Sim_RSS_2013

Sim_RSS_2013

Sim_RSS_2013(
  dag,
  terms,
  distance = "longest_distances_via_LCA",
  verbose = simona_opt$verbose
)

Methods

Sim_RSS_2013

The similarity is adjusted by the positions of term a, b and the LCA term c in the DAG. The similarity is defined as:

sim = max_depth/(max_depth + d(a, b)) * alpha/(alpha + beta)

where d(a, b) is the distance between a and b which can be the shortest distance or the longest distance via LCA.

In the tuning factor, alpha is the distance of LCA to root, which is depth(c). beta is the distance to leaves, which is the minimal distance (or the minimal height) of term a and b:

alpha/(alpha + beta) = depth(c)/(depth(c) + min(height(a), height(b)))

Paper link: doi:10.1371/journal.pone.0066745 .

There is a parameter distance which takes value of "longest_distances_via_LCA" (the default) or "shortest_distances_via_NCA":

term_sim(dag, terms, method = "Sim_RSS_2013",
    control = list(distance = "shortest_distances_via_NCA"))