Nothing
permCR = function(target, dataset, xIndex, csIndex, wei = NULL, univariateModels=NULL, hash = FALSE, stat_hash=NULL, pvalue_hash=NULL,
threshold = 0.05, R = 999){
# 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;
thres <- threshold * R + 1
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];
#if the censored indicator is empty, a dummy variable is created
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 <- anova(cox_results)[2, 2]
if (stat > 0) {
step <- 0
j <- 1
n <- length(x)
while (j <= R & step < thres ) {
xb <- sample(x, n)
bit2 <- survival::coxph( target ~ xb, weights = wei )
step <- step + ( anova(bit2)[2, 2] > stat )
j <- j + 1
}
pvalue <- log( (step + 1) / (R + 1) )
}
} else {
cox_results_full <- survival::coxph(target ~ ., data = as.data.frame( dataset[ , c(csIndex, xIndex)] ), weights = wei)
res <- anova(cox_results_full)
pr <- nrow(res)
stat <- res[pr, 2]
if (stat > 0) {
j <- 1
step <- 0
n <- length(x)
while (j <= R & step < thres ) {
xb <- sample(x, n)
bit2 <- survival::coxph( target ~ ., data = as.data.frame( cbind( dataset[, csIndex], xb ) ), weights = wei )
step <- step + ( anova(bit2)[pr, 2] > stat )
j <- j + 1
}
pvalue <- log( (step + 1) / (R + 1) )
}
}
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);
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.