R help - May 2012 - Data frame vs matrix quirk: Hinky error message?

AdvisoRs:

Is the following a bug, feature, hinky error message, or dumb Bert?
> mtest <- matrix(1:12,nr=4)
> dftest <- data.frame(mtest)
> ix <- cbind(1:2,2:3)
> mtest[ix] <- NA
> mtest
     [,1] [,2] [,3]
[1,]    1   NA    9
[2,]    2    6   NA
[3,]    3    7   11
[4,]    4    8   12

## But ...
> dftest[ix] <- NA
Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
  only logical matrix subscripts are allowed in replacement

Obviously, I was expecting matrix indexing for replacement to work
similarly in both cases; however, I can see why it would be
problematic for data frames (mixed types), but was a bit nonplussed by
the error message, which seems hinky to me.

Cheers,
Bert

-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

Hi Bert,

The failure itself is the documented behavior: ?'[.data.frame' says

"Matrix indexing ('x[i]' with a logical or a 2-column integer
     matrix 'i') using '[' is not recommended, and barely
supported.
     For extraction, 'x' is first coerced to a matrix.  For
     replacement, a logical matrix (only) can be used to select the
     elements to be replaced in the same way as for a matrix."

The error message may be a bit hinky, as obviously data.frames can be
indexed by things other than logical matricies. Or is there another
reason this strikes you as odd?

Best,
Ista

On Tue, May 1, 2012 at 1:33 PM, Bert Gunter <gunter.berton at gene.com>
wrote:
> AdvisoRs:
>
> Is the following a bug, feature, hinky error message, or dumb Bert?
>
>> mtest <- matrix(1:12,nr=4)
>> dftest <- data.frame(mtest)
>> ix <- cbind(1:2,2:3)
>> mtest[ix] <- NA
>> mtest
> ? ? [,1] [,2] [,3]
> [1,] ? ?1 ? NA ? ?9
> [2,] ? ?2 ? ?6 ? NA
> [3,] ? ?3 ? ?7 ? 11
> [4,] ? ?4 ? ?8 ? 12
>
> ## But ...
>> dftest[ix] <- NA
> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
> ?only logical matrix subscripts are allowed in replacement
>
> Obviously, I was expecting matrix indexing for replacement to work
> similarly in both cases; however, I can see why it would be
> problematic for data frames (mixed types), but was a bit nonplussed by
> the error message, which seems hinky to me.
>
> Cheers,
> Bert
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
>
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

On 01-May-2012 17:33:23 Bert Gunter wrote:
> AdvisoRs:
> 
> Is the following a bug, feature, hinky error message, or dumb Bert?
> 
>   mtest <- matrix(1:12,nr=4)
>   dftest <- data.frame(mtest)
>   ix <- cbind(1:2,2:3)
>   mtest[ix] <- NA
>   mtest
>      [,1] [,2] [,3]
> [1,]    1   NA    9
> [2,]    2    6   NA
> [3,]    3    7   11
> [4,]    4    8   12
> 
>## But ...
>   dftest[ix] <- NA
> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>   only logical matrix subscripts are allowed in replacement
> 
> Obviously, I was expecting matrix indexing for replacement to
> work similarly in both cases; however, I can see why it would
> be problematic for data frames (mixed types), but was a bit
> nonplussed by the error message, which seems hinky to me.
> 
> Cheers,
> Bert
Also interesting is that, prior to the substitution commands,

  mtest[ix]
  # [1]  5 10
  dftest[ix]
  # [1]  5 10

both as one would expect on Bert's "naive" gounds (which, I
confess,
I also share[d]).

Ted.

-------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at wlandres.net>
Date: 01-May-2012  Time: 19:03:14
This message was sent by XFMail

On May 1, 2012, at 1:33 PM, Bert Gunter wrote:
> AdvisoRs:
>
> Is the following a bug, feature, hinky error message, or dumb Bert?
>
>> mtest <- matrix(1:12,nr=4)
>> dftest <- data.frame(mtest)
>> ix <- cbind(1:2,2:3)
>> mtest[ix] <- NA
>> mtest
>    [,1] [,2] [,3]
> [1,]    1   NA    9
> [2,]    2    6   NA
> [3,]    3    7   11
> [4,]    4    8   12
>
> ## But ...
>> dftest[ix] <- NA
> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
> only logical matrix subscripts are allowed in replacement
I'm not sure _I_ would have expected '[<-.data.frame' to
recognize
that a matrix was being offered because the "[.]" formalism  without a
comma (called "i-indexing" on the help page) would generally be  
referencing only columns (i.e. list elements). I had not realized the  
possibilitiy of offering a logical matrix to df but it does succeed as  
predicted by

?"[.data.frame"

" For replacement, a logical matrix (only) can be used to select the  
elements to be replaced in the same way as for a matrix."

So how you want to characterize documented behavior is your call. I  
would never choose the label you offered.


 > mtest <- matrix(FALSE, 4,4)
 > ix <- cbind(1:2,2:3)
 > dftest <- data.frame(mtest)
 > mtest[ix] <- TRUE
 > dftest[mtest] <- "a"
 > dftest
     X1    X2    X3    X4
1 FALSE     a FALSE FALSE
2 FALSE FALSE     a FALSE
3 FALSE FALSE FALSE FALSE
4 FALSE FALSE FALSE FALSE

The nonassignment operation still succeeds:

 > dftest[ix]
[1] "a" "a"

> Obviously, I was expecting matrix indexing for replacement to work
> similarly in both cases; however, I can see why it would be
> problematic for data frames (mixed types), but was a bit nonplussed by
> the error message, which seems hinky to me.
>
> Cheers,
> Bert
>
> -- 
-- 

David Winsemius, MD
Heritage Laboratories
West Hartford, CT