I am trying to understand the underlying calculations performed by omicade4 on the function mcia. How can I extract the position of the samples in the new shared sample space? How is defined this sample space on a matrix where each row and column is each dataset on the list used as input?

Following the Momix-notebook I used:

out <-  mcia(data)
out$mcoa$SynVar

However, this doesn't explain how is the matrix of the relationships on mcia.

              data[[1]]      data[[2]]
data[[1]]      0                1
data[[2]]      1                0

or

              data[[1]]      data[[2]]
data[[1]]      1                1
data[[2]]      1                1

or something else