed also R2.7.2 (see details
below)
> 
> In R 2.6.0, the following script using the function 'var'
(cor(stats)):
> 
> x.test <- c(NA, NA, NA, NA)
> 
> var(x.test, na.rm=T)        
> 
> gives the output: 
> 
> NA
> 
> In R2.7.2 the output of the same script generates an error message and
stops R:
> 
>  'Error in var(x.test, na.rm = T) : no complete element pairs'
> 
> R2.7.2 can handle it if there is just one non-NA value in the list but not
if
they are all NA.
> 
> I prefer the output of 2.6.0. Is this a bug in 2.7.2 or is it a deliberate
change compare to previous versions?
> Or is there a way to make R2.7.2 give NA as output?
> 
> Thank you for any helo/comments! 
> 
> Best regards,
> 
> Klaus
   This is a deliberate change, but the behavior will
(more or less) revert in version 2.8.0.  

 From the NEWS file for 2.7 (in bug fixes):

 o	co[rv](use = "complete.obs") now always gives an error if there
	are no complete cases: they used to give NA if
	method = "pearson" but an error for the other two methods.
	(Note that this is pretty arbitrary, but zero-length vectors
	always give an error so it is at least consistent.)

	Since sd(na.rm=TRUE) and var(na.rm=TRUE) both call cov(use 
"complete.obs"), this applies also to them.

	cor(use="pair") used to give diagonal 1 even if the variable
	was completely missing for the rank methods but NA for the
	Pearson method: it now gives NA in all cases.

	cor(use="pair") for the rank methods gave a matrix result with
	dimensions > 0 even if one of the inputs had 0 columns.


  From the NEWS file for the development version

   o   var(),cov(),cor() etc now by default (when 'use' is not
specified)
    	return NA in many cases where they signalled an error before.

I don't know of a really easy way to make the behavior revert, perhaps
the easiest workaround is to make a 'my.var' function that first
tests if(all(is.na(x))) -- if you want to live really dangerously
you could even call it 'var' and have it mask the built-in function,
but that's probably a bad idea.

  Ben Bolker