From d8d213c35cc8dc84c2a6c1aa302de6d412e81663 Mon Sep 17 00:00:00 2001
From: Andrew Pulsipher <a.pulsipher@utah.edu>
Date: Thu, 5 Dec 2024 15:06:14 -0700
Subject: [PATCH] Update namespace and build docs

---
 NAMESPACE     | 14 +++++++-------
 man/LFMCMC.Rd | 40 ++++++++++++++++++++--------------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index aac1efb..645ac01 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -135,10 +135,12 @@ export(get_hist_tool)
 export(get_hist_total)
 export(get_hist_transition_matrix)
 export(get_hist_virus)
-export(get_n_parameters)
+export(get_mean_params)
+export(get_mean_stats)
+export(get_n_params)
 export(get_n_replicates)
 export(get_n_samples)
-export(get_n_statistics)
+export(get_n_stats)
 export(get_n_tools)
 export(get_n_viruses)
 export(get_name)
@@ -147,12 +149,10 @@ export(get_name_virus)
 export(get_ndays)
 export(get_network)
 export(get_param)
-export(get_params_mean)
 export(get_reproductive_number)
+export(get_sample_stats)
 export(get_state)
 export(get_states)
-export(get_statistics_hist)
-export(get_stats_mean)
 export(get_today_total)
 export(get_tool)
 export(get_transition_probability)
@@ -199,8 +199,8 @@ export(set_name)
 export(set_name_tool)
 export(set_name_virus)
 export(set_observed_data)
-export(set_par_names)
 export(set_param)
+export(set_param_names)
 export(set_prob_death)
 export(set_prob_death_fun)
 export(set_prob_death_ptr)
@@ -215,7 +215,7 @@ export(set_recovery_enhancer)
 export(set_recovery_enhancer_fun)
 export(set_recovery_enhancer_ptr)
 export(set_simulation_fun)
-export(set_stats_names)
+export(set_stat_names)
 export(set_summary_fun)
 export(set_susceptibility_reduction)
 export(set_susceptibility_reduction_fun)
diff --git a/man/LFMCMC.Rd b/man/LFMCMC.Rd
index 24623b1..f80605a 100644
--- a/man/LFMCMC.Rd
+++ b/man/LFMCMC.Rd
@@ -11,16 +11,16 @@
 \alias{set_summary_fun}
 \alias{set_kernel_fun}
 \alias{use_kernel_fun_gaussian}
-\alias{set_par_names}
-\alias{set_stats_names}
-\alias{get_params_mean}
-\alias{get_stats_mean}
+\alias{set_param_names}
+\alias{set_stat_names}
+\alias{get_mean_params}
+\alias{get_mean_stats}
 \alias{print.epiworld_lfmcmc}
 \alias{get_accepted_params}
 \alias{get_accepted_stats}
-\alias{get_statistics_hist}
-\alias{get_n_parameters}
-\alias{get_n_statistics}
+\alias{get_sample_stats}
+\alias{get_n_params}
+\alias{get_n_stats}
 \alias{get_n_samples}
 \title{Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)}
 \usage{
@@ -42,13 +42,13 @@ set_kernel_fun(lfmcmc, fun)
 
 use_kernel_fun_gaussian(lfmcmc)
 
-set_par_names(lfmcmc, names)
+set_param_names(lfmcmc, names)
 
-set_stats_names(lfmcmc, names)
+set_stat_names(lfmcmc, names)
 
-get_params_mean(lfmcmc)
+get_mean_params(lfmcmc)
 
-get_stats_mean(lfmcmc)
+get_mean_stats(lfmcmc)
 
 \method{print}{epiworld_lfmcmc}(x, burnin = 0, ...)
 
@@ -56,11 +56,11 @@ get_accepted_params(lfmcmc)
 
 get_accepted_stats(lfmcmc)
 
-get_statistics_hist(lfmcmc)
+get_sample_stats(lfmcmc)
 
-get_n_parameters(lfmcmc)
+get_n_params(lfmcmc)
 
-get_n_statistics(lfmcmc)
+get_n_stats(lfmcmc)
 
 get_n_samples(lfmcmc)
 }
@@ -132,13 +132,13 @@ samples and the number of columns equal to the number of statistics.
 }
 
 \itemize{
-\item The function \code{get_statistics_hist} returns a matrix of statistics
+\item The function \code{get_sample_stats} returns a matrix of statistics
 for the given LFMCMC model. with the number of rows equal to the number of
 samples and the number of columns equal to the number of statistics.
 }
 
 \itemize{
-\item The functions \code{get_n_parameters}, \code{get_n_statistics}, and \code{get_n_samples}
+\item The functions \code{get_n_params}, \code{get_n_stats}, and \code{get_n_samples}
 return the number of parameters, statistics, and samples for the given
 LFMCMC model, respectively.
 }
@@ -209,12 +209,12 @@ run_lfmcmc(
 )
 
 # Print the results
-set_stats_names(lfmcmc_model, get_states(model_sir))
-set_par_names(lfmcmc_model, c("Immune recovery", "Infectiousness"))
+set_stat_names(lfmcmc_model, get_states(model_sir))
+set_param_names(lfmcmc_model, c("Immune recovery", "Infectiousness"))
 
 print(lfmcmc_model)
 
-get_stats_mean(lfmcmc_model)
-get_params_mean(lfmcmc_model)
+get_mean_stats(lfmcmc_model)
+get_mean_params(lfmcmc_model)
 
 }