Nothing
compute_intern_achaz <- function(bial,populations,outgroup){
npops <- length(populations)
Achaz.value <- rep(NaN,npops)
if(outgroup[1]==FALSE){
for (xx in 1:npops ){
pop.matrix <- bial[populations[[xx]],,drop=FALSE]
FREQ_ERG <- .Call("compute_FREQ_C",pop.matrix)
FREQ_ERG <- rowSums(FREQ_ERG)
init <- vector(,floor(length(populations[[xx]])/2))
w1 <- init
w2 <- init
sfreqn <- init
popsize <- length(populations[[xx]])
sfreq <- FREQ_ERG[2:popsize] # monomorph positions are not relevant # ACHTUNG bei sehr kleinen Populationen !!!
for(x in 1:floor(popsize/2)) {
if(x == 1) {w1[x] <- 0
}else{
if(x == popsize-x){w1[x] <- popsize/2.0
}else{w1[x] <- popsize}
}
if(x == 1){w2[x] <- 0
}else{
if(x == popsize-x){ w2[x] <- popsize/(x*(popsize - x)*2.0)
}else{ w2[x] <- popsize/(x*(popsize - x))}
}
if(x == popsize-x){ sfreqn[x] <- as.integer(((sfreq[x]+ sfreq[popsize-x])/2))
}else{sfreqn[x] <- sfreq[x] + sfreq[popsize-x]
}
}
Achaz.value[xx] <- freqtestn_achaz(popsize,sfreqn,0,w1,w2)
# print(Achaz.value)
}# End over all pops
return(Achaz.value)
}# End no Outgroup
#------------------------------------- WITH OUTGROUP !!!
if(outgroup[1]!=FALSE){
for (xx in 1:npops ){
popsize <- length(populations[[xx]])
pop.matrix <- bial[populations[[xx]],,drop=FALSE]
out.matrix <- bial[outgroup,,drop=FALSE]
# Get ANCESTRAL
ancestral <- .Call("verify_ancestral_C",out.matrix)
#------------
all.matrix <- rbind(pop.matrix,ancestral)
FREQ_ERG <- .Call("compute_FREQOUT_C",all.matrix)
FREQ_ERG <- rowSums(FREQ_ERG)
w1 <- c(0, seq(length(populations[[xx]])-2,1)) # ?? 0 3 2 1 # Population size 5
w2 <- c(0,1/(3:length(populations[[xx]])-1)) # ?? 0 1/2 1/3 1/4 # Population size 5
# Yach[xx] <- freqtesto_achaz(length(populations[[xx]]),FREQ_ERG[[xx]],THETA_ERG["S",xx],w1,w2)
Achaz.value[xx] <- freqtesto_achaz(popsize,FREQ_ERG,0,w1,w2)
}
return(Achaz.value)
}# End of outgroup included
}
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