Modified function to generate interspecies distance matrices in R

sppDistMatrix2.R

# load libs
require("spider")
#source(file="sppDistMatrix2.R")#can source the function

# load the example data
data(dolomedes)
doloDist <- dist.dna(dolomedes)
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)

# you have three options for dist, which are min, mean and max
sppDistMatrix2(distobj=doloDist, sppVector=doloSpp, dist=min)

# load the new function
sppDistMatrix2 <- function (distobj, sppVector, dist) 
{
    dat <- as.matrix(distobj)
    attr(dat, "dimnames")[[1]] <- sppVector
    taxa <- unique(sppVector)
    pair.mat <- matrix(data = NA, nrow = length(taxa), ncol = length(taxa), 
        dimnames = list(one = taxa, two = taxa))
    for (i in 1:length(taxa)) {
        for (j in 1:length(taxa)) {
            sppMat <- dat[which(dimnames(dat)[[1]] == taxa[i]), 
                which(dimnames(dat)[[1]] == taxa[j])]
            if (taxa[i] == taxa[j]) 
                pair.mat[i, j] <- dist(sppMat[lower.tri(sppMat)])
            else pair.mat[i, j] <- dist(sppMat)
        }
    }
    return(pair.mat)
}