[R] strange behavior of cor() with pairwise.complete.obs

[Hilmar Berger]

Sorry, 

I obviously did not state clearly what the problem is (thanks Daniel):

1. minor problem: cor() does return different types of variables for
methods "kendall" and pearson (matrix vs. scalar) when 
pairwise.complete.obs is selected. 

2. major problem: cor() does return with an error if both x and y 
are matrices with method="kendall" when pairwise.complete.obs is
selected and one column of one of the two matrices is completely NA.
This does not happen for method "pearson".

Regards,
Hilmar

Hilmar Berger <hilmar.berger <at> imise.uni-leipzig.de> writes:
> 
> Hi all, 
> 
> I'm not quite sure if this is a feature or a bug or if I just fail to
> understand
> the documentation: 
> 
> If I use cor() with pairwise.complete.obs and method=pearson, the
> result is a
> scalar: 
> 
> ->cor(c(1,2,3),c(3,4,6),use="pairwise.complete.obs",method="pearson")
> [1] 0.9819805
> 
> The documentation says that 
> " '"pairwise.complete.obs"' only works with the '"pearson"' method
>      for 'cov' and 'var'."
> 
> Thus, I guess that cor() should work for pairwise.complete.obs and
> method =
> "kendall", or am I misinterpreting that statement ?
> 
> -> c(1,2,3),c(3,4,6),use="pairwise.complete.obs",method="kendall")
>      [,1]
> [1,]    1
> 
> Now the result is a matrix with dimensions (1,1) - strange enough.
> 
> Note that when I use "all.obs" or "complete.obs" I get a scalar for
> method
> kendall, too.
> 
> It gets worse if one tries to calculate the correlation between the
> columns of
> two matrices (i.e. cor(x,y) with x and y being a matrix). Then
> 
> -> c=matrix(c(1,2,3,3,4,5),nrow=3,ncol=2)
> -> d=matrix(c(2,3,4,NA,NA,NA),nrow=3,ncol=2)
> -> cor(c,d,use="pairwise.complete.obs",method="pearson")
>      [,1] [,2]
> [1,]    1   NA
> [2,]    1   NA
> 
> -> cor(c,d,use="pairwise.complete.obs",method="kendall")
> Error: 'x' is empty (*translated from german error message*)
> 
> The behavior is reproducible in R 2.4.1 and 2.6.1 (WinXP). I noticed
> that in
> 2.7.0 something was fixed in cor() related to "complete.obs" handling
> - would
> that fix my problems ?
>
> Any suggestions ?
> 
> Thanks, 
> Hilmar
> 
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