Hello,
I have written a small function ('JostD' based upon a recent molecular
ecology paper) to calculate genetic distance between populations (columns in
my data set). As I have it now I have to tell it which 2 columns to use (X,
Y). I would like it to automatically calculate 'JostD' for all combinations
of columns, perhaps returning a matrix of distances. Thanks for any help or
suggestions.
Cheers
Colin
Function:
JostD <- function(DF, X, Y) {
Ni1 <- DF[,X]
Ni2 <- DF[,Y]
N1 <- sum(Ni1)
N2 <- sum(Ni2)
pi1 <-Ni1/N1
pi2 <-Ni2/N2
pisqr <- ((pi1+pi2)/2)^2
H1 <- 1 - sum(pi1^2)
H2 <- 1 - sum(pi2^2)
Ha <- 0.5*(H1+H2)
Da <- 1/(1-Ha)
Dg <- 1/sum(pisqr)
Db <- Dg/Da
D <- -2*((1/Db) - 1)
D
}
Sample data:
e<-c(0,0,0,4,27)
r<-c(0,1,0,7,16)
t<-c(1,0,0,16,44)
y<-c(0,0,0,2,39)
df<-cbind(e,r,t,y)
rownames(df)<-q
colnames(df)<-w
> df
P01 P02 P03 P04
L01.1 0 0 1 0
L01.2 0 1 0 0
L01.3 0 0 0 0
L01.4 4 7 16 2
L01.5 27 16 44 39
> JostD(df, 1, 2)
[1] 0.0535215
> JostD(df, 1, 3)
[1] 0.02962404
>
--
Colin Garroway (PhD candidate)
Wildlife Research and Development Section
Ontario Ministry of Natural Resources
Trent University, DNA Building
2140 East Bank Drive
Peterborough, ON, K9J 7B8
Canada
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