Reads the neomorphic character matrix for a given project and extracts only those characters that are informative (i.e., showing more than one repeated state across taxa). Returns per-taxon counts of neomorphic cell states, together with proportions and overall counts.
InfNeo(pID)InfNeo() invisibly returns a list with elements:
"0"Vector of per-taxon counts of cells scored as 0.
"1"Vector of per-taxon counts of cells scored as 1.
"?"Vector of per-taxon counts of ambiguous cells.
"p1"Vector of proportions of 1-cells among scored cells.
"count"Named vector giving total counts of 0-, 1-, and 0/1-cells across all taxa.
"p"Named vector giving overall proportions of 0 and 1 states among scored cells.
The function reads the neomorphic matrix file "neo.nex" associated with
the given project ID, filters out uninformative characters, and calculates for
each taxon:
Number of cells with state 0 ("0")
Number of cells with state 1 ("1")
Number of ambiguous cells ("?")
Proportion of 1 cells among those scored as 0 or 1 ("p1")