removed last dynamic memory call, modified .Rbuildignore to ignore th…

…e new top level directory, 'docs'
neurodata · Jul 28, 2018 · 73b896f · 73b896f
1 parent 248e10c
commit 73b896f
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Showing 9 changed files with 42 additions and 6 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,4 @@
 ^travisTest$
+^docs$
 ^\.travis\.yml$
 ^.*\\.gz$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rerf
 Type: Package
 Title: Randomer Forest
-Version: 1.1.2
+Version: 1.1.3
 Date: 2018-07-05
 Authors@R: c(person("James", "Browne", role = c("aut", "cre"),
 	   	    email = "jbrowne6@jhu.edu"),

diff --git a/docs/subsampling/bootstrap_subsample.Rmd b/docs/subsampling/bootstrap_subsample.Rmd
diff --git a/docs/subsampling/bootstrap_subsample.html b/docs/subsampling/bootstrap_subsample.html
diff --git a/docs/subsampling/figure.pdf b/docs/subsampling/figure.pdf
diff --git a/man/RerF.Rd b/man/RerF.Rd
diff --git a/src/forestPacking.cpp b/src/forestPacking.cpp
@@ -1,5 +1,6 @@
 #include <RcppArmadillo.h>
 #include <improv8.h>
+#include <vector>
 // [[Rcpp::depends(RcppArmadillo)]]
 
 using namespace Rcpp;
@@ -21,7 +22,7 @@ Rcpp::NumericVector predictRF(const NumericMatrix mat, const int numCores){
 		int numObservations = mat.nrow();
 			int numFeatures = mat.ncol();
 
-			double *currObs = new double[numFeatures];
+			std::vector<double> currObs(numFeatures);
 			Rcpp::NumericVector predictions(numObservations);
 
 			const std::string packedFileName = "forest.out";
@@ -30,10 +31,8 @@ Rcpp::NumericVector predictRF(const NumericMatrix mat, const int numCores){
 				for(int j = 0; j < numFeatures; j++){
 					currObs[j] = mat(i,j);
 				}
-				//predictions[i] = tester.makePrediction(currObs,numCores)+1;
 				predictions[i] = tester.makePrediction(currObs)+1;
 			}
-			delete currObs;	
 			return predictions;
 }
 

diff --git a/src/forestPacking/improv8.cpp b/src/forestPacking/improv8.cpp
@@ -282,6 +282,41 @@ void improv8::makePrediction(double* observation, double* preds, int numFeatures
 }
 
 
+int improv8::makePrediction(std::vector<double>& observation){
+
+	std::vector<int> predictions(numOfClasses);
+	std::vector<int> currentNode(forestRoots[0].numOfTreesInBin);
+	int numberNotInLeaf;
+	int k, q;
+
+	for( k=0; k < numOfBins;k++){
+
+		for( q=0; q<forestRoots[k].numOfTreesInBin; q++){
+			currentNode[q] = q;
+			__builtin_prefetch(&forestRoots[k].bin[currentNode[q]], 0, 3);
+		}
+
+		do{
+			numberNotInLeaf = forestRoots[k].numOfTreesInBin;
+
+			for( q=0; q<forestRoots[k].numOfTreesInBin; q++){
+
+				if(forestRoots[k].bin[currentNode[q]].isInternalNode()){
+					currentNode[q] = forestRoots[k].bin[currentNode[q]].nextNode(observation[forestRoots[k].bin[currentNode[q]].returnFeature()]);
+					__builtin_prefetch(&forestRoots[k].bin[currentNode[q]], 0, 3);
+					continue;
+				}
+				--numberNotInLeaf;
+			}
+		}while(numberNotInLeaf > 0);
+
+		for( q=0; q<forestRoots[k].numOfTreesInBin; q++){
+			++predictions[forestRoots[k].bin[currentNode[q]].returnRightNode()];
+		}
+	}
+	return returnClassPrediction(predictions, numOfClasses);
+}
+
 int improv8::makePrediction(double*& observation){
 
 	std::vector<int> predictions(numOfClasses);

diff --git a/src/forestPacking/improv8.h b/src/forestPacking/improv8.h
@@ -23,6 +23,7 @@ class improv8: public padForest
 		void makePredictions(const inferenceSamples& observations);
 		void makePrediction(double* observation, double* preds, int numFeatures, int numObservations, int numCores);
 		int makePrediction(double*& observation);
+		int makePrediction(std::vector<double>& observation);
 		int makePrediction(double*& observation, int numCore);
 		void writeForest(const std::string& forestFileName);
 		void changeNumBins(int newBinNum){