sppDist {spider}

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 <[e-mail]>

See Also

sppDistMatrix.

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)