distanceMatrix: Calculate a distance matrix of an alignment

In KonstantinHoffmann/ABVDTools: Some useful tools for processing data from the ABVD database abvd.shh.mpg.de

Description

Create a matrix of pariwise distances between languages. Takes as input eighter a set of languages or an alignment matrix

Usage

distanceMatrix(languages = NULL, alignment = NULL, type = "Hamming",
  silent = FALSE, ...)

Arguments

languages	ids of the languages
alignment	alignment matrix consisting of 0, 1, ?. If alignment=NULL, then it will be created with the language IDs.
type	one of "Hamming" or "Jaccard"
silent	report progress or not
...	further arguments

Details

Optional arguments are:

• removeMissings: (default TRUE): removes all ? in the sequence and only considers entries, where both languages in comparison have data

• removeZeroes: (default: FALSE): if TRUE, only consider entries, where at least one of the two languages have a 1

Value

a matrix of pairwise distances

KonstantinHoffmann/ABVDTools documentation built on Dec. 14, 2021, 11:48 a.m.