Nothing
permClogit = function(target, dataset, xIndex, csIndex, wei = NULL, univariateModels=NULL, hash = FALSE, stat_hash=NULL, pvalue_hash=NULL,
threshold = 0.05, R = 999) {
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]) ) {
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);
clogit_results = NULL;
clogit_results_full = NULL;
id = target[, 2] #the patient id
x = dataset[ , xIndex];
cs = dataset[, csIndex];
case = as.logical(target[, 1]); ## case control, 0 is the control
#if the conditioningset (cs) is empty, lets take it easy.
res <- tryCatch(
{
if (is.na(csIndex) || length(csIndex) == 0 || csIndex == 0) {
clogit_results <- survival::clogit(case ~ x + strata(id) )
#retrieve the p value and stat.
dof = length( coef(clogit_results) )
stat = abs( diff(clogit_results$loglik) )
step <- 0
j <- 1
n <- length(target)
while (j <= R & step < thres ) {
xb <- sample(x, n)
bit2 <- survival::clogit( case ~ xb + strata(id) )
step <- step + ( abs( diff(bit2$loglik) ) > stat )
j <- j + 1
}
stat <- 2 * stat
pvalue <- (step + 1) / (R + 1)
if ( hash ) { #update hash objects
stat_hash[key] <- stat; #.set(stat_hash , key , stat)
pvalue_hash[key] <- pvalue; #.set(pvalue_hash , key , pvalue)
}
} else {
clogit_results <- survival::clogit(case ~ . + strata(id), data = as.data.frame( dataset[ , c(csIndex)] ) )
#fitting the full model
clogit_results_full <- survival::clogit(case ~ . + strata(id), data = as.data.frame( dataset[ , c(csIndex, xIndex)] ) )
#retrieving the p value
stat = anova(clogit_results_full, clogit_results)[2, 2]
step <- 0
j <- 1
n <- length(x)
while (j <= R & step < thres ) {
xb <- sample(x, n)
bit2 <- survival::clogit( case ~ cbind(cs, xb) + strata(id) )
step <- step + ( anova(bit2, clogit_results)[2, 2] > stat )
j <- j + 1
}
pvalue <- log( (step + 1) / (R + 1) )
if( hash ) { #update hash objects
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);
},
error=function(cond) {
pvalue = log(1);
stat = 0;
results <- list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
},
finally={}
)
return(res);
}
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