[R] Compare two distance matrices

[Martin Maechler]

>>>>> "bady" == bady  <bady at univ-lyon1.fr>
>>>>>     on Thu, 06 Oct 2005 14:39:27 +0200 writes:

    bady> Hi, hi all,
    >> I am trying to compare two distance matrices with R. I would like to
    >> create a XY plot of these matrices and do some linear regression on
    >> it. But, I am a bit new to R, so i have a few questions (I searched in
    >> the documentation with no success).
    >> The first problem is loading a distance matrix into R. This matrix is
    >> the output of a the Phylip program Protdist and lookes like this:
    >> I tried with the scan() function to load the files, but with no
    >> success. How should i load in these files? ....
    >> 

    bady> you can separately load each matrix with two text files.

    bady> require(ade4)
    bady> mat1 <- read.table("mat1.txt")
    bady> nam1 <- mat1[,1]
    bady> mat1 <- mat1[,-1]
    bady> row.names(mat1) <- names(mat1) <- nam1
    bady> mat2 <- read.table("mat2.txt")
    bady> nam2 <- mat2[,1]
    bady> mat2 <- mat2[,-1]
    bady> row.names(mat2) <- names(mat2) <- nam2

    bady> dist1 <- mat2dist(mat1)
    bady> dist2 <- mat2dist(mat2)

but I don't see why you would need an extra package "ade4" and
its "extra - function"  mat2dist().


when the 'stats' package already provides the function
as.dist(.)  {the help page of which was mentioned by the
original poster}.


Here is a reproducible example showing how I think as.dist()
works sufficiently:

> (m <- toeplitz(round(rnorm(6),2)))
      [,1]  [,2]  [,3]  [,4]  [,5]  [,6]
[1,] -0.42 -0.78 -0.42 -2.24  0.74  1.31
[2,] -0.78 -0.42 -0.78 -0.42 -2.24  0.74
[3,] -0.42 -0.78 -0.42 -0.78 -0.42 -2.24
[4,] -2.24 -0.42 -0.78 -0.42 -0.78 -0.42
[5,]  0.74 -2.24 -0.42 -0.78 -0.42 -0.78
[6,]  1.31  0.74 -2.24 -0.42 -0.78 -0.42
> as.dist(m)
      1     2     3     4     5
2 -0.78                        
3 -0.42 -0.78                  
4 -2.24 -0.42 -0.78            
5  0.74 -2.24 -0.42 -0.78      
6  1.31  0.74 -2.24 -0.42 -0.78
> ## it also works for data frames {if really needed}:
> dm <- as.data.frame(m)
> as.dist(dm)
      1     2     3     4     5
2 -0.78                        
3 -0.42 -0.78                  
4 -2.24 -0.42 -0.78            
5  0.74 -2.24 -0.42 -0.78      
6  1.31  0.74 -2.24 -0.42 -0.78
>