pis: Number of Potentially-Informative Sites

In ips: Interfaces to Phylogenetic Software in R

Number of Potentially-Informative Sites

Description

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 indices 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

data(ips.16S)	

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

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

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

ips documentation built on May 29, 2024, 4:39 a.m.