pathdist: Graph extension of dissimilarities

In phiala/ecodist: Dissimilarity-Based Functions for Ecological Analysis

Graph extension of dissimilarities

Description

Uses the shortest path connecting sites to estimate the distance between samples with pairwise distances greater than maxv.

Usage

pathdist(v, maxv = 1)

Arguments

v	lower-triangular distance vector, possibly as produced by dist() or distance().
maxv	cutoff for distances: values greater or equal to this will be estimated from the minimum spanning tree.

Details

Pairwise samples with no species will have distances greater than a cutoff. A distance-weighted graph connecting these samples by way of intermediate samples with some species in common can be used to interpolate distances by adding up the path length connecting those samples. This function will fail if there are completely disconnected subsets.

Value

Returns a lower-triangular distance matrix.

Author(s)

Sarah Goslee

See Also

dist, distance

Examples

	# samples 1 and 2, and 3 and 4, have no species in common
	x <- matrix(c(	1, 0, 1, 0,
			0, 1, 0, 1,
			1, 0, 0, 0,
			0, 1, 1, 1,
			1, 1, 1, 0,
			1, 0, 1, 1,
			0, 0, 1, 1), ncol = 4, byrow = TRUE)

	# the maximum Jaccard distance is 1
	# regardless of how different the samples are
	x.jd <- dist(x, "binary")

	# estimate the true distance between those pairs
	# by following the shorted path along connected sites
	pathdist(x.jd)

phiala/ecodist documentation built on Nov. 5, 2023, 10:47 a.m.