Reading a symmetric matrix from file that omits upper triangular part - r

Question

Using R, what is the best way to read a symmetric matrix from a file that omits the upper triangular part. For example,
1.000
.505 1.000
.569 .422 1.000
.602 .467 .926 1.000
.621 .482 .877 .874 1.000
.603 .450 .878 .894 .937 1.000
I have tried read.table, but haven't been successful.

Answer 1

Here's a read.table and loopless and *apply-less solution:
txt <- "1.000
.505 1.000
.569 .422 1.000
.602 .467 .926 1.000
.621 .482 .877 .874 1.000
.603 .450 .878 .894 .937 1.000"
# Could use clipboard or read this from a file as well.
mat <- data.matrix( read.table(text=txt, fill=TRUE, col.names=paste("V", 1:6)) )
mat[upper.tri(mat)] <- t(mat)[upper.tri(mat)]
> mat
V1 V2 V3 V4 V5 V6
[1,] 1.000 0.505 0.569 0.602 0.621 0.603
[2,] 0.505 1.000 0.422 0.467 0.482 0.450
[3,] 0.569 0.422 1.000 0.926 0.877 0.878
[4,] 0.602 0.467 0.926 1.000 0.874 0.894
[5,] 0.621 0.482 0.877 0.874 1.000 0.937
[6,] 0.603 0.450 0.878 0.894 0.937 1.000

Answer 2

I copied your text, and then used tt <- file('clipboard','rt') to import it. For a standard file:
tt <- file("yourfile.txt",'rt')
a <- readLines(tt)
b <- strsplit(a," ") #insert delimiter here; can use regex
b <- lapply(b,function(x) {
x <- as.numeric(x)
length(x) <- max(unlist(lapply(b,length)));
return(x)
})
b <- do.call(rbind,b)
b[is.na(b)] <- 0
#kinda kludgy way to get the symmetric matrix
b <- b + t(b) - diag(b[1,1],nrow=dim(b)[1],ncol=dim(b)[2]

Answer 3

I'm posting but I like Blue Magister's approach wat better. But maybe there's something in this that's of use.
mat <- readLines(n=6)
1.000
.505 1.000
.569 .422 1.000
.602 .467 .926 1.000
.621 .482 .877 .874 1.000
.603 .450 .878 .894 .937 1.000
nmat <- lapply(mat, function(x) unlist(strsplit(x, "\\s+")))
lens <- sapply(nmat, length)
dlen <- max(lens) -lens
bmat <- lapply(seq_along(nmat), function(i) {
as.numeric(c(nmat[[i]], rep(NA, dlen[i])))
})
mat <- do.call(rbind, bmat)
mat[upper.tri(mat)] <- t(mat)[upper.tri(mat)]
mat

Answer 4

Here is an approach which also works if the dimensions of the matrix are unknown.
# read file as a vector
mat <- scan("file.txt", what = numeric())
# calculate the number of columns (and rows)
ncol <- (sqrt(8 * length(mat) + 1) - 1) / 2
# index of the diagonal values
diag_idx <- cumsum(seq.int(ncol))
# generate split index
split_idx <- cummax(sequence(seq.int(ncol)))
split_idx[diag_idx] <- split_idx[diag_idx] - 1
# split vector into list of rows
splitted_rows <- split(mat, f = split_idx)
# generate matrix
mat_full <- suppressWarnings(do.call(rbind, splitted_rows))
mat_full[upper.tri(mat_full)] <- t(mat_full)[upper.tri(mat_full)]
[,1] [,2] [,3] [,4] [,5] [,6]
0 1.000 0.505 0.569 0.602 0.621 0.603
1 0.505 1.000 0.422 0.467 0.482 0.450
2 0.569 0.422 1.000 0.926 0.877 0.878
3 0.602 0.467 0.926 1.000 0.874 0.894
4 0.621 0.482 0.877 0.874 1.000 0.937
5 0.603 0.450 0.878 0.894 0.937 1.000

Answer 5

This won't work in the OP's case because the diagonal was 1, but if the diagonal is zero or missing, then you can use as.dist%>%as.matrix to copy the lower diagonal to the upper diagonal and set the diagonal to zero:
input=" Pop0 Pop1 Pop2
Pop0
Pop1 0.015
Pop2 0.079 0.083
Pop3 0.014 0.016 0.073"
as.matrix(as.dist(cbind(read.table(text=input,fill=T),NA)))
Result:
Pop0 Pop1 Pop2 Pop3
Pop0 0.000 0.015 0.079 0.014
Pop1 0.015 0.000 0.083 0.016
Pop2 0.079 0.083 0.000 0.073
Pop3 0.014 0.016 0.073 0.000
In my case the input had column names, so read.table(fill=T) was automatically able to determine the number of columns and IRTFM's trick of specifying col.names=1:4 was not neeeded.