Bug repair to compile last changes

src/dcModelTerm.cpp

@@ -74,8 +74,9 @@ dcModelTerm::dcModelTerm(std::string modelTerm, Rcpp::DataFrame &d) :
             }
             else {
                varianceObjects.push_back(getVariableObject(d,varianceNames[i]));
-               if(varianceObjects.back() == R_NilValue)
+               if(varianceObjects.back() == R_NilValue) {
                   throw generalRbayzError("Kernel object not found: "+varianceNames[i]);
+               }
                varianceType=2; // flag variance type 2 if some matrices are not IDEN, WEI, MIXT
             }
          }

src/kernelMatrix.h

@@ -33,6 +33,11 @@ class kernelMatrix : public labeledMatrix {
    	}
    	Rcpp::NumericVector eigvalues = eigdecomp["values"];
 	   Rcpp::NumericMatrix eigvectors = eigdecomp["vectors"];
+      // re-attach the dimnames again to the eigvectors matrix for correct further processing
+      if (kerneldata.hasAttribute("dimnames")) {
+         Rcpp::List dimnames = Rcpp::as<Rcpp::List>(kerneldata.attr("dimnames"));
+         eigvectors.attr("dimnames") = dimnames;
+      }
       // Determine how many evectors to keep
       double rrankpct=90;          // rrankpct not coming correctly from the modelterm now
       size_t nColUsed = 0;
@@ -41,10 +46,9 @@ class kernelMatrix : public labeledMatrix {
       double eval_cutoff = rrankpct * sumeval / 100.0l;
       sumeval = 0.0l;
       while (sumeval < eval_cutoff) sumeval += eigvalues[nColUsed++];
-      // this message can be moved to the modelTerm routine; and it must be different for ran2f_2cor.
       Rcpp::Rcout << "For kernel " << name << " with rrankpct=" << rrankpct << " using "
                   << nColUsed << " eigenvectors\n";
-      this->initWith(eigvectors, nColUsed);
+      this->initWith(eigvectors, name, nColUsed);
       weights.initWith(eigvalues, nColUsed);
    }
 
@@ -99,14 +103,14 @@ class kernelMatrix : public labeledMatrix {
             tempLabels.push_back(this->rownames[rowi]+"%"+K2->rownames[rowj]);
          }
       }
+      Rcpp::Rcout << "Interaction kernel retains " << nEvalUsed << " eigenvalues\n";
       // Swap the old data with the new data.
       // Note the old data is removed when tempEvecs, tempEvals and tempLabels here go out of scope.
       this->swap(&tempEvecs);
       weights.swap(&tempEvals);
       std::swap(rownames,tempLabels);
    }
 
-   std::vector<std::string> rownames, colnames;
    simpleDblVector weights;
 
 };

src/labeledMatrix.h

@@ -22,7 +22,8 @@ class labeledMatrix : public simpleMatrix {
 
 public:
 
-   labeledMatrix() : simpleMatrix() {  }
+   labeledMatrix() : simpleMatrix() {  
+   }
 
    labeledMatrix(Rcpp::RObject col, std::string & name) : simpleMatrix(col) {
       // I need to temporarily redo the conversion of the input Robject to
@@ -34,13 +35,12 @@ class labeledMatrix : public simpleMatrix {
       addMatrixNames(colnames, tempdata, 2); // no throw here, colnames are optional
    }
 
-   void initWith(Rcpp::NumericMatrix M, size_t useCol) {
+   void initWith(Rcpp::NumericMatrix & M, std::string & name, size_t useCol) {
       simpleMatrix::initWith(M, useCol);
       if (addMatrixNames(rownames, M, 1) >0) {
-         throw generalRbayzError("No rownames on matrix xxx\n");  // no name available here!
+         throw generalRbayzError("No rownames on matrix "+name);
       }
       addMatrixNames(colnames, M, 2); // no throw here, colnames are optional
-
    }
 
    ~labeledMatrix() {

src/modelRanf_cor.h

@@ -36,19 +36,21 @@ class modelRanf_cor : public modelFactor {
       }
       // Get the first kernel and then add (making kronecker products) with second etc., if available
       K = new kernelMatrix(modeldescr.varianceObjects[0], modeldescr.varianceNames[0]);
+      Rcpp::Rcout << "1\n";
       if (modeldescr.varianceNames.size()==2) {  // combine with a second kernel if present
+         Rcpp::Rcout << "2\n";
          kernelMatrix* K2 = new kernelMatrix(modeldescr.varianceObjects[1], modeldescr.varianceNames[1]);
+         Rcpp::Rcout << "3\n";
          K->addKernel(K2);
+         Rcpp::Rcout << "4\n";
          delete K2;
       }
+      Rcpp::Rcout << "5\n";
       if (modeldescr.varianceNames.size()>2) {  // need to think if I can keep combining kernels with addKernel()
          throw(generalRbayzError("Not yet ready to combine more than 2 kernels for interaction"));
       }
-      // note: modelled parameters are regressions on the eigenvectors and are stored in separate
-      // vector regcoeff (size K->ncol). The par-vector has backtransfor to random effects
-      // (eigen-vectors x regressions, size K->nrow).
-      par.initWith(K->nrow,0.0l);
-      parLabels = K->rownames; // I believe this makes a deep copy, but a shallow copy would be enough
+      // note: par-vector and names are set-up in modelFactor and follow levels of the data factor.
+      // Here add a vector regcoeff (size K->ncol) to hold the regresssion on eigenvectors.
       regcoeff.initWith(K->ncol, 0.0l);
       builObsIndex(obsIndex,F,K);
    }

src/nameTools.cpp

@@ -29,28 +29,30 @@ inline bool compString2Pair(const std::pair<std::string, size_t> & p, const std:
     return p.first < s;
 }
 
