removed timing and cleaned up

Author: osorensen

src/parameter_tracer.cpp

@@ -1,7 +1,4 @@
-#include <sys/stat.h>
 #include <string>
-#include <cstdlib>
-#include <sstream>
 #include "parameter_tracer.h"
 using namespace arma;
 

src/particle.cpp

@@ -33,12 +33,6 @@ Particle::Particle(const Options& options, const StaticParameters& parameters,
     }
   }
 
-std::vector<std::pair<std::string, int>>::const_iterator findIntInPairs(const std::vector<std::pair<std::string, int>>& vec, int a) {
-  return std::find_if(vec.begin(), vec.end(), [a](const std::pair<std::string, int>& element) {
-    return element.second == a;
-  });
-}
-
 void Particle::run_particle_filter(
     unsigned int t, const Prior& prior,
     const std::unique_ptr<Data>& data,

src/run_smc.cpp

@@ -1,8 +1,5 @@
 // [[Rcpp::depends(RcppArmadillo)]]
 #include <RcppArmadillo.h>
-#include <numeric>
-#include <limits>
-#include <chrono>
 #include "prior.h"
 #include "data.h"
 #include "distances.h"
@@ -46,7 +43,6 @@ Rcpp::List run_smc(
 
   for(size_t t{}; t < T; t++) {
     reporter.report_time(t);
-    auto start = std::chrono::steady_clock::now();
 
     for(auto& p : particle_vector) {
       p.run_particle_filter(t, prior, data, pfun, distfun, resampler,
@@ -115,9 +111,6 @@ Rcpp::List run_smc(
     tracer.update_trace(particle_vector, t);
     n_particle_filters(t) = options.n_particle_filters;
 
-    auto end = std::chrono::steady_clock::now();
-    auto duration = std::chrono::duration_cast<std::chrono::nanoseconds>(end - start).count();
-    iteration_times.push_back(static_cast<double>(duration));
   }
 
   mat alpha(prior.n_clusters, particle_vector.size());
@@ -146,7 +139,6 @@ Rcpp::List run_smc(
     Rcpp::Named("ESS") = ESS,
     Rcpp::Named("resampling") = resampling,
     Rcpp::Named("n_particle_filters") = n_particle_filters,
-    Rcpp::Named("iteration_times") = iteration_times,
     Rcpp::Named("importance_weights") = exp(normalize_log_importance_weights(particle_vector)),
     Rcpp::Named("log_marginal_likelihood") = log_marginal_likelihood,
     Rcpp::Named("alpha_traces") = tracer.alpha_traces,

src/sample_latent_rankings.cpp

@@ -1,12 +1,8 @@
 #include <RcppArmadillo.h>
-#include <filesystem>
-#include <vector>
-#include <iterator>
 #include "sample_latent_rankings.h"
 #include "data.h"
 #include "misc.h"
 using namespace arma;
-namespace fs = std::filesystem;
 
 uvec shuffle_rcpp(const uvec& values_in) {
   ivec inds = Rcpp::sample(values_in.size(), values_in.size(), false) - 1;