This script obtains the distribution if Sannon's Index of diversity for all the AFLP loci

Shannon_from_aflps_in_msap.R

# Assuming you have your aflp matrix data with samples in rows and 
# loci in columns. The file is a csv file with the format of msap

#Read data
data <- read.csv("aflp.csv", header=TRUE)

#convert to matrix
matN <- as.matrix(data[,4:length(data[1,])])

#Function for sannon index
shannon <-function(x){
	#Calculate Shannon's Diversity Index given a list of binomial alleles
	t <- table(x)
	if (length(t)<2) return(NaN)
	P=t[1]/sum(t)
	Q=t[2]/sum(t)
	S=-(P*log(P)+Q*log(Q))
	return(S)
}

#Apply the funtion to your data
Sannon.I <- apply(matM, 2, shannon)

summary(Sannon.I)
hist(Sannon.I)