mcmc.sumstat<-function(ms.output,gene.prior){
sum.stat<-NULL
for (j in 1:length(ms.output)){
ss<-as.numeric(strsplit(ms.output[[j]][3]," ")[[1]][2])
if(ss==0){
pi=0
H=c(0,0)
TD<-NA
} else {
x<-ms.output[[j]][5:length(ms.output[[j]])]
x<-gsub("0","A",x)
x<-gsub("1","C",x)
se<-list(NULL,NULL,NULL,NULL)
names(se)<-c("nb","seq","nam","com")
se$nb<-length(x) # number of samples
se$seq<-x # sequencies
se$nam<-c(1:length(x)) # sequence names, just numbers
se$com<-NA
class(se)<-"alignment" # this is an alignment
x<-as.DNAbin(se)
pi<-nuc.div(x)*ss/gene.prior[j,5]
H<-H.div(x)[2]
TD<-tajima.test(x)$D
}
SS<-c(pi[[1]],ss,H,TD[1])
sum.stat<-rbind(sum.stat,SS)
}
return(sum.stat)
}
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