[R] more woes trying to convert a data.frame to a numerical matrix

[Marc Schwartz]

On Wed, 2007-05-16 at 08:40 -0400, Andrew Yee wrote:
> Thanks for the suggestion and the explanation for why I was running
> into these troubles.
> 
> I've tried:
> 
> as.numeric(as.matrix(sample.data[-1, -1]))
> 
> However, this creates another vector rather than a matrix. 

Right. That's because I'm an idiot and need more caffeine... :-)

>  Is there a straight forward way to convert this directly into a
> numeric matrix rather than a vector? 

Yeah, Dimitris' approach below of using data.matrix().

You could also use:

mat <- sapply(sample.data[-1, -1], as.numeric)
rownames(mat) <- rownames(sample.data[-1, -1])

> mat
  x y z
2 1 1 1
3 2 2 2
4 3 3 3

Though, this is essentially what data.matrix() does internally.

> Additionally, I've also considered:
> 
> data.matrix(sample.data[-1,-1]
> 
> but bizarrely, it returns:
> 
>   x y z
> 2 1 1 1
> 3 2 2 2
> 4 3 3 3

That is a numeric matrix:

> str(data.matrix(sample.data[-1, -1]))
 int [1:3, 1:3] 1 2 3 1 2 3 1 2 3
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:3] "2" "3" "4"
  ..$ : chr [1:3] "x" "y" "z"

HTH,

Marc

> 
> Thanks,
> Andrew
> 
> 
> On 5/16/07, Marc Schwartz <marc_schwartz at comcast.net> wrote:
>         On Wed, 2007-05-16 at 08:10 -0400, Andrew Yee wrote:
>         > I have the following csv file:
>         >
>         > name,x,y,z
>         > category,delta,gamma,epsilon
>         > a,1,2,3
>         > b,4,5,6
>         > c,7,8,9
>         >
>         > I'd like to create a numeric matrix of just the numbers in
>         this csv dataset. 
>         >
>         > I've tried the following program:
>         >
>         > sample.data <- read.csv("sample.csv")
>         > numerical.data <- as.matrix(sample.data[-1,-1])
>         >
>         > However, print(numerical.data ) returns what appears to be a
>         matrix of
>         > characters:
>         >
>         >   x   y   z
>         > 2 "1" "2" "3"
>         > 3 "4" "5" "6"
>         > 4 "7" "8" "9" 
>         >
>         > How do I force it to be numbers rather than characters?
>         >
>         > Thanks,
>         > Andrew
>         
>         The problem is that you have two rows which contain alpha
>         entries.
>         
>         The first row is treated as the header, but the second row is
>         treated as 
>         actual data, thus overriding the numeric values in the
>         subsequent rows.
>         
>         You could use:
>         
>           as.numeric(as.matrix(sample.data[-1, -1]))
>         
>         to coerce the matrix to numeric, or if you don't need the
>         alpha entries, 
>         you could modify the read.csv() call to something like:
>         
>           read.csv("sample.csv", header = FALSE, skip = 2, row.names =
>         1,
>                    col.names = c("name", "x", "y", "z") 
>         
>         This will skip the first two rows, set the first column to the
>         row names
>         and give you a data frame with numeric columns, which in most
>         cases can
>         be treated as a numeric matrix and/or you could explicitly
>         coerce it to 
>         one.
>         
>         HTH,
>         
>         Marc Schwartz
>         
>         
>