Fix naming conventions to match C++ library (#58)

* Copy changes to C++ library

* Rename relevant variables and methods to be consistent with latest C++ changes

* Update namespace and build docs

* Pull in latest changes from C++ library

* Update R API to match C++ changes to set_stat_names and set_param_names

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: epiworldR
 Type: Package
 Title: Fast Agent-Based Epi Models
-Version: 0.5-0
+Version: 0.6-0
 Authors@R: c(
   person(given="George", family="Vega Yon", role=c("aut","cre"),
   email="[email protected]", comment = c(ORCID = "0000-0002-3171-0844")),

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_params_names)
 export(set_prob_death)
 export(set_prob_death_fun)
 export(set_prob_death_ptr)

R/LFMCMC.R

@@ -77,12 +77,12 @@ stopifnot_lfmcmc <- function(x) {
 #'
 #' # Print the results
 #' set_stats_names(lfmcmc_model, get_states(model_sir))
-#' set_par_names(lfmcmc_model, c("Immune recovery", "Infectiousness"))
+#' set_params_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)
 #'
 #' @export
 LFMCMC <- function(model = NULL) {
@@ -228,10 +228,10 @@ use_kernel_fun_gaussian <- function(lfmcmc) {
 #' @param names The model parameter names
 #' @returns The lfmcmc model with the parameter names added
 #' @export
-set_par_names <- function(lfmcmc, names) {
+set_params_names <- function(lfmcmc, names) {
 
   stopifnot_lfmcmc(lfmcmc)
-  set_par_names_cpp(lfmcmc, names)
+  set_params_names_cpp(lfmcmc, names)
   invisible(lfmcmc)
 
 }
@@ -253,21 +253,21 @@ set_stats_names <- function(lfmcmc, names) {
 #' @param lfmcmc LFMCMC model
 #' @returns The param means for the given lfmcmc model
 #' @export
-get_params_mean <- function(lfmcmc) {
+get_mean_params <- function(lfmcmc) {
 
   stopifnot_lfmcmc(lfmcmc)
-  get_params_mean_cpp(lfmcmc)
+  get_mean_params_cpp(lfmcmc)
 
 }
 
 #' @rdname LFMCMC
 #' @param lfmcmc LFMCMC model
 #' @returns The stats means for the given lfmcmc model
 #' @export
-get_stats_mean <- function(lfmcmc) {
+get_mean_stats <- function(lfmcmc) {
 
   stopifnot_lfmcmc(lfmcmc)
-  get_stats_mean_cpp(lfmcmc)
+  get_mean_stats_cpp(lfmcmc)
 
 }
 
@@ -301,7 +301,7 @@ get_accepted_params <- function(lfmcmc) {
 
   stopifnot_lfmcmc(lfmcmc)
   a_params <- get_accepted_params_cpp(lfmcmc)
-  n_params <- get_n_parameters(lfmcmc)
+  n_params <- get_n_params(lfmcmc)
 
   matrix(
     a_params,
@@ -322,7 +322,7 @@ get_accepted_stats <- function(lfmcmc) {
 
   stopifnot_lfmcmc(lfmcmc)
   a_stats <- get_accepted_stats_cpp(lfmcmc)
-  n_stats <- get_n_statistics(lfmcmc)
+  n_stats <- get_n_stats(lfmcmc)
 
   matrix(
     a_stats,
@@ -335,14 +335,14 @@ get_accepted_stats <- function(lfmcmc) {
 #' @export
 #' @rdname LFMCMC
 #' @returns
-#' - The function `get_statistics_hist` returns a matrix of statistics
+#' - The function `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.
-get_statistics_hist <- function(lfmcmc) {
+get_sample_stats <- function(lfmcmc) {
 
   stopifnot_lfmcmc(lfmcmc)
-  stats <- get_statistics_hist_cpp(lfmcmc)
-  n_stats <- get_n_statistics(lfmcmc)
+  stats <- get_sample_stats_cpp(lfmcmc)
+  n_stats <- get_n_stats(lfmcmc)
 
