fix import

jdtuck · Dec 21, 2023 · 1ffa6f9 · 1ffa6f9
1 parent 5739cbe
commit 1ffa6f9
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Showing 7 changed files with 41 additions and 64 deletions.
diff --git a/src/Makevars b/src/Makevars
@@ -1,4 +1,4 @@
-SOURCES1 = registerDynamicSymbol.cpp wrapper.cpp fdasrsf/DP.cpp fdasrsf/dp_grid.cpp fdasrsf/dp_nbhd.cpp fdasrsf/DynamicProgrammingQ2.cpp fdasrsf/misc_funcs.cpp fdasrsf/mlogit_warp_grad.cpp \
+SOURCES1 = registerDynamicSymbol.cpp wrapper.cpp wrapper_rbfgs.cpp fdasrsf/DP.cpp fdasrsf/dp_grid.cpp fdasrsf/dp_nbhd.cpp fdasrsf/DynamicProgrammingQ2.cpp fdasrsf/misc_funcs.cpp fdasrsf/mlogit_warp_grad.cpp \
   fdasrsf/bayesian.cpp fdasrsf/pair_align_functions_expomap.cpp
 SOURCES2 = fdaqmap/src/myVector.cpp fdaqmap/src/UnitSquareImage.cpp
 

diff --git a/src/Makevars.win b/src/Makevars.win
@@ -1,5 +1,5 @@
 ##split sources to ensure the commands for linking are not too long!
-SOURCES1 = registerDynamicSymbol.cpp wrapper.cpp fdasrsf/DP.cpp fdasrsf/dp_grid.cpp fdasrsf/dp_nbhd.cpp fdasrsf/DynamicProgrammingQ2.cpp fdasrsf/misc_funcs.cpp fdasrsf/mlogit_warp_grad.cpp \
+SOURCES1 = registerDynamicSymbol.cpp wrapper.cpp wrapper_rbfgs.cpp fdasrsf/DP.cpp fdasrsf/dp_grid.cpp fdasrsf/dp_nbhd.cpp fdasrsf/DynamicProgrammingQ2.cpp fdasrsf/misc_funcs.cpp fdasrsf/mlogit_warp_grad.cpp \
   fdasrsf/bayesian.cpp fdasrsf/pair_align_functions_expomap.cpp
 SOURCES2 = fdaqmap/src/myVector.cpp fdaqmap/src/UnitSquareImage.cpp
 

diff --git a/src/fdasrsf/pair_align_functions_expomap.cpp b/src/fdasrsf/pair_align_functions_expomap.cpp
@@ -92,8 +92,9 @@ RcppExport SEXP trapzCpp(SEXP R_x, SEXP R_y) {
 
 // order vectors and calculate l2 norm, for f.L2norm()
 //RcppExport double order_l2norm(NumericVector x, NumericVector y) {
-RcppExport double order_l2norm(vec x, vec y) {
-
+RcppExport SEXP order_l2norm(SEXP R_x, SEXP R_y) {
+  vec x = as<vec>(R_x);
+  vec y = as<vec>(R_y);
   int n = x.size();
   // get ordering of x
   // borrowed from Hadley Wickhams adv-r/extras/cpp/order.cpp
@@ -126,5 +127,5 @@ RcppExport double order_l2norm(vec x, vec y) {
   for (int i = 0; i<(n-1); i++) {
     area2 += (xSort[i+1] - xSort[i]) * (ySortSq[i+1] + ySortSq[i]);
   }
-  return sqrt(area2 / 2.0);
+  return wrap(sqrt(area2 / 2.0));
 }
diff --git a/src/fdasrsf/rbfgs.cpp b/src/fdasrsf/rbfgs.cpp
diff --git a/src/fdasrsf/rbfgs.h b/src/fdasrsf/rbfgs.h
@@ -1,8 +1,8 @@
 #ifndef RBFGS_H
 #define RBFGS_H
-
-#include <iostream>
-#include "armadillo"
+#include <RcppArmadillo.h>
+// Correctly setup the build environment
+// [[Rcpp::depends(RcppArmadillo)]]
 
 using namespace arma;
 using namespace std;
@@ -541,4 +541,14 @@ class rlbfgs {
   }
 };
 
