void getCRPerformance (uint mode,
uint obsSize,
double **responsePtr,
double **conditionalMortality,
uint *ensembleDenPtr,
double *performanceVector) {
uint mRecordSize;
int **mpSign;
uint *mRecordIndex;
uint *meIndividualSize;
uint **eIndividual;
double concordanceIndex;
uint j;
if (!(RF_opt & OPT_COMP_RISK)) {
Rprintf("\nRF-SRC: *** ERROR *** ");
Rprintf("\nRF-SRC: Attempt at conditional performance updates in a non-CR analysis.");
Rprintf("\nRF-SRC: Please Contact Technical Support.");
error("\nRF-SRC: The application will now exit.\n");
}
if (RF_mStatusSize > 0) {
if (mode != RF_PRED) {
mRecordSize = RF_mRecordSize;
mpSign = RF_mpSign;
mRecordIndex = RF_mRecordIndex;
}
else {
mRecordSize = RF_fmRecordSize;
mpSign = RF_fmpSign;
mRecordIndex = RF_fmRecordIndex;
}
meIndividualSize = uivector(1, RF_eventTypeSize);
eIndividual = (uint **) new_vvector(1, RF_eventTypeSize, NRUTIL_UPTR);
for (j = 1; j <= RF_eventTypeSize; j++) {
eIndividual[j] = uivector(1, RF_eIndividualSize[j] + RF_mStatusSize + 1);
}
updateEventTypeSubsets(responsePtr[RF_statusIndex], mRecordSize, mpSign, mRecordIndex, meIndividualSize, eIndividual);
}
else {
meIndividualSize = RF_eIndividualSize;
eIndividual = RF_eIndividualIn;
}
double *subsettedTime = dvector(1, obsSize);
double *subsettedStatus = dvector(1, obsSize);
double *subsettedMortality = dvector(1, obsSize);
uint *subsettedEnsembleDen = uivector(1, obsSize);
for (j = 1; j <= RF_eventTypeSize; j++) {
getConditionalConcordanceArrays(j,
responsePtr[RF_timeIndex],
responsePtr[RF_statusIndex],
conditionalMortality[j],
ensembleDenPtr,
meIndividualSize,
eIndividual,
subsettedTime,
subsettedStatus,
subsettedMortality,
subsettedEnsembleDen);
concordanceIndex = getConcordanceIndex(1,
meIndividualSize[j],
subsettedTime,
subsettedStatus,
subsettedMortality,
subsettedEnsembleDen);
if (ISNA(concordanceIndex)) {
performanceVector[j] = NA_REAL;
}
else {
performanceVector[j] = concordanceIndex;
}
}
if (RF_mStatusSize > 0) {
free_uivector(meIndividualSize, 1, RF_eventTypeSize);
for (j = 1; j <= RF_eventTypeSize; j++) {
free_uivector(eIndividual[j], 1, RF_eIndividualSize[j] + RF_mStatusSize + 1);
}
free_new_vvector(eIndividual, 1, RF_eventTypeSize, NRUTIL_UPTR);
}
free_dvector(subsettedTime, 1, obsSize);
free_dvector(subsettedStatus, 1, obsSize);
free_dvector(subsettedMortality, 1, obsSize);
free_uivector(subsettedEnsembleDen, 1, obsSize);
}
void finalizeVariableImportance(uint mode,
uint rejectedTreeCount,
char **dmRecordBootFlag,
double ***dmvImputation) {
uint obsSize = 0;
uint varCount = 0;
double *statusPtr = NULL;
double *timePtr = NULL;
uint *ensembleDenPtr = NULL;
double concordanceIndex;
int concordancePolarity;
char concordanceImputeFlag;
double *crPerformanceVector;
double ***crVimpMortality;
double value;
uint *denominatorCount;
uint i, j, k, p;
if (!(rejectedTreeCount < _forestSize)) {
Rprintf("\nRSF: *** WARNING *** ");
Rprintf("\nRSF: Insufficient trees for VIMP analysis. \n");
return;
}
if (!(_opt & OPT_VIMP)) {
Rprintf("\nRSF: *** WARNING *** ");
Rprintf("\nRSF: VIMP analysis requested while OPT bit not set. \n");
return;
}
crPerformanceVector = NULL;
crVimpMortality = NULL;
if (_opt & (OPT_POUT_TYPE)) {
concordancePolarity = -1;
}
else {
concordancePolarity = 1;
}
concordanceImputeFlag = FALSE;
