Computes similarity index between two encodings.
calc_si(a, b)
a | encoding (see |
---|---|
b | encoding to which |
the value of similarity index.
Briefly, the similarity index is a fraction of elements that have the same pairing in both encodings. Pairing is a binary variable, that has value 1 if two elements are in the same group and 0 if not. For more details, see references.
Stephenson, J.D., and Freeland, S.J. (2013). Unearthing the Root of Amino Acid Similarity. J Mol Evol 77, 159-169.
calc_ed
: calculate the encoding distance between two encodings.
# example from Stephenson & Freeland, 2013 (Fig. 6) enc1 <- list(`1` = "A", `2` = c("F", "E"), `3` = c("C", "D", "G")) enc2 <- list(`1` = c("A", "G"), `2` = c("C", "D", "E", "F")) enc3 <- list(`1` = c("D", "G"), `2` = c("E", "F"), `3` = c("A", "C")) calc_si(enc1, enc2)#> [1] 0.5333333calc_si(enc2, enc3)#> Warning: 'a' must be longer than 'b'. Reverting a and b.#> [1] 0.4666667calc_si(enc1, enc3)#> [1] 0.8