void omxExpectation::loadFromR()
{
if (!rObj || !data) return;
auto ox = this;
int numCols=0;
bool isRaw = strEQ(omxDataType(data), "raw");
if (isRaw || data->hasSummaryStats()) {
ProtectedSEXP Rdcn(R_do_slot(rObj, Rf_install("dataColumnNames")));
loadCharVecFromR(name, Rdcn, dataColumnNames);
ProtectedSEXP Rdc(R_do_slot(rObj, Rf_install("dataColumns")));
numCols = Rf_length(Rdc);
ox->saveDataColumnsInfo(Rdc);
if(OMX_DEBUG) mxPrintMat("Variable mapping", base::getDataColumns());
if (isRaw) {
auto dc = base::getDataColumns();
for (int cx=0; cx < numCols; ++cx) {
int var = dc[cx];
data->assertColumnIsData(var);
}
}
}
if (R_has_slot(rObj, Rf_install("thresholds"))) {
if(OMX_DEBUG) {
mxLog("Accessing Threshold matrix.");
}
ProtectedSEXP threshMatrix(R_do_slot(rObj, Rf_install("thresholds")));
if(INTEGER(threshMatrix)[0] != NA_INTEGER) {
ox->thresholdsMat = omxMatrixLookupFromState1(threshMatrix, ox->currentState);
ox->loadThresholds();
} else {
if (OMX_DEBUG) {
mxLog("No thresholds matrix; not processing thresholds.");
}
ox->numOrdinal = 0;
}
}
}
void omxInitWLSFitFunction(omxFitFunction* oo) {
omxMatrix *cov, *means, *weights;
if(OMX_DEBUG) { mxLog("Initializing WLS FitFunction function."); }
int vectorSize = 0;
omxSetWLSFitFunctionCalls(oo);
if(OMX_DEBUG) { mxLog("Retrieving expectation.\n"); }
if (!oo->expectation) { Rf_error("%s requires an expectation", oo->fitType); }
if(OMX_DEBUG) { mxLog("Retrieving data.\n"); }
omxData* dataMat = oo->expectation->data;
if (dataMat->hasDefinitionVariables()) Rf_error("%s: def vars not implemented", oo->name());
if(!strEQ(omxDataType(dataMat), "acov") && !strEQ(omxDataType(dataMat), "cov")) {
char *errstr = (char*) calloc(250, sizeof(char));
sprintf(errstr, "WLS FitFunction unable to handle data type %s. Data must be of type 'acov'.\n", omxDataType(dataMat));
omxRaiseError(errstr);
free(errstr);
if(OMX_DEBUG) { mxLog("WLS FitFunction unable to handle data type %s. Aborting.", omxDataType(dataMat)); }
return;
}
omxWLSFitFunction *newObj = (omxWLSFitFunction*) R_alloc(1, sizeof(omxWLSFitFunction));
OMXZERO(newObj, 1);
oo->argStruct = (void*)newObj;
oo->units = FIT_UNITS_SQUARED_RESIDUAL;
/* Get Expectation Elements */
newObj->expectedCov = omxGetExpectationComponent(oo->expectation, "cov");
newObj->expectedMeans = omxGetExpectationComponent(oo->expectation, "means");
// FIXME: threshold structure should be asked for by omxGetExpectationComponent
/* Read and set expected means, variances, and weights */
cov = omxDataCovariance(dataMat);
means = omxDataMeans(dataMat);
weights = omxDataAcov(dataMat);
newObj->observedCov = cov;
newObj->observedMeans = means;
newObj->weights = weights;
newObj->n = omxDataNumObs(dataMat);
// NOTE: If there are any continuous columns then these vectors
// will not match because eThresh is indexed by column number
// not by ordinal column number.
std::vector< omxThresholdColumn > &oThresh = omxDataThresholds(oo->expectation->data);
std::vector< omxThresholdColumn > &eThresh = oo->expectation->thresholds;
// Error Checking: Observed/Expected means must agree.
