Nothing
waldCR <- function(target, dataset, xIndex, csIndex, wei = NULL, univariateModels=NULL, hash = FALSE, stat_hash=NULL, pvalue_hash=NULL){
# Conditional independence test based on the Log Likelihood ratio test
if ( !survival::is.Surv(target) ) stop('The survival test can not be performed without a Surv object target');
csIndex[ which( is.na(csIndex) ) ] <- 0;
if ( hash ) {
csIndex2 <- csIndex[which(csIndex!=0)]
csIndex2 <- sort(csIndex2)
xcs <- c(xIndex,csIndex2)
key <- paste(as.character(xcs) , collapse=" ");
if ( is.null(stat_hash[key]) == FALSE ) {
stat <- stat_hash[key];
pvalue <- pvalue_hash[key];
results <- list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
}
}
#initialization: these values will be returned whether the test cannot be carried out
pvalue <- log(1);
stat <- 0;
results <- list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
cox_results <- NULL;
cox_results_full <- NULL;
event <- target[,2]
x <- dataset[ , xIndex];
numCases <- dim(dataset)[1];
oop <- options(warn = -1)
on.exit( options(oop) )
if ( length(event) == 0 ) event = vector('numeric',numCases) + 1;
if ( length(csIndex) == 0 || sum(csIndex == 0, na.rm = TRUE) > 0 ) {
cox_results <- survival::coxph(target ~ x, weights = wei )
stat <- cox_results$wald.test
pvalue <- pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE);
} else {
cox_results_full <- survival::coxph(target ~ ., data = as.data.frame( dataset[ , c(csIndex, xIndex)] ), weights = wei)
res <- summary(cox_results_full)[[ 7 ]]
pr <- dim(res)[1]
stat <- res[pr, 4]^2
pvalue < pchisq(stat, 1, lower.tail = FALSE, log.p = TRUE)
}
if ( is.na(pvalue) || is.na(stat) ) {
pvalue <- log(1);
stat <- 0;
} else {
#update hash objects
if( hash ) {
stat_hash[key] <- stat; #.set(stat_hash , key , stat)
pvalue_hash[key] <- pvalue; #.set(pvalue_hash , key , pvalue)
}
}
results <- list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
}
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