In TraMineR I might compute dissimilarities as such:
properties <- matrix(c(# left, married, child ,divorced
0, 0, 0, 0, # parent
1, 0, 0, 0, # left
0, 1, .5, 0, # marr
1, 1, 0, 0, # left+marr
0, 0, 1, 0, # child
1, 0, 1, 0, # left+child
1, 1, 1, 0, # left+marr+child
.5, 1, .5, 1 # divorced
), 8, 4, byrow=TRUE)
sm <- as.matrix(dist(properties))
indel <- .5*max(sm)
dOM <- seqdist(biofam.seq, method="OM", indel=indel, sm=sm)
Why do I provide both indel costs (indel) and substitution cost matrix (sm)? I thought they were one and the same? Please help me to understand the relationship between the substitution cost matrix and the indel costs.