switch (mode) {
case RSF_GROW:
obsSize = _observationSize;
varCount = _xSize;
statusPtr = _status;
timePtr = _time;
ensembleDenPtr = _oobEnsembleDen;
if (_mRecordSize > 0) {
concordanceImputeFlag = TRUE;
}
break;
case RSF_PRED:
obsSize = _fobservationSize;
varCount = _xSize;
statusPtr = _fstatus;
timePtr = rsf_ftime;
ensembleDenPtr = _fullEnsembleDen;
if (_fmRecordSize > 0) {
concordanceImputeFlag = TRUE;
}
break;
case RSF_INTR:
obsSize = _fobservationSize;
if (_opt & (~OPT_VIMP) & OPT_VIMP_JOIN) {
varCount = 1;
}
else {
varCount = _intrPredictorSize;
}
statusPtr = _fstatus;
timePtr = rsf_ftime;
ensembleDenPtr = _oobEnsembleDen;
if (_fmRecordSize > 0) {
concordanceImputeFlag = TRUE;
}
break;
default:
Rprintf("\nRSF: *** ERROR *** ");
Rprintf("\nRSF: Unknown case in switch encountered. ");
Rprintf("\nRSF: Please Contact Technical Support.");
error("\nRSF: The application will now exit.\n");
break;
}
if (_opt & OPT_VOUT_TYPE) {
denominatorCount = uivector(1, obsSize);
}
else {
denominatorCount = ensembleDenPtr;
}
if (_eventTypeSize > 1) {
crVimpMortality = dmatrix3(1, varCount, 1, _eventTypeSize, 1, obsSize);
crPerformanceVector = dvector(1, _eventTypeSize);
for (p=1; p <= varCount; p++) {
for (i = 1; i <= obsSize; i++) {
for (j = 1; j <= _eventTypeSize; j++) {
for (k = 1; k <= _sortedTimeInterestSize; k++) {
if(_crVimpEnsemble[p][j][k][i] > 0) {
if (_crVimpPOE[p][j][i] > 0) {
value = _crVimpEnsemble[p][j][k][i] / _crVimpPOE[p][j][i];
value = (value <= 1.0) ? value : 1.0;
_crVimpEnsemble[p][j][k][i] = - log (value);
}
else {
value = _crVimpEnsemble[p][j][k][i] / 1.0;
value = (value <= 1.0) ? value : 1.0;
_crVimpEnsemble[p][j][k][i] = - log (value);
}
}
else {
if (_crVimpPOE[p][j][i] > 0) {
if (k > 1) {
_crVimpEnsemble[p][j][k][i] = _crVimpEnsemble[p][j][k-1][i];
}
else {
_crVimpEnsemble[p][j][k][i] = 0.0;
}
}
else {
_crVimpEnsemble[p][j][k][i] = 1.0;
}
}
}
}
}
}
for (p = 1; p <= varCount; p++) {
for (j = 1; j <= _eventTypeSize; j++) {
for (i = 1; i <= obsSize; i++) {
crVimpMortality[p][j][i] = 0.0;
for (k = 1; k <= _sortedTimeInterestSize; k++) {
crVimpMortality[p][j][i] += _crVimpEnsemble[p][j][k][i];
}
}
}
}
}
if (concordanceImputeFlag == TRUE) {
imputeConcordance(mode,
_forestSize,
dmRecordBootFlag,
dmvImputation,
statusPtr,
timePtr);
}
for (p=1; p <= varCount; p++) {
for (i = 1; i <= obsSize; i++) {
if (_opt & OPT_VOUT_TYPE) {
denominatorCount[i] = ensembleDenPtr[i] - _oobVimpInvalidDen[p][i];
}
if (denominatorCount[i] != 0) {
_vimpMortality[p][i] = _vimpMortality[p][i] / denominatorCount[i];
}
}
concordanceIndex = getConcordanceIndex(concordancePolarity,
obsSize,
statusPtr,
timePtr,
_vimpMortality[p],
denominatorCount);
if (ISNA(concordanceIndex)) {
_importancePtr[1][p] = NA_REAL;
}
else {
_importancePtr[1][p] = 1 - concordanceIndex;
}
if (_eventTypeSize > 1) {
getConditionalPerformance(mode,
concordancePolarity,
obsSize,
statusPtr,
timePtr,
crVimpMortality[p],
denominatorCount,
crPerformanceVector);
for (j=1; j <=_eventTypeSize; j++) {
_importancePtr[1+j][p] = crPerformanceVector[j];
}
}
}
if (_eventTypeSize > 1) {
free_dvector(crPerformanceVector, 1, _eventTypeSize);
free_dmatrix3(crVimpMortality, 1, varCount, 1, _eventTypeSize, 1, obsSize);
}
if (_opt & OPT_VOUT_TYPE) {
free_uivector(denominatorCount, 1, obsSize);
}
}
