R help - Apr 2008 - Transposing Data Frame does not return numeric entries

x <- read.table("LittleGarvin.csv", sep=",", header=TRUE)
y <- t(x)
str(y)

chr [1:193, 1:288] "oligocha" "0" " 0" "
0" " 0" "0" ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:193] "X" "upwd1201" "upwd0502"
"upwd0702" ...
  ..$ : NULL

x is a data frame with a whole bunch of numeric vectors I would like for the
rows and columns to be reversed == transposed but with the same attributes.
I am trying to feed the transposed data frame to metaMDS(vegan).  I am
stumped- sorry for the large attached file- I am at a loss.

Stephen Sefick


-- 
Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make us
feel like gods. We are mammals, and have not exhausted the annoying little
problems of being mammals.

-K. Mullis

I have a species as rows and sites as columns matrix.  I would like to
tranpose this matrix so that I can do an NMDS analysis with the vegan
package.  I have used

y <- t(x)

and it indeed transposes the matrix, but it changes the whole make up

chr [1:193, 1:288] "oligocha" "0" " 0" "
0" " 0" "0" ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:193] "X" "upwd1201" "upwd0502"
"upwd0702" ...
  ..$ : NULL

the original matrix is numeric when I use str(x).  I would post the data but
it is large for a mailing list.  I have read help and I can't figure it out.

-- 
Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make us
feel like gods. We are mammals, and have not exhausted the annoying little
problems of being mammals.

-K. Mullis

	[[alternative HTML version deleted]]

RML:  *** Data frames are NOT matrices!!! ***

On 16/04/2008, at 10:35 AM, stephen sefick wrote:
>  x <- read.table("LittleGarvin.csv", sep=",",
header=TRUE)
> y <- t(x)
> str(y)
>
> chr [1:193, 1:288] "oligocha" "0" " 0" "
0" " 0" "0" ...
>  - attr(*, "dimnames")=List of 2
>   ..$ : chr [1:193] "X" "upwd1201" "upwd0502"
"upwd0702" ...
>   ..$ : NULL
>
> x is a data frame with a whole bunch of numeric vectors I would  
> like for the
> rows and columns to be reversed == transposed but with the same  
> attributes.
> I am trying to feed the transposed data frame to metaMDS(vegan).  I am
> stumped- sorry for the large attached file- I am at a loss.
	Although it is possible, transposition makes little to no sense
	for data frames.  If you want to transpose something you are
	thinking of it as being a *matrix* not a data frame.  The result
	of transposing a data frame is in fact a matrix.

	There is as far as I know no structure in R whereby the rows of
	a matrix-like object can have different characteristics.  (The
	term ``attributes'' has a technical meaning in R which is probably
	not what you intend --- but even if you do intend that, it's not
	possible.)

	The complaint made in your subject line is that the result of
	your transposition is not numeric.  It is in fact character.
	That's because there is character data in the data frame x.
	When you transpose x, it is first coerced into a matrix.  If there
	are any character or factor columns in x the coercion will result
	in a character matrix, the transpose of which will of course be a
	character matrix.

	The solution is of course to remove the character or factor columns
	from x before transposition.

	If you ``can't'' do this, then you ***can't*** transpose ---  
transposition
	just doesn't make any sense at all.  Simple as that.

		cheers,

			Rolf Turner

	

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