   matrix(
     stats,
@@ -355,22 +355,22 @@ get_statistics_hist <- function(lfmcmc) {
 #' @export
 #' @rdname LFMCMC
 #' @returns
-#' - The functions `get_n_parameters`, `get_n_statistics`, and `get_n_samples`
+#' - The functions `get_n_params`, `get_n_stats`, and `get_n_samples`
 #' return the number of parameters, statistics, and samples for the given
 #' LFMCMC model, respectively.
-get_n_parameters <- function(lfmcmc) {
+get_n_params <- function(lfmcmc) {
 
   stopifnot_lfmcmc(lfmcmc)
-  get_n_parameters_cpp(lfmcmc)
+  get_n_params_cpp(lfmcmc)
 
 }
 
 #' @export
 #' @rdname LFMCMC
-get_n_statistics <- function(lfmcmc) {
+get_n_stats <- function(lfmcmc) {
 
   stopifnot_lfmcmc(lfmcmc)
-  get_n_statistics_cpp(lfmcmc)
+  get_n_stats_cpp(lfmcmc)
 
 }
 

R/cpp11.R

@@ -256,28 +256,28 @@ use_kernel_fun_gaussian_cpp <- function(lfmcmc) {
   .Call(`_epiworldR_use_kernel_fun_gaussian_cpp`, lfmcmc)
 }
 
-set_par_names_cpp <- function(lfmcmc, names) {
-  .Call(`_epiworldR_set_par_names_cpp`, lfmcmc, names)
+set_params_names_cpp <- function(lfmcmc, names) {
+  .Call(`_epiworldR_set_params_names_cpp`, lfmcmc, names)
 }
 
 set_stats_names_cpp <- function(lfmcmc, names) {
   .Call(`_epiworldR_set_stats_names_cpp`, lfmcmc, names)
 }
 
-get_params_mean_cpp <- function(lfmcmc) {
-  .Call(`_epiworldR_get_params_mean_cpp`, lfmcmc)
+get_mean_params_cpp <- function(lfmcmc) {
+  .Call(`_epiworldR_get_mean_params_cpp`, lfmcmc)
 }
 
-get_stats_mean_cpp <- function(lfmcmc) {
-  .Call(`_epiworldR_get_stats_mean_cpp`, lfmcmc)
+get_mean_stats_cpp <- function(lfmcmc) {
+  .Call(`_epiworldR_get_mean_stats_cpp`, lfmcmc)
 }
 
 print_lfmcmc_cpp <- function(lfmcmc, burnin) {
   .Call(`_epiworldR_print_lfmcmc_cpp`, lfmcmc, burnin)
 }
 
-get_statistics_hist_cpp <- function(lfmcmc) {
-  .Call(`_epiworldR_get_statistics_hist_cpp`, lfmcmc)
+get_sample_stats_cpp <- function(lfmcmc) {
+  .Call(`_epiworldR_get_sample_stats_cpp`, lfmcmc)
 }
 
 get_accepted_params_cpp <- function(lfmcmc) {
@@ -292,12 +292,12 @@ get_n_samples_cpp <- function(lfmcmc) {
   .Call(`_epiworldR_get_n_samples_cpp`, lfmcmc)
 }
 
-get_n_statistics_cpp <- function(lfmcmc) {
-  .Call(`_epiworldR_get_n_statistics_cpp`, lfmcmc)
+get_n_stats_cpp <- function(lfmcmc) {
+  .Call(`_epiworldR_get_n_stats_cpp`, lfmcmc)
 }
 
-get_n_parameters_cpp <- function(lfmcmc) {
-  .Call(`_epiworldR_get_n_parameters_cpp`, lfmcmc)
+get_n_params_cpp <- function(lfmcmc) {
+  .Call(`_epiworldR_get_n_params_cpp`, lfmcmc)
 }
 
 print_cpp <- function(m, lite) {

inst/include/epiworld/epiworld.hpp

@@ -18,7 +18,7 @@
 
 /* Versioning */
 #define EPIWORLD_VERSION_MAJOR 0
-#define EPIWORLD_VERSION_MINOR 5
+#define EPIWORLD_VERSION_MINOR 6
 #define EPIWORLD_VERSION_PATCH 0
 
 static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;