ips (version 0.0.11)

pis: Number of Potentially-Informative Sites

Description

This function returns the number or positions of potentially-informative (parsimony-informative, phylogenetically-informative) sites in DNA sequence alignment.

Usage

pis(x, what = "fraction", use.ambiguities = FALSE)

Arguments

x

An object of class DNAbin.

what

Either of "absolute", "fraction", or "index", which will return the absolute number, the relative number or the indeces of the potentially-informative sites.

use.ambiguities

Not yet available.

Value

Numeric (depending on what, the number, fraction, or indices of potentially-informative nucleotide sites).

Examples

# NOT RUN {
# example data:
# -------------
data(ips.16S)	

# number of potentially-informative sites:
# ----------------------------------------
pis(ips.16S, what = "abs")
	
# proportion of potentially-informative sites:
# --------------------------------------------
pis(ips.16S, what = "frac")

# indeces of potentially-informative sites:
# --------------------------------------------
pis(ips.16S, what = "ind")
# }