#Cai JJ (2008) PGEToolbox: A Matlab toolbox for population genetics and evolution
#Journal of Heredity Jul-Aug;99(4):438-40. doi:10.1093/jhered/esm127
#modified
########################################################
###################### MKTEST ##########################
########################################################
# unused
mktest <- function(seq,taxset1,taxset2){
# In der Funktion DsPsDnPn wird gesplittet !
O <- DsPsDnPn(seq,taxset1,taxset2)
Ds <- O$Ds
Ps <- O$Ps
Dn <- O$Dn
Pn <- O$Pn
#p <- fisherextest(round(Ds),round(Ps),round(Dn),round(Pn))
#cat("Ds - Syn. Divergences; Ps - Syn. Polymorphisms","\n")
#cat("Dn - Nonsyn. Divergences; Pn - Nonsyn. Polymorphisms","\n")
#cat("\n")
#cat("Fisher''s exact test","\n","P-value (two tailed):",p,"-->","significant ? :",sigtag(p))
#cat("\n")
X <- gtest(Ds,Ps,Dn,Pn)
P <- X$P
G <- X$G
#cat("G TEST, G value:",G,"\n")
#cat("P-value:",P)
#if(P!="NaN"){
# cat("--> significant ? :",sigtag(P))
#}
#cat("\n")
if(Ps!=0 && Dn!=0 && Ds!=0){
NI <- (Pn/Dn)/(Ps/Ds)
alphax <- 1-(Pn*Ds)/(Ps*Dn)
}else{
NI <- 0
alphax <- "NaN"
}
#cat("Neutrality Index (NI), [(Pn/Dn)/(Ps/Ds)]:",NI,"\n")
#cat("Alpha [1-(Pn*Ds)/(Ps*Dn)]:",alphax,"\n")
return(list(Ps=Ps,Pn=Pn,Ds=Ds,Dn=Dn,NI=NI,alphax=alphax,G=G,P=P))
}
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