// ^ is XOR: true when one is false and the other is not.
if((newObj->expectedMeans == NULL) ^ (newObj->observedMeans == NULL)) {
if(newObj->expectedMeans != NULL) {
omxRaiseError("Observed means not detected, but an expected means matrix was specified.\n If you wish to model the means, you must provide observed means.\n");
return;
} else {
omxRaiseError("Observed means were provided, but an expected means matrix was not specified.\n If you provide observed means, you must specify a model for the means.\n");
return;
}
}
if((eThresh.size()==0) ^ (oThresh.size()==0)) {
if (eThresh.size()) {
omxRaiseError("Observed thresholds not detected, but an expected thresholds matrix was specified.\n If you wish to model the thresholds, you must provide observed thresholds.\n ");
return;
} else {
omxRaiseError("Observed thresholds were provided, but an expected thresholds matrix was not specified.\nIf you provide observed thresholds, you must specify a model for the thresholds.\n");
return;
}
}
/* Error check weight matrix size */
int ncol = newObj->observedCov->cols;
vectorSize = (ncol * (ncol + 1) ) / 2;
if(newObj->expectedMeans != NULL) {
vectorSize = vectorSize + ncol;
}
for(int i = 0; i < int(oThresh.size()); i++) {
vectorSize = vectorSize + oThresh[i].numThresholds;
}
if(OMX_DEBUG) { mxLog("Intial WLSFitFunction vectorSize comes to: %d.", vectorSize); }
if(weights != NULL && (weights->rows != weights->cols || weights->cols != vectorSize)) {
omxRaiseError("Developer Error in WLS-based FitFunction object: WLS-based expectation specified an incorrectly-sized weight matrix.\nIf you are not developing a new expectation type, you should probably post this to the OpenMx forums.");
return;
}
// FIXME: More Rf_error checking for incoming Fit Functions
/* Temporary storage for calculation */
newObj->observedFlattened = omxInitMatrix(vectorSize, 1, TRUE, oo->matrix->currentState);
newObj->expectedFlattened = omxInitMatrix(vectorSize, 1, TRUE, oo->matrix->currentState);
newObj->standardExpectedFlattened = omxInitMatrix(vectorSize, 1, TRUE, oo->matrix->currentState);
newObj->P = omxInitMatrix(1, vectorSize, TRUE, oo->matrix->currentState);
newObj->B = omxInitMatrix(vectorSize, 1, TRUE, oo->matrix->currentState);
newObj->standardExpectedCov = omxInitMatrix(ncol, ncol, TRUE, oo->matrix->currentState);
if (oo->expectation->thresholdsMat) {
newObj->standardExpectedThresholds = omxInitMatrix(oo->expectation->thresholdsMat->rows, oo->expectation->thresholdsMat->cols, TRUE, oo->matrix->currentState);
}
if(means){
newObj->standardExpectedMeans = omxInitMatrix(1, ncol, TRUE, oo->matrix->currentState);
}
omxMatrix *obsThresholdsMat = oo->expectation->data->obsThresholdsMat;
flattenDataToVector(newObj->observedCov, newObj->observedMeans, obsThresholdsMat, oThresh, newObj->observedFlattened);
flattenDataToVector(newObj->expectedCov, newObj->expectedMeans, oo->expectation->thresholdsMat,
eThresh, newObj->expectedFlattened);
}
void omxInitExpectationBA81(omxExpectation* oo) {
omxState* currentState = oo->currentState;
SEXP rObj = oo->rObj;
SEXP tmp;
if(OMX_DEBUG) {
mxLog("Initializing %s.", oo->name);
}
if (!Glibrpf_model) {
#if USE_EXTERNAL_LIBRPF
get_librpf_t get_librpf = (get_librpf_t) R_GetCCallable("rpf", "get_librpf_model_GPL");
(*get_librpf)(LIBIFA_RPF_API_VERSION, &Glibrpf_numModels, &Glibrpf_model);
#else
// if linking against included source code
Glibrpf_numModels = librpf_numModels;
Glibrpf_model = librpf_model;
#endif
}
BA81Expect *state = new BA81Expect;
// These two constants should be as identical as possible