+vec rlbfgs_optim(vec q1, vec q2, vec time, int maxiter=30, double lam=0.0, int penalty=0){
+  uword T = time.n_elem;
+  vec time1 = arma::linspace(0, 1, T);
+
+  rlbfgs myObj(q1, q2, time1);
+  myObj.solve(maxiter, lam, penalty);
+
+  return myObj.gammaOpt;
+}
+
 #endif // end of RBFGS_H
diff --git a/src/wrapper.cpp b/src/wrapper.cpp
@@ -1,42 +1,11 @@
 
 #include "fdasrsf/DynamicProgrammingQ2.h"
 #include "fdasrsf/mlogit_warp_grad.h"
-#include "fdasrsf/rbfgs.h"
 #include "fdasrsf/DP.h"
-#include <iostream>
-#include <RcppArmadillo.h>
-// Correctly setup the build environment
-// [[Rcpp::depends(RcppArmadillo)]]
+#include <Rcpp.h>
 
-using namespace arma;
 using namespace Rcpp;
 
-vec rlbfgs_optim(vec q1, vec q2, vec time, int maxiter=30, double lam=0.0, int penalty=0){
-  uword T = time.n_elem;
-  vec time1 = arma::linspace(0, 1, T);
-
-  rlbfgs myObj(q1, q2, time1);
-  myObj.solve(maxiter, lam, penalty);
-
-  return myObj.gammaOpt;
-}
-
-RcppExport SEXP _fdasrvf_rlbfgs_optim(SEXP q1SEXP, SEXP q2SEXP, SEXP timeSEXP, SEXP maxiterSEXP, SEXP lamSEXP, SEXP penaltySEXP) {
-  BEGIN_RCPP
-  Rcpp::RObject rcpp_result_gen;
-  Rcpp::RNGScope rcpp_rngScope_gen;
-  Rcpp::traits::input_parameter< vec >::type q1(q1SEXP);
-  Rcpp::traits::input_parameter< vec >::type q2(q2SEXP);
-  Rcpp::traits::input_parameter< vec >::type time(timeSEXP);
-  Rcpp::traits::input_parameter< int >::type maxiter(maxiterSEXP);
-  Rcpp::traits::input_parameter< double >::type lam(lamSEXP);
-  Rcpp::traits::input_parameter< int >::type penalty(penaltySEXP);
-  rcpp_result_gen = Rcpp::wrap(rlbfgs_optim(q1, q2, time, maxiter, lam, penalty));
-  return rcpp_result_gen;
-  END_RCPP
-}
-
-
 RcppExport SEXP mlogit_warp_grad_wrap(SEXP m1, SEXP m2, SEXP alpha, SEXP beta, SEXP ti, SEXP gami, SEXP q, SEXP y, SEXP max_itri, SEXP toli, SEXP deltai, SEXP displayi, SEXP gamout){
   NumericVector alphai(alpha);
   NumericVector betai(beta);

diff --git a/src/wrapper_rbfgs.cpp b/src/wrapper_rbfgs.cpp
@@ -0,0 +1,21 @@
+#include "fdasrsf/rbfgs.h"
+#include <RcppArmadillo.h>
+// Correctly setup the build environment
+// [[Rcpp::depends(RcppArmadillo)]]
+
+using namespace arma;
+using namespace Rcpp;
+using namespace std;
+
+RcppExport SEXP _fdasrvf_rlbfgs_optim(SEXP q1SEXP, SEXP q2SEXP, SEXP timeSEXP, SEXP maxiterSEXP, SEXP lamSEXP, SEXP penaltySEXP) {
+  vec q1 = as<vec>(q1SEXP);
+  vec q2 = as<vec>(q2SEXP);
+  vec time = as<vec>(timeSEXP);
+  int maxiter = as<int>(maxiterSEXP);
+  int len = q1.size();
+  double lam = as<double>(lamSEXP);
+  int penalty = as<int>(penaltySEXP);
+  vec gam(len);
+  gam = rlbfgs_optim(q1, q2, time, maxiter, lam, penalty);
+  return wrap(gam);
+}