resurrect command-line interface for DM

Author: msuchard

src/cyclops/engine/ModelSpecifics.hpp

@@ -24,10 +24,6 @@
 #include "ParallelLoops.h"
 #include "Ranges.h"
 
-#include "R.h"
-
-//#include "Rcpp.h"
-
 #ifdef CYCLOPS_DEBUG_TIMING
 	#include "Timing.h"
 	namespace bsccs {

standalone/CMakeLists.txt

@@ -15,12 +15,22 @@ endif(APPLE)
 
 #find_package(CUDA)
 
-set(BOOST_ROOT 
-	 ~/Dropbox/Projects)
-	 
+
+	
+if(DEFINED R_LIBRARIES)
+	set(BOOST_ROOT
+		${R_LIBRARIES}/BH/include)
+	set(RCPP_PARALLEL_ROOT
+		${R_LIBRARIES}/RcppParallel)
+else()
+	message(FATAL_ERROR "RCPP_PARALLEL_ROOT is not defined")
+endif()	
+			 
+include_directories(${RCPP_PARALLEL_ROOT}/include)			 
+			 
 find_package(Boost)
 
-add_subdirectory(${CMAKE_SOURCE_DIR}/codebase/CCD)
+#add_subdirectory(${CMAKE_SOURCE_DIR}/codebase/CCD)
 add_subdirectory(${CMAKE_SOURCE_DIR}/codebase/CCD-DP)
 
 #if(CUDA_FOUND)

standalone/codebase/CCD/CmdLineCcdInterface.cpp

@@ -432,17 +432,17 @@ void CmdLineCcdInterface::initializeModelImpl(
 	using namespace bsccs::priors;
 	PriorPtr singlePrior;
 	if (arguments.useNormalPrior) {
-		singlePrior = std::make_shared<NormalPrior>();
+		singlePrior = std::make_shared<NormalPrior>(arguments.hyperprior);
 	} else if (arguments.computeMLE) {
 		if (arguments.fitMLEAtMode) {
 			cerr << "Unable to compute MLE at posterior mode, if mode is not first explored." << endl;
 			exit(-1);
 		}
 		singlePrior = std::make_shared<NoPrior>();
 	} else {
-		singlePrior = std::make_shared<LaplacePrior>();
+		singlePrior = std::make_shared<LaplacePrior>(arguments.hyperprior);
 	}
-	singlePrior->setVariance(arguments.hyperprior);
+	//singlePrior->setVariance(arguments.hyperprior);
 
 	JointPriorPtr prior;
 	if (arguments.flatPrior.size() == 0) {
@@ -469,7 +469,7 @@ void CmdLineCcdInterface::initializeModelImpl(
 	//Hierarchy prior
 	if (arguments.useHierarchy) {
 		std::shared_ptr<HierarchicalJointPrior> hierarchicalPrior = std::make_shared<HierarchicalJointPrior>(singlePrior, 2); //Depth of hierarchy fixed at 2 right now
-		PriorPtr classPrior = std::make_shared<NormalPrior>();
+		PriorPtr classPrior = std::make_shared<NormalPrior>(arguments.hyperprior);
 		hierarchicalPrior->changePrior(classPrior,1);
         hierarchicalPrior->setHierarchy(
                 hierarchyData->returnGetParentMap(),

standalone/codebase/CCD/ccd.cpp

@@ -66,7 +66,8 @@ int main(int argc, char* argv[]) {
 	bsccs::ProfileInformationMap profileMap;
 	if (arguments.profileCI.size() > 0) {
 		doProfile = true;
-		timeProfile = interface.profileModel(ccd, modelData, arguments.profileCI, profileMap);
+		timeProfile = interface.profileModel(ccd, modelData, arguments.profileCI, profileMap,
+			1 /* threads */);
 	}	
 
 	if (std::find(arguments.outputFormat.begin(),arguments.outputFormat.end(), "estimates")