state->name = oo->name;
if (0) {
state->LogLargestDouble = 0.0;
state->LargestDouble = 1.0;
} else {
state->LogLargestDouble = log(std::numeric_limits<double>::max()) - 1;
state->LargestDouble = exp(state->LogLargestDouble);
ba81NormalQuad &quad = state->getQuad();
quad.setOne(state->LargestDouble);
}
state->expectedUsed = false;
state->estLatentMean = NULL;
state->estLatentCov = NULL;
state->type = EXPECTATION_OBSERVED;
state->itemParam = NULL;
state->EitemParam = NULL;
state->itemParamVersion = 0;
state->latentParamVersion = 0;
oo->argStruct = (void*) state;
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("data")));
state->data = omxDataLookupFromState(tmp, currentState);
}
if (strcmp(omxDataType(state->data), "raw") != 0) {
omxRaiseErrorf("%s unable to handle data type %s", oo->name, omxDataType(state->data));
return;
}
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("verbose")));
state->verbose = Rf_asInteger(tmp);
}
int targetQpoints;
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("qpoints")));
targetQpoints = Rf_asInteger(tmp);
}
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("qwidth")));
state->grp.setGridFineness(Rf_asReal(tmp), targetQpoints);
}
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("ItemSpec")));
state->grp.importSpec(tmp);
if (state->verbose >= 2) mxLog("%s: found %d item specs", oo->name, state->numItems());
}
state->_latentMeanOut = omxNewMatrixFromSlot(rObj, currentState, "mean");
state->_latentCovOut = omxNewMatrixFromSlot(rObj, currentState, "cov");
state->itemParam = omxNewMatrixFromSlot(rObj, currentState, "item");
state->grp.param = state->itemParam->data; // algebra not allowed yet TODO
const int numItems = state->itemParam->cols;
if (state->numItems() != numItems) {
omxRaiseErrorf("ItemSpec length %d must match the number of item columns (%d)",
state->numItems(), numItems);
return;
}
if (state->itemParam->rows != state->grp.impliedParamRows) {
omxRaiseErrorf("item matrix must have %d rows", state->grp.impliedParamRows);
return;
}
state->grp.paramRows = state->itemParam->rows;
// for algebra item param, will need to defer until later?
state->grp.learnMaxAbilities();
int maxAbilities = state->grp.itemDims;
state->grp.setFactorNames(state->itemParam->rownames);
{
ProtectedSEXP tmp2(R_do_slot(rObj, Rf_install(".detectIndependence")));
state->grp.detectIndependence = Rf_asLogical(tmp2);
}
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("EstepItem")));
if (!Rf_isNull(tmp)) {
int rows, cols;
getMatrixDims(tmp, &rows, &cols);
if (rows != state->itemParam->rows || cols != state->itemParam->cols) {
Rf_error("EstepItem must have the same dimensions as the item MxMatrix");
}
state->EitemParam = REAL(tmp);
}
}
oo->computeFun = ba81compute;
oo->setVarGroup = ignoreSetVarGroup;
oo->destructFun = ba81Destroy;
oo->populateAttrFun = ba81PopulateAttributes;
oo->componentFun = getComponent;
oo->canDuplicate = false;
// TODO: Exactly identical rows do not contribute any information.
// The sorting algorithm ought to remove them so we get better cache behavior.
// The following summary stats would be cheaper to calculate too.
omxData *data = state->data;
if (data->hasDefinitionVariables()) Rf_error("%s: not implemented yet", oo->name);
std::vector<int> &rowMap = state->grp.rowMap;
int weightCol;
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("weightColumn")));
weightCol = INTEGER(tmp)[0];
}
if (weightCol == NA_INTEGER) {
// Should rowMap be part of omxData? This is essentially a
// generic compression step that shouldn't be specific to IFA models.
