Nothing
testIndClogit = 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 ( !is.matrix(target) || ( is.matrix(target) & ncol(target) != 2 ) ) stop('The testIndClogit test can not be performed without a 2 column matrix 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]) ) {
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];
case = target[, 1] ## case control, 1 is the case, 0 is the control
res <- tryCatch(
{
if ( length(csIndex) == 0 || sum(csIndex == 0, na.rm = TRUE) > 0 ) {
clogit_results <- survival::clogit(case ~ x + strata(id) )
dof = length( coef(clogit_results) )
stat = 2 * abs( diff(clogit_results$loglik) )
pvalue = pchisq(stat, dof, lower.tail = FALSE, log.p = TRUE);
} else {
clogit_results <- survival::clogit(case ~ . + strata(id), data = data.frame( dataset[ , csIndex] ) )
clogit_results_full <- survival::clogit(case ~ . + strata(id), data = data.frame( dataset[ , c(csIndex, xIndex)] ) )
res = anova(clogit_results_full, clogit_results)
stat = res[2, 2]
dF = res[2, 3]
pvalue = pchisq(stat, dF, 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)
}
}
#testerrorcaseintrycatch(4);
results <- list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
},
error=function(cond) {
# message(paste("error in try catch of the testIndZIP test"))
# message("Here's the original error message:")
# message(cond)
# # #for debug
# # print("\nxIndex = \n");
# # print(xIndex);
# # print("\ncsindex = \n");
# # print(csIndex);
# stop();
#error case
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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