-// getMatrixNames: retrieve row or col-names (use dim=1 or 2 as in apply()) from an Rcpp
-//     NumericMatrix, returns NULL vector when dimnames not present or the requested dim is empty.
 // addMatrixNames: fills matrix row or col-names (dim=1 or 2) in an c++ vector<string>,
 //     return value 0 for success, 1 for errors (missing names).
 // Note: addMatrixNames uses push_back, typical use is to pass an empty vector<string> as 'names'
-// argument and it will be filled.
+// argument and it will be filled. 
 
-Rcpp::CharacterVector getMatrixNames(Rcpp::NumericMatrix & mat, int dim) {
+int addMatrixNames(std::vector<std::string> & names, Rcpp::NumericMatrix & mat, int dim) {
    if (mat.hasAttribute("dimnames")) {
       Rcpp::List dimnames = Rcpp::as<Rcpp::List>(mat.attr("dimnames"));
-      if(dim==1) return dimnames[0];
-      else return dimnames[1];
+      if(dim==1 && dimnames[0] != R_NilValue) {
+         Rcpp::CharacterVector matNames = Rcpp::as<Rcpp::CharacterVector>(dimnames[0]);
+         CharVec2cpp(names, matNames);
+         return 0;  // sucess
+      }
+      else if (dim==2 && dimnames[1] != R_NilValue) {
+         Rcpp::CharacterVector matNames = Rcpp::as<Rcpp::CharacterVector>(dimnames[1]);
+         CharVec2cpp(names, matNames);
+         return 0;  // sucess
+      }
+      else {
+         return 1;  // the dimnames for the requested dim must have been empty
+      }
    }
-   else return R_NilValue;
-}
-
-int addMatrixNames(std::vector<std::string> & names, Rcpp::NumericMatrix & mat, int dim) {
-   Rcpp::CharacterVector matNames = getMatrixNames(mat, dim);
-   if(matNames.isNULL()) return 1;
    else {
-      CharVec2cpp(names, matNames);
-      return 0;
+      return 1;    // no dimnames attributes
    }
 }
 

src/rbayz.cpp

@@ -38,8 +38,8 @@ void collectLoggedSamples(std::vector<modelBase *> & model, Rcpp::IntegerVector
 
 // [[Rcpp::export]]
 Rcpp::List rbayz_cpp(Rcpp::Formula modelFormula, Rcpp::DataFrame inputData,
-                     Rcpp::IntegerVector chain, int silent) {
-
+                     Rcpp::IntegerVector chain, int silent)
+{
    // Some check of chain settings is needed. Also the rbayz wrapper function now
    // handles chain being NULL, but it can be done here, so that warning message
    // can come in output.
@@ -97,8 +97,8 @@ Rcpp::List rbayz_cpp(Rcpp::Formula modelFormula, Rcpp::DataFrame inputData,
       size_t nEstimates = estimNames.size();
 
       // Check the chain settings and make list of output sample cycle-numbers.
-      if (chain[1]==0 && chain[2]==0 && chain[3]==0) {  // chain was not set
-         chain[1]=1100; chain[2]=100; chain[3]=10;
+      if (chain[0]==0 && chain[1]==0 && chain[2]==0) {  // chain was not set
+         chain[0]=1100; chain[1]=100; chain[2]=10;
          Rcpp::Rcout << "Warning: chain was not set, running 1100 cycles but it may be too short for many analyses\n";
       }
       if (chain.size() != 3) throw (generalRbayzError("The chain settings do not have 3 elements"));

src/simpleMatrix.h

@@ -23,7 +23,8 @@ class simpleMatrix {
 
 public:
 
-   simpleMatrix() { }
+   simpleMatrix() { 
+   }
 
    simpleMatrix(size_t nr, size_t nc) {
       doalloc(nr, nc);

src/simpleVector.h

@@ -79,7 +79,7 @@ class simpleDblVector {
 
 public:
 
-   simpleDblVector() : nelem(0) { }
+   simpleDblVector() { }
 
    simpleDblVector(size_t n) {
       doalloc(n);
@@ -107,7 +107,7 @@ class simpleDblVector {
          throw(generalRbayzError("useElem is larger than actual nelem in simpleDblVector"));
       }
       doalloc(useElem);
-      for(size_t i=0; i<nelem; i++)
+      for(size_t i=0; i<useElem; i++)
          data[i] = v[i];
    }
 
@@ -131,7 +131,7 @@ class simpleDblVector {
    }
 
    double *data;
-   size_t nelem;
+   size_t nelem=0;
 
 private:
    void doalloc(size_t n) {