state->grp.rowWeight = (double*) R_alloc(data->rows, sizeof(double));
rowMap.resize(data->rows);
int numUnique = 0;
for (int rx=0; rx < data->rows; ) {
int rw = 1;
state->grp.rowWeight[numUnique] = rw;
rowMap[numUnique] = rx;
rx += rw;
++numUnique;
}
rowMap.resize(numUnique);
state->weightSum = state->data->rows;
}
else {
if (omxDataColumnIsFactor(data, weightCol)) {
omxRaiseErrorf("%s: weightColumn %d is a factor", oo->name, 1 + weightCol);
return;
}
state->grp.rowWeight = omxDoubleDataColumn(data, weightCol);
state->weightSum = 0;
for (int rx=0; rx < data->rows; ++rx) { state->weightSum += state->grp.rowWeight[rx]; }
rowMap.resize(data->rows);
for (size_t rx=0; rx < rowMap.size(); ++rx) {
rowMap[rx] = rx;
}
}
// complain about non-integral rowWeights (EAP can't work) TODO
auto colMap = oo->getDataColumns();
for (int cx = 0; cx < numItems; cx++) {
int *col = omxIntDataColumnUnsafe(data, colMap[cx]);
state->grp.dataColumns.push_back(col);
}
// sanity check data
for (int cx = 0; cx < numItems; cx++) {
if (!omxDataColumnIsFactor(data, colMap[cx])) {
data->omxPrintData("diagnostic", 3);
omxRaiseErrorf("%s: column %d is not a factor", oo->name, int(1 + colMap[cx]));
return;
}
}
// TODO the max outcome should be available from omxData
for (int rx=0; rx < data->rows; rx++) {
int cols = 0;
for (int cx = 0; cx < numItems; cx++) {
const int *col = state->grp.dataColumns[cx];
int pick = col[rx];
if (pick == NA_INTEGER) continue;
++cols;
const int no = state->grp.itemOutcomes[cx];
if (pick > no) {
Rf_error("Data for item '%s' has at least %d outcomes, not %d",
state->itemParam->colnames[cx], pick, no);
}
}
if (cols == 0) {
Rf_error("Row %d has all NAs", 1+rx);
}
}
if (state->_latentMeanOut && state->_latentMeanOut->rows * state->_latentMeanOut->cols != maxAbilities) {
Rf_error("The mean matrix '%s' must be a row or column vector of size %d",
state->_latentMeanOut->name(), maxAbilities);
}
if (state->_latentCovOut && (state->_latentCovOut->rows != maxAbilities ||
state->_latentCovOut->cols != maxAbilities)) {
Rf_error("The cov matrix '%s' must be %dx%d",
state->_latentCovOut->name(), maxAbilities, maxAbilities);
}
state->grp.setLatentDistribution(state->_latentMeanOut? state->_latentMeanOut->data : NULL,
state->_latentCovOut? state->_latentCovOut->data : NULL);
{
EigenArrayAdaptor Eparam(state->itemParam);
Eigen::Map< Eigen::VectorXd > meanVec(state->grp.mean, maxAbilities);
Eigen::Map< Eigen::MatrixXd > covMat(state->grp.cov, maxAbilities, maxAbilities);
state->grp.quad.setStructure(state->grp.qwidth, state->grp.qpoints,
Eparam, meanVec, covMat);
}
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("minItemsPerScore")));
state->grp.setMinItemsPerScore(Rf_asInteger(tmp));
}
state->grp.buildRowSkip();
if (isErrorRaised()) return;
{ScopedProtect p1(tmp, R_do_slot(rObj, Rf_install("debugInternal")));
state->debugInternal = Rf_asLogical(tmp);
}
state->ElatentVersion = 0;
if (state->_latentMeanOut) {
state->estLatentMean = omxInitMatrix(maxAbilities, 1, TRUE, currentState);
omxCopyMatrix(state->estLatentMean, state->_latentMeanOut); // rename matrices TODO
}
if (state->_latentCovOut) {
state->estLatentCov = omxInitMatrix(maxAbilities, maxAbilities, TRUE, currentState);
omxCopyMatrix(state->estLatentCov, state->_latentCovOut);
}
}