R: Intra and inter-specific distances

sppDist

R Documentation

Intra and inter-specific distances

Description

Separates a distance matrix into its inter- and intra-specific components.

Usage

sppDist(distobj, sppVector)

Arguments

`distobj`	A distance matrix.
`sppVector`	The species vector (see `sppVector`).

Details

This function can be used to produce histograms and other charts exploring the ‘barcode gap’, such as in the examples below.

Value

A list with two elements:

`inter`	A numeric vector containing ALL inter-specific pairwise distances.
`intra`	A numeric vector containing ALL intra-specific pairwise distances.

Author(s)

Samuel Brown <s_d_j_brown@hotmail.com>

Examples


data(dolomedes)
doloDist <- ape::dist.dna(dolomedes)
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)

doloSpDist <- sppDist(doloDist, doloSpp)

doloSpDist

#Histogram of the barcode gap
transGreen <- rgb(0, 1, 0, 0.5) #Make a slightly transparent colour to see some overlap
graphics::hist(doloSpDist$inter, col="grey")
graphics::hist(doloSpDist$intra, col=transGreen, add=TRUE)

#Boxplot of the same
graphics::boxplot(doloSpDist)