Nothing
permDcor = function(target, dataset, xIndex, csIndex, wei = NULL, statistic = FALSE, univariateModels=NULL, hash = FALSE, stat_hash = NULL,
pvalue_hash = NULL, threshold = 0.05, R = 499) {
# TESTINDFISHER Fisher Conditional Independence Test for continous class variables
# PVALUE = TESTINDFISHER(Y, DATA, XINDEX, CSINDEX)
# This test provides a p-value PVALUE for the NULL hypothesis H0 which is
# X is independent by TARGET given CS. The pvalue is calculated following
# Fisher's method (see reference below)
# This method requires the following inputs
# TARGET: a numeric vector containing the values of the target (continuous) variable.
# Its support can be R or any number betweeen 0 and 1, i.e. it contains proportions.
# DATASET: a numeric data matrix containing the variables for performing the test. They can be only be continuous variables.
# XINDEX: the index of the variable whose association with the target we want to test.
# CSINDEX: the indices if the variable to condition on.
# this method returns: the pvalue PVALUE, the statistic STAT.
# Copyright 2012 Vincenzo Lagani and Ioannis Tsamardinos
# R Implementation by Giorgos Athineou (10/2013)
#if the test cannot performed succesfully these are the returned values
pvalue = log(1)
stat = 0;
if ( !is.list(target) ) {
n = length( 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);
}
}
#if the xIndex is contained in csIndex, x does not bring any new information with respect to cs
if ( !is.na( match(xIndex, csIndex) ) ) {
if ( hash ) { #update hash objects
stat_hash[key] <- 0; #.set(stat_hash , key , 0)
pvalue_hash[key] <- 1; #.set(pvalue_hash , key , 1)
}
results <- list(pvalue = 1, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
}
#check input validity
if ( any(xIndex < 0) || any(csIndex < 0) ) {
message(paste("error in testIndFisher : wrong input of xIndex or csIndex"))
results <- list(pvalue = pvalue, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
}
xIndex = unique(xIndex);
csIndex = unique(csIndex);
#extract the data
x = dataset[ , xIndex];
cs = dataset[ , csIndex];
#That means that the x variable does not add more information to our model due to an exact copy of this in the cs, so it is independent from the target
if ( length(cs) != 0 ) {
if ( is.null(dim(cs)[2]) ) { #cs is a vector
if ( identical(x, cs) ) { #if(!any(x == cs) == FALSE)
if ( hash ) { #update hash objects
stat_hash[key] <- 0; #.set(stat_hash , key , 0)
pvalue_hash[key] <- 1; #.set(pvalue_hash , key , 1)
}
results <- list(pvalue = 1, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
}
} else { #more than one var
for (col in 1:dim(cs)[2]) {
if ( identical(x, cs[, col]) ) { #if(!any(x == cs) == FALSE)
if ( hash ) { #update hash objects
stat_hash[key] <- 0; #.set(stat_hash , key , 0)
pvalue_hash[key] <- 1; #.set(pvalue_hash , key , 1)
}
results <- list(pvalue = 1, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
}
}
}
}
res <- tryCatch(
{
#if the conditioning set (cs) is empty, we use a simplified formula
if (length(cs) == 0) {
if ( !is.null(univariateModels) ) {
pvalue = univariateModels$pvalue[[xIndex]];
stat = univariateModels$stat[[xIndex]];
results <- list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
}
#compute the correlation coefficient between x,target directly
mod <- energy::dcov.test(target, x, R = R)
stat <- mod$statistic
pvalue <- mod$p.value
} else {
#perform the test with the cs
mod <- energy::pdcor.test(target, x, cs, R)
stat <- mod$statistic
pvalue <- mod$p.value
}
#last error check
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);
},
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={}
)
###########################
## meta-analytic approach
###########################
} else {
D = length(target)
pva = numeric(D)
aa <- list()
