After finding the
lineagePath of a phylogenetic
sitesMinEntropy perform entropy minimization on every site of
the sequence to group the tips according to amino acid/nucleotide.
sitesMinEntropy(x, ...) # S3 method for lineagePath sitesMinEntropy( x, minEffectiveSize = NULL, searchDepth = 1, method = c("compare", "insert", "delete"), ... )
lineagePath object returned from
further arguments passed to or from other methods.
The minimum number of tips in a group.
The function uses heuristic search but the termination of
the search cannot be intrinsically decided.
searchDepth is needed to
tell the search when to stop.
The strategy for predicting the fixation. The basic approach is entropy minimization and can be achieved by adding or removing fixation point, or by comparing the two.