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censIndER = 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);
expo_results = NULL;
expo_results_full = NULL;
#timeIndex = dim(dataset)[2];
event = target[,2]
x = dataset[ , xIndex];
#if the censored indicator is empty, a dummy variable is created
numCases = dim(dataset)[1];
if (length(event) == 0) event = vector('numeric',numCases) + 1;
if ( length(csIndex) == 0 || sum(csIndex == 0, na.rm = TRUE) > 0 ) {
expo_results <- try( survival::survreg(target ~ x, dist = "exponential", weights = wei), silent = TRUE )
if ( identical( class(expo_results), "try-error" ) ) {
stat <- NA
} else {
dof <- length( coef(expo_results) ) - 1
stat = 2 * abs( diff(expo_results$loglik) )
pvalue = pchisq(stat, dof, lower.tail = FALSE, log.p = TRUE);
}
} else {
expo_results <- try( survival::survreg(target ~ ., data = as.data.frame( dataset[ , c(csIndex)] ), dist = "exponential", weights = wei), silent = TRUE)
expo_results_full <- try( survival::survreg(target ~ ., data = as.data.frame( dataset[ , c(csIndex, xIndex)] ), dist = "exponential", weights = wei ), silent = TRUE)
if ( identical( class(expo_results), "try-error" ) | identical( class(expo_results_full), "try-error" ) ) {
stat <- NA
} else {
res = anova(expo_results, expo_results_full)
stat = abs( res[2, 6] );
dof = abs( res[2, 5] );
pvalue = pchisq(stat, dof, 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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