Nothing
preprocessX <- function(data.x) {
#------------------------------------------------------------------#
# Verify sufficient number of columns in datasets #
#------------------------------------------------------------------#
nc <- ncol(data.x)
if( nc < 3L ) {
stop("data.x must include {ID, time, measurement(s)}.",
call. = FALSE)
}
#------------------------------------------------------------------#
# ensure that patient ids are integers #
#------------------------------------------------------------------#
if( !is.integer(data.x[,1L]) ) {
data.x[,1L] <- as.integer(round(data.x[,1L],0))
message("patient IDs in data.x were coerced to integer.\n")
}
intPresent <- FALSE
if( nc > 2L ) {
for( i in 3L:nc ) {
if( isTRUE(all.equal(data.x[,i], 1.0)) ) {
intPresent <- TRUE
break
}
}
}
#------------------------------------------------------------------#
# Remove any cases for which all covariates are NA #
#------------------------------------------------------------------#
rmRow <- apply(data.x, 1, function(x){all(is.na(x))})
data.x <- data.x[!rmRow,]
#------------------------------------------------------------------#
# Determine total number of covariates. #
# Note this includes an intercept #
#------------------------------------------------------------------#
if( intPresent ){
nCov <- ncol(data.x) - 2L
} else {
nCov <- ncol(data.x) - 2L + 1L
#----------------------------------------------------------------#
# Add intercept to data.x #
#----------------------------------------------------------------#
nms <- colnames(data.x)
if( nc > 2L ) {
data.x <- cbind(data.x[,1L:2L], 1.0, data.x[,3L:nc])
colnames(data.x) <- c(nms[1L:2L], "(Intercept)", nms[3L:nc])
} else {
data.x <- cbind(data.x[,1L:2L], 1.0)
colnames(data.x) <- c(nms[1L:2L], "(Intercept)")
}
}
#------------------------------------------------------------------#
# Set missing cases to 0.0 #
#------------------------------------------------------------------#
tst <- is.na(data.x)
data.x[tst] <- 0.0
#------------------------------------------------------------------#
# Determine if any times in data.x are < 0 #
#------------------------------------------------------------------#
if( any(data.x[,2L] < {-1.5e-8}) ) {
stop("Time is negative in data.x.", call. = FALSE)
}
return(data.x)
}
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