R devel - Apr 2002 - Problem handling NA indexes for character matrixes (PR#1447)

In a package I've been developing for manipulating genetic data I discovered
a problem when indexing into character arrays using NA's:

Create a character matrix and a numeric matrix

	> cmat <- matrix( letters[1:4], ncol=2, nrow=2)
	> nmat <- matrix( 1:4, ncol=2, nrow=2)

Create an index vector containing an NA value

	> indvec <- c(1,2,NA)

Indexing works fine for both matrixes when we only pull off *one* column:

	> cmat[ indvec, 1 ]
	[1] "a"  "b"  "NA"
	> nmat[ indvec, 1 ]
	[1]  1  2 NA

	> cmat[ indvec, 2 ]
	[1] "c"  "d"  "NA"
	> nmat[ indvec, 2 ]
	[1]  3  4 NA

However, when we pull off both columns, we get "" where we should have
NA
for cmat but it works properly for nmat:

	> cmat[ indvec,  ]
	     [,1] [,2]
	[1,] "a"  "c" 
	[2,] "b"  "d" 
	[3,] "NA" ""  
	> nmat[ indvec,  ]
	     [,1] [,2]
	[1,]    1    3
	[2,]    2    4
	[3,]   NA   NA

	> cmat[ indvec, c(1,2) ]
	     [,1] [,2]
	[1,] "a"  "c" 
	[2,] "b"  "d" 
	[3,] "NA" ""  

	> nmat[ indvec, c(1,2) ]
	     [,1] [,2]
	[1,]    1    3
	[2,]    2    4
	[3,]   NA   NA


The problem persists with other matrix sizes:

	> cmat <- matrix( letters[1:6], ncol=3, nrow=2)
	> nmat <- matrix( 1:6, ncol=3, nrow=2)
	> cmat[ indvec,  ]
	     [,1] [,2] [,3]
	[1,] "a"  "c"  "e" 
	[2,] "b"  "d"  "f" 
	[3,] "NA" ""   ""  
	> nmat[ indvec,  ]
	     [,1] [,2] [,3]
	[1,]    1    3    5
	[2,]    2    4    6
	[3,]   NA   NA   NA

Also we get a strange result if the only index is NA:

	> cmat[NA,]
	     [,1] [,2] [,3]
	[1,] "NA" ""   ""  
	[2,] "NA" ""   ""  
	> nmat[NA,]
	     [,1] [,2] [,3]
	[1,]   NA   NA   NA
	[2,]   NA   NA   NA

I would expect to get a single row for these cases rather than the whole
matrix replicated and (incorrectly for the cmat) filled with NA.

I'm reporting this now to get it in.  I'll download the 1.5.0  source
code
now and muck about to see if I can locate the problem.  

-Greg
> version
         _                   
platform sparc-sun-solaris2.8
arch     sparc               
os       solaris2.8          
system   sparc, solaris2.8   
status                       
major    1                   
minor    4.1                 
year     2002                
month    01                  
day      30                  
language R                   


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gregory_r_warnes@groton.pfizer.com writes:
> In a package I've been developing for manipulating genetic data I
discovered
> a problem when indexing into character arrays using NA's:
> 	> cmat[ indvec,  ]
> 	     [,1] [,2]
> 	[1,] "a"  "c" 
> 	[2,] "b"  "d" 
> 	[3,] "NA" ""  
> 	> nmat[ indvec,  ]
> 	     [,1] [,2]
> 	[1,]    1    3
> 	[2,]    2    4
> 	[3,]   NA   NA
This seems to have vanished in R-1.5.0pre, likely as a (fortunate, if
unexpected) side effect of the character NA changes:
> cmat[ indvec,  ]
     [,1] [,2]
[1,] "a"  "c" 
[2,] "b"  "d" 
[3,] NA   NA  
> nmat[ indvec,  ]
     [,1] [,2]
[1,]    1    3
[2,]    2    4
[3,]   NA   NA

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907
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