Add Nei's DA distance (1983)

[pascalangst]

Hi @lpembleton

StAMPP is a cool package and I've used it a lot. Thanks!

Have you thought about adding more functions to the package? For example, since we can calculate Nei's D with StAMPP, I assume it would not be too difficult to implement Nei's D_A distance. Having this measure would allow to build more reliable trees.

I was looking around in your code and found sections in the NeisD function that one could modify to get a new NeisDA function. However, I'm not 100 % sure what your variables code for. E.g.

StAMPP/R/stamppNeisD.R

Lines 263 to 277 in 346815e

	p.dup <- (p[p.dup.ids[((pre.split*split.size)+1):(totalind*totalind)],]) #matrix of allele frequencies to calculate squared allele freq, jx & jy
	m.dup <- (m[m.dup.ids[((pre.split*split.size)+1):(totalind*totalind)],]) #matrix of true false (1/0) missing genotype of each ind & loci to adjust p.dup matrix for missing alleles
	m.dup2 <- (m[p.dup.ids[((pre.split*split.size)+1):(totalind*totalind)],])
	jxjy <- c(jxjy, sum((p.dup*m.dup)^2)+sum(((1-p.dup)*m.dup*m.dup2)^2)) #sum of square allele freq
	}
	#########################
	sq.jxjy <- sqrt(matrix(jxjy, nrow=totalind, ncol=totalind)) #square root of the sum of squared allele freq
	i <- jxy/sq.jxjy
	i <- i/t(sq.jxjy) #normalised identity averaged across loci
	d <- -log(i) #Nei's genetic distance

Would you be willing to add this function or could you give me a hint how I could modify the existing code to do so?

Cheers
Pascal

[lpembleton]

Thanks for the feature request @pascalangst
I have been working to incorporate this and will hopefully push to GitHub soon so you can test it.
Cheers,
Luke

[lpembleton]

A alpha/beta release is now available with this requested feature (https://github.com/lpembleton/StAMPP/releases/tag/v1.6.3.9000).
@pascalangst do you have any example datasets with known results to test the implementation of this formula?

[pascalangst]

Hi @lpembleton

Thanks for implementing. Unfortunately, I don't have datasets with known results. Therefore, I cannot do a proper test. However, I can check if it is running ok on my machine.