From 15842ee87e5c443746a0238af67f6278738a5ae6 Mon Sep 17 00:00:00 2001
From: Andrew Pulsipher <a.pulsipher@utah.edu>
Date: Mon, 25 Nov 2024 13:11:14 -0700
Subject: [PATCH] Add latest changes from C++ library

---
 .../epiworld/math/lfmcmc/lfmcmc-meat-print.hpp   | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp b/inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp
index 1bd5879..b2860a0 100755
--- a/inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp
+++ b/inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp
@@ -5,15 +5,18 @@ template<typename TData>
 inline void LFMCMC<TData>::print(size_t burnin) const
 {
 
+    // For each statistic or parameter in the model, we print three values: 
+    // - mean, the 2.5% quantile, and the 97.5% quantile
     std::vector< epiworld_double > summ_params(n_parameters * 3, 0.0);
     std::vector< epiworld_double > summ_stats(n_statistics * 3, 0.0);
 
+    // Compute the number of samples to use based on burnin rate
     size_t n_samples_print = n_samples;
     if (burnin > 0)
     {
         if (burnin >= n_samples)
             throw std::length_error(
-                "The burnin is greater than the number of samples."
+                "The burnin is greater than or equal to the number of samples."
                 );
 
         n_samples_print = n_samples - burnin;
@@ -24,6 +27,7 @@ inline void LFMCMC<TData>::print(size_t burnin) const
         n_samples_print
         );
 
+    // Compute parameter summary values
     for (size_t k = 0u; k < n_parameters; ++k)
     {
 
@@ -31,8 +35,8 @@ inline void LFMCMC<TData>::print(size_t burnin) const
         std::vector< epiworld_double > par_i(n_samples_print);
         for (size_t i = burnin; i < n_samples; ++i)
         {
-            par_i[i] = accepted_params[i * n_parameters + k];
-            summ_params[k * 3] += par_i[i]/n_samples_dbl;
+            par_i[i-burnin] = accepted_params[i * n_parameters + k];
+            summ_params[k * 3] += par_i[i-burnin]/n_samples_dbl;
         }
 
         // Computing the 95% Credible interval
@@ -45,6 +49,7 @@ inline void LFMCMC<TData>::print(size_t burnin) const
 
     }
 
+    // Compute statistics summary values
     for (size_t k = 0u; k < n_statistics; ++k)
     {
 
@@ -52,13 +57,12 @@ inline void LFMCMC<TData>::print(size_t burnin) const
         std::vector< epiworld_double > stat_k(n_samples_print);
         for (size_t i = burnin; i < n_samples; ++i)
         {
-            stat_k[i] = accepted_stats[i * n_statistics + k];
-            summ_stats[k * 3] += stat_k[i]/n_samples_dbl;
+            stat_k[i-burnin] = accepted_stats[i * n_statistics + k];
+            summ_stats[k * 3] += stat_k[i-burnin]/n_samples_dbl;
         }
 
         // Computing the 95% Credible interval
         std::sort(stat_k.begin(), stat_k.end());
-
         summ_stats[k * 3 + 1u] = 
             stat_k[std::floor(.025 * n_samples_dbl)];
         summ_stats[k * 3 + 2u] =