for ( i in 1:D ) {
targ = target[[ i ]]
data = dataset[[ i ]]
n = length( targ )
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];
aa[[ i ]] <- list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
}
}
#if the xIndex is contained in csIndex, x does not bring any new
#information with respect to cs
if ( !is.na( match(xIndex, csIndex) ) ) {
if ( hash ) { #update hash objects
stat_hash[key] <- 0; #.set(stat_hash , key , 0)
pvalue_hash[key] <- 1; #.set(pvalue_hash , key , 1)
}
aa[[ i ]] <- list(pvalue = 1, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
}
#check input validity
if ( any(xIndex < 0) || any(csIndex < 0) ) {
message(paste("error in testIndFisher : wrong input of xIndex or csIndex"))
aa[[ i ]] <- list(pvalue = pvalue, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
}
xIndex = unique(xIndex);
csIndex = unique(csIndex);
x = data[ , xIndex];
cs = data[ , csIndex];
#That means that the x variable does not add more information to our model due to an exact copy of this in the cs, so it is independent from the target
if ( length(cs) != 0 ) {
if ( is.null( dim(cs )[2]) ) { #cs is a vector
if (any(x != cs) == FALSE) { #if(!any(x == cs) == FALSE)
if ( hash ) { #update hash objects
stat_hash[key] <- 0; #.set(stat_hash , key , 0)
pvalue_hash[key] <- 1; #.set(pvalue_hash , key , 1)
}
aa[[ i ]] <- list(pvalue = 1, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
}
} else { #more than one var
for ( col in 1:ncol(cs) ) {
if (any(x != cs[, col]) == FALSE) { #if(!any(x == cs) == FALSE)
if ( hash ) { #update hash objects
stat_hash[key] <- 0; #.set(stat_hash , key , 0)
pvalue_hash[key] <- 1; #.set(pvalue_hash , key , 1)
}
aa[[ i ]] <- list(pvalue = 1, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
}
}
}
}
#if x or target is constant then there is no point to perform the test
if ( Rfast::Var(x) == 0 ) {
if ( hash ) { #update hash objects
stat_hash[key] <- 0; #.set(stat_hash , key , 0)
pvalue_hash[key] <- 1; #.set(pvalue_hash , key , 1)
}
aa[[ i ]] <- list(pvalue = 1, stat = 0, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
}
#remove constant columns of cs
cs = cs[, apply(cs, 2, var, na.rm=TRUE) != 0]
aa[[ i ]] <- tryCatch(
{
#if the conditioning set (cs) is empty, we use a simplified formula
if (length(cs) == 0) {
if ( !is.null(univariateModels) ) {
pvalue = univariateModels$pvalue[[xIndex]];
stat = univariateModels$stat[[xIndex]];
results <- list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
return(results);
}
#compute the correlation coefficient between x, target directly
mod <- energy::dcov.test(target, x, R = R)
stat <- mod$statistic
pvalue <- mod$p.value
} else {
#perform the test with the cs
mod <- energy::pdcor.test(target, x, cs, R)
stat <- mod$statistic
pvalue <- mod$p.value
}
#last error check
if (is.na(pvalue) || is.na(stat) ) {
pvalue = log(1)
stat = 0;
} else {
if( hash ) {
stat_hash[key] <- stat; #.set(stat_hash , key , stat)
pvalue_hash[key] <- pvalue; #.set(pvalue_hash , key , pvalue)
}
}
#testerrorcaseintrycatch(4);
list(pvalue = pvalue, nu = n, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
},
error=function(cond) {
#error case (we are pretty sure that the only error case is when x,cs are highly correlated and the inversion of the matrix is not possible)
pvalue = log(1)
stat = 0;
list(pvalue = pvalue, nu = n, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
},
finally={}
)
}
pva <- numeric(D)
for ( j in 1:D ) pva[j] = -2 * aa[[ j ]]$pvalue
stat = sum(pva)
pvalue = pchisq( stat, 2 * D, lower.tail = FALSE, log.p = TRUE )
if ( hash ) {
stat_hash[key] <- stat
pvalue_hash[key] <- pvalue
}
res = list(pvalue = pvalue, stat = stat, stat_hash=stat_hash, pvalue_hash=pvalue_hash);
}
return(res)
}
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