First install ripser.
Then make it locatable on your system PATH, something like:
$ ln -s /home/clark/dev/ripser/ripser /usr/local/bin/ripser
After this your system should be able to find ripser:
$ which ripser
/usr/local/bin/ripser
Now you can do something like this in R:
# Operate on a data point cloud represented as a matrix
m = matrix(c(1,0,
0,1,
-1,0,
0,-1)
, byrow = TRUE, ncol = 2)
# Ripser likes to read files in, so use a temporary file
f = tempfile()
write.table(m, f, col.names = FALSE, row.names = FALSE)
output = system2("ripser", args = c("--format point-cloud", f)
, stdout = TRUE)output is a character vector in R which needs to be parsed to perform any
analysis.
> output
[1] "point cloud with 4 points in dimension 2"
[2] "distance matrix with 4 points"
[3] "value range: [1.41421,2]"
[4] "persistence intervals in dim 0:"
[5] " [0,1.41421)"
[6] " [0,1.41421)"
[7] " [0,1.41421)"
[8] " [0, )"
[9] "persistence intervals in dim 1:"
[10] " [1.41421,2)"
Ripser only displays output through stdout.
If it had a more programmatic interface we could do
richer things without using R's system2() call or having to parse this text.