almost lower triangular matrices

I have output from a program which produces a distance matrix I want to
read into a clustering program in R.

 

The output is a .txt file and is 'almost' lower triangular in the sense
that it is just the triangle below the diagonal.

 

So for example a 4-by-4 distance matrix appears as,

 

1

2 3

4 5 6

 

i.e. it looks like a lower triangular of a 3-by3.

 

I thought I might be able to use "diag" to add zeros but apparently not.

 

It's a problem because my matrix is actually 1989-by-1989 not 4-by-4

 

I would not be at all surprised if the solution is obvious but I cannot
quite see how to read this into R.

Michael Anyadike-Danes wrote:

I have output from a program which produces a distance matrix I want to
read into a clustering program in R.

 

The output is a .txt file and is 'almost' lower triangular in the sense
that it is just the triangle below the diagonal.

 

So for example a 4-by-4 distance matrix appears as,

 

1

2 3

4 5 6

 

i.e. it looks like a lower triangular of a 3-by3.

 

I thought I might be able to use "diag" to add zeros but apparently not.

 

It's a problem because my matrix is actually 1989-by-1989 not 4-by-4

 

I would not be at all surprised if the solution is obvious but I cannot
quite see how to read this into R.

You can use scan to get the entries from the file in row order.  Then 
create the matrix to hold the result and overwrite the elements in the 
upper triangle with scanned vector.  (R stores matrices in 
column-major order so the row-major order from your file corresponds 
to the upper triangle, not the lower triangle).  I'll leave it to you 
to work out the  symmetrization operation.

file.show("/tmp/tri.dat")

1
2 3
4 5 6
7 8 9 10

mm <- array(0, c(4,4))
mm[upper.tri(mm, diag = TRUE)] <- scan("/tmp/tri.dat")

Read 10 items

mm

     [,1] [,2] [,3] [,4]
[1,]    1    2    4    7
[2,]    0    3    5    8
[3,]    0    0    6    9
[4,]    0    0    0   10

(res <- mm + t(mm))

     [,1] [,2] [,3] [,4]
[1,]    2    2    4    7
[2,]    2    6    5    8
[3,]    4    5   12    9
[4,]    7    8    9   20

diag(res) <- diag(res)/2
res

     [,1] [,2] [,3] [,4]
[1,]    1    2    4    7
[2,]    2    3    5    8
[3,]    4    5    6    9
[4,]    7    8    9   10