sppDist: Intra and inter-specific distances
In spider: Species Identity and Evolution in R

Description Usage Arguments Details Value Author(s) See Also Examples

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

1	sppDist(distobj, sppVector)

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

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

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.

Samuel Brown <s_d_j_brown@hotmail.com>

sppDistMatrix.

data(dolomedes)
doloDist <- 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
hist(doloSpDist$inter, col="grey")
hist(doloSpDist$intra, col=transGreen, add=TRUE)

#Boxplot of the same
boxplot(doloSpDist)