R/dataprep.R

In kkholst/mcif: What the package does (short line)

#-----------------------------------------------------------------------
# Time transforming function g(t)
#-----------------------------------------------------------------------
# Transformation g
g <- function(x,delta){
     atanh((x-delta/2)/(delta/2))
}

# Derivative of g
dg <- function(x,delta){
     (1/2)*delta/(x*(delta-x))
}

#-----------------------------------------------------------------------
# Data preparing function
#-----------------------------------------------------------------------
data.prep <- function(data, time, status, ID, w, cova=NULL){

datao <- data[order(data[,ID]),]

#-----------------------------------------------------------------------
# Causes of failure
#-----------------------------------------------------------------------
causes <- cbind(datao[, paste(status, 1, sep="")], datao[, paste(status, 2, sep="")])

#-----------------------------------------------------------------------
# Xs
#-----------------------------------------------------------------------
n <- nrow(datao)

if (!is.null(cova)){
    x1 <- paste(cova, "1", sep="")
    x2 <- paste(cova, "2", sep="")
}
if (is.null(cova)){
    x1 <- cova
    x2 <- cova
}
x.1 <- as.matrix(cbind(rep(1,n),datao[,x1]))
x.2 <- as.matrix(cbind(rep(1,n),datao[,x2]))

#-----------------------------------------------------------------------
# Transformation g(t)
#-----------------------------------------------------------------------
# Time points
t1 <- datao[, paste(time, 1, sep="")]
t2 <- datao[, paste(time, 2, sep="")]

# Max. time
delta <- max(t1,t2)

# Transformed timepoints
gt1 <- g(t1,delta)
gt2 <- g(t2,delta)

#-----------------------------------------------------------------------
# Derivative of g(t)
#-----------------------------------------------------------------------
dgt1 <- dg(t1,delta)
dgt2 <- dg(t2,delta)

#-----------------------------------------------------------------------
# ID
#-----------------------------------------------------------------------
ID <- datao[, ID]

#-----------------------------------------------------------------------
# Weights
#-----------------------------------------------------------------------
w <- datao[, w]

#-----------------------------------------------------------------------
# EB0
#-----------------------------------------------------------------------
eb0 <- matrix(0, nrow=nrow(causes), ncol=2)

#-----------------------------------------------------------------------
# Return
#-----------------------------------------------------------------------
res <- list("causes"=causes, "x.1"=x.1, "x.2"=x.2, "gt1"=gt1, "dgt1"=dgt1, "gt2"=gt2, "dgt2"=dgt2, "delta"=delta, "weights"=w, "ID"=ID, "eb0"=eb0)
return(res)
}