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

From: Daniel Malter <>
Date: Wed, 2 Jan 2008 14:07:48 -0500

Sorry, I did not get it at first. Now I see your problem. I accidentally used pearson. So it does not work for kendall's tau or spearman's rho. The reason why it does not work is because there is one column full of NAs in the second matrix. It works if you have more than one valid value to compare to in each of the matrix columns:



I don't know if that helps, but it is an explanation. Why pearson works and spearman and kendall don't, I don't know.


cuncta stricte discussurus

-----Ursprüngliche Nachricht-----
Von: [] Im Auftrag von Hilmar Berger
Gesendet: Wednesday, January 02, 2008 12:39 PM An:
Betreff: [R] strange behavior of cor() with pairwise.complete.obs

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

->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

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 ?

Hilmar mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. Received on Wed 02 Jan 2008 - 19:10:44 GMT

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