Remove src files, update exports, WIP #146

src/RcppExports.cpp

@@ -1,6 +1,7 @@
 // Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+#include "../inst/include/finalsize.h"
 #include <RcppEigen.h>
 #include <Rcpp.h>
 
@@ -11,42 +12,20 @@ Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
 Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
 #endif
 
-// solve_final_size_iterative
-Eigen::ArrayXd solve_final_size_iterative(const Eigen::MatrixXd& contact_matrix, const Eigen::VectorXd& demography_vector, const Eigen::VectorXd& susceptibility, const int iterations, const double tolerance, double step_rate, const bool adapt_step);
-RcppExport SEXP _finalsize_solve_final_size_iterative(SEXP contact_matrixSEXP, SEXP demography_vectorSEXP, SEXP susceptibilitySEXP, SEXP iterationsSEXP, SEXP toleranceSEXP, SEXP step_rateSEXP, SEXP adapt_stepSEXP) {
+// final_size
+Eigen::ArrayXd final_size(const Rcpp::List& parameters);
+RcppExport SEXP _finalsize_final_size(SEXP parametersSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Eigen::MatrixXd& >::type contact_matrix(contact_matrixSEXP);
-    Rcpp::traits::input_parameter< const Eigen::VectorXd& >::type demography_vector(demography_vectorSEXP);
-    Rcpp::traits::input_parameter< const Eigen::VectorXd& >::type susceptibility(susceptibilitySEXP);
-    Rcpp::traits::input_parameter< const int >::type iterations(iterationsSEXP);
-    Rcpp::traits::input_parameter< const double >::type tolerance(toleranceSEXP);
-    Rcpp::traits::input_parameter< double >::type step_rate(step_rateSEXP);
-    Rcpp::traits::input_parameter< const bool >::type adapt_step(adapt_stepSEXP);
-    rcpp_result_gen = Rcpp::wrap(solve_final_size_iterative(contact_matrix, demography_vector, susceptibility, iterations, tolerance, step_rate, adapt_step));
-    return rcpp_result_gen;
-END_RCPP
-}
-// solve_final_size_newton
-Eigen::ArrayXd solve_final_size_newton(const Eigen::MatrixXd& contact_matrix, const Eigen::VectorXd& demography_vector, const Eigen::VectorXd& susceptibility, const int iterations, const double tolerance);
-RcppExport SEXP _finalsize_solve_final_size_newton(SEXP contact_matrixSEXP, SEXP demography_vectorSEXP, SEXP susceptibilitySEXP, SEXP iterationsSEXP, SEXP toleranceSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< const Eigen::MatrixXd& >::type contact_matrix(contact_matrixSEXP);
-    Rcpp::traits::input_parameter< const Eigen::VectorXd& >::type demography_vector(demography_vectorSEXP);
-    Rcpp::traits::input_parameter< const Eigen::VectorXd& >::type susceptibility(susceptibilitySEXP);
-    Rcpp::traits::input_parameter< const int >::type iterations(iterationsSEXP);
-    Rcpp::traits::input_parameter< const double >::type tolerance(toleranceSEXP);
-    rcpp_result_gen = Rcpp::wrap(solve_final_size_newton(contact_matrix, demography_vector, susceptibility, iterations, tolerance));
+    Rcpp::traits::input_parameter< const Rcpp::List& >::type parameters(parametersSEXP);
+    rcpp_result_gen = Rcpp::wrap(final_size(parameters));
     return rcpp_result_gen;
 END_RCPP
 }
 
 static const R_CallMethodDef CallEntries[] = {
-    {"_finalsize_solve_final_size_iterative", (DL_FUNC) &_finalsize_solve_final_size_iterative, 7},
-    {"_finalsize_solve_final_size_newton", (DL_FUNC) &_finalsize_solve_final_size_newton, 5},
+    {"_finalsize_final_size", (DL_FUNC) &_finalsize_final_size, 1},
     {NULL, NULL, 0}
 };
 

src/finalsize.cpp

@@ -0,0 +1,29 @@
+// Copyright 2023 'finalsize' authors. See repository licence in LICENSE.md.
+#include <Rcpp.h>
+#include <finalsize.h>
+#include <string.h>
+
+//' @title Calculate the final size of an epidemic
+//' @description An internal function that interfaces between the R function
+//' `final_size()` and functions in the package header.
+//' @param parameters A named list of parameters for the final size calculation.
+//' See the R function documentation for details and input checking.
+//'
+// [[Rcpp::export(name=".final_size")]]
+Eigen::ArrayXd final_size(const Rcpp::List &parameters) {
+
+  if (strcmp(parameters["solver"], "iterative") == 0) {
+    return finalsize::solve_final_size_iterative(
+      parameters["contact_matrix"], parameters["demography_vector"],
+      parameters["susceptibility"], parameters["iterations"],
+      parameters["tolerance"], parameters["step_rate"],
+      parameters["adapt_step"]
+    );
+  } else {
+    return finalsize::solve_final_size_newton(
+      parameters["contact_matrix"], parameters["demography_vector"],
+      parameters["susceptibility"], parameters["iterations"],
+      parameters["tolerance"]
+    );
+  }
+}