## LSD bootstrap solo addition to pick up where it has failed...
## function declaration
LSD_Data_Frame <- function(data,n.bs=100,reps=10,mu=0.0001,R0=2,Tg=2.6,size=c(0,0.1,10),
dir="C:/Users/Oliver/Google Drive/Academic Work/Imperial/O15-12/BEAST/Data Collection/VarianceCheck/",
dir.names = c("NoVariance","Size0.1","Size10")){
## EXTRA FUNCTIONS ##
## HANDLE VARIABLES ##
##########################################################
param.dir <- paste(dir,"mu_",mu,"_R0_",R0,"_Tg_",Tg,"/",sep="")
rows <- length(size)*reps*n.bs
res <- as.data.frame(list("Var"=rep(0,rows),"Tree"=rep(0,rows),"Time"=rep(0,rows),"O_TMRCA"=rep(0,rows),"E_mu"=rep(0,rows),"O_mu"=rep(0,rows)))
## MAIN LOOP ##
##########################################################
for (d in 1:length(dir.names)){
main.dir <- paste(param.dir,dir.names[d],"/",sep="")
if(d==1){
res$Var[(((d-1)*(reps*n.bs))+1):(((d)*(reps*n.bs)))] <- 0
} else {
res$Var[(((d-1)*(reps*n.bs))+1):(((d)*(reps*n.bs)))] <- size[d]
}
for (r in 1:reps){
rep.dir <- paste(main.dir,rep.name,r,"/",sep="")
## collect tree
load(paste(rep.dir,"casetree.RData",sep=""))
res$O_TMRCA[((((d-1)*(reps*n.bs))+((r-1)*n.bs)):((d-1)*(reps*n.bs)+((r)*n.bs)))] <- data[[d]][,r]
res$O_mu[((((d-1)*(reps*n.bs))+((r-1)*n.bs)):((d-1)*(reps*n.bs)+((r)*n.bs)))] <- data[[d+length(dir.names)]][,r]
res$Tree[((((d-1)*(reps*n.bs))+((r-1)*n.bs)):((d-1)*(reps*n.bs)+((r)*n.bs)))] <- r
res$Time[((((d-1)*(reps*n.bs))+((r-1)*n.bs)):((d-1)*(reps*n.bs)+((r)*n.bs)))] <- max(case.tree$Time)
res$E_mu[((((d-1)*(reps*n.bs))+((r-1)*n.bs)):((d-1)*(reps*n.bs)+((r)*n.bs)))] <- mu
}
}
return(res)
}
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