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

UofUEpiBio · Dec 9, 2024 · 50346c8 · 50346c8
1 parent b3096c6
commit 50346c8
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Showing 8 changed files with 36 additions and 36 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -200,7 +200,7 @@ export(set_name_tool)
 export(set_name_virus)
 export(set_observed_data)
 export(set_param)
-export(set_param_names)
+export(set_params_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_stat_names)
+export(set_stats_names)
 export(set_summary_fun)
 export(set_susceptibility_reduction)
 export(set_susceptibility_reduction_fun)

diff --git a/R/LFMCMC.R b/R/LFMCMC.R
@@ -76,8 +76,8 @@ stopifnot_lfmcmc <- function(x) {
 #' )
 #'
 #' # Print the results
-#' set_stat_names(lfmcmc_model, get_states(model_sir))
-#' set_param_names(lfmcmc_model, c("Immune recovery", "Infectiousness"))
+#' set_stats_names(lfmcmc_model, get_states(model_sir))
+#' set_params_names(lfmcmc_model, c("Immune recovery", "Infectiousness"))
 #'
 #' print(lfmcmc_model)
 #'
@@ -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_param_names <- function(lfmcmc, names) {
+set_params_names <- function(lfmcmc, names) {
 
   stopifnot_lfmcmc(lfmcmc)
-  set_param_names_cpp(lfmcmc, names)
+  set_params_names_cpp(lfmcmc, names)
   invisible(lfmcmc)
 
 }
@@ -241,10 +241,10 @@ set_param_names <- function(lfmcmc, names) {
 #' @param names The model stats names
 #' @returns The lfmcmc model with the stats names added
 #' @export
-set_stat_names <- function(lfmcmc, names) {
+set_stats_names <- function(lfmcmc, names) {
 
   stopifnot_lfmcmc(lfmcmc)
-  set_stat_names_cpp(lfmcmc, names)
+  set_stats_names_cpp(lfmcmc, names)
   invisible(lfmcmc)
 
 }

diff --git a/R/cpp11.R b/R/cpp11.R
@@ -256,12 +256,12 @@ use_kernel_fun_gaussian_cpp <- function(lfmcmc) {
   .Call(`_epiworldR_use_kernel_fun_gaussian_cpp`, lfmcmc)
 }
 
-set_param_names_cpp <- function(lfmcmc, names) {
-  .Call(`_epiworldR_set_param_names_cpp`, lfmcmc, names)
+set_params_names_cpp <- function(lfmcmc, names) {
+  .Call(`_epiworldR_set_params_names_cpp`, lfmcmc, names)
 }
 
-set_stat_names_cpp <- function(lfmcmc, names) {
-  .Call(`_epiworldR_set_stat_names_cpp`, lfmcmc, names)
+set_stats_names_cpp <- function(lfmcmc, names) {
+  .Call(`_epiworldR_set_stats_names_cpp`, lfmcmc, names)
 }
 
 get_mean_params_cpp <- function(lfmcmc) {

diff --git a/inst/tinytest/test-lfmcmc.R b/inst/tinytest/test-lfmcmc.R
@@ -68,8 +68,8 @@ expect_silent(run_lfmcmc(
   seed = model_seed
 ))
 
-expect_silent(set_stat_names(lfmcmc_model, get_states(model_sir)))
-expect_silent(set_param_names(lfmcmc_model, c("Immune recovery", "Infectiousness")))
+expect_silent(set_stats_names(lfmcmc_model, get_states(model_sir)))
+expect_silent(set_params_names(lfmcmc_model, c("Immune recovery", "Infectiousness")))
 
 # Check printing LFMCMC --------------------------------------------------------
 expect_stdout(print(lfmcmc_model))
@@ -233,8 +233,8 @@ expect_error(set_summary_fun(not_lfmcmc, sumfun), expected_error_msg)
 expect_error(set_kernel_fun(not_lfmcmc, kernelfun), expected_error_msg)
 expect_error(use_kernel_fun_gaussian(not_lfmcmc), expected_error_msg)
 
-expect_error(set_param_names(not_lfmcmc, c("Par 1", "Par 2")), expected_error_msg)
-expect_error(set_stat_names(not_lfmcmc, get_states(model_sir)), expected_error_msg)
+expect_error(set_params_names(not_lfmcmc, c("Par 1", "Par 2")), expected_error_msg)
+expect_error(set_stats_names(not_lfmcmc, get_states(model_sir)), expected_error_msg)
 
 expect_error(get_mean_params(not_lfmcmc), expected_error_msg)
 expect_error(get_mean_stats(not_lfmcmc), expected_error_msg)

diff --git a/man/LFMCMC.Rd b/man/LFMCMC.Rd
diff --git a/src/cpp11.cpp b/src/cpp11.cpp
@@ -454,17 +454,17 @@ extern "C" SEXP _epiworldR_use_kernel_fun_gaussian_cpp(SEXP lfmcmc) {
   END_CPP11
 }
 // lfmcmc.cpp
-SEXP set_param_names_cpp(SEXP lfmcmc, std::vector< std::string > names);
-extern "C" SEXP _epiworldR_set_param_names_cpp(SEXP lfmcmc, SEXP names) {
+SEXP set_params_names_cpp(SEXP lfmcmc, std::vector< std::string > names);
+extern "C" SEXP _epiworldR_set_params_names_cpp(SEXP lfmcmc, SEXP names) {
   BEGIN_CPP11
-    return cpp11::as_sexp(set_param_names_cpp(cpp11::as_cpp<cpp11::decay_t<SEXP>>(lfmcmc), cpp11::as_cpp<cpp11::decay_t<std::vector< std::string >>>(names)));
+    return cpp11::as_sexp(set_params_names_cpp(cpp11::as_cpp<cpp11::decay_t<SEXP>>(lfmcmc), cpp11::as_cpp<cpp11::decay_t<std::vector< std::string >>>(names)));
   END_CPP11
 }
 // lfmcmc.cpp
-SEXP set_stat_names_cpp(SEXP lfmcmc, std::vector< std::string > names);
-extern "C" SEXP _epiworldR_set_stat_names_cpp(SEXP lfmcmc, SEXP names) {
+SEXP set_stats_names_cpp(SEXP lfmcmc, std::vector< std::string > names);
+extern "C" SEXP _epiworldR_set_stats_names_cpp(SEXP lfmcmc, SEXP names) {
   BEGIN_CPP11
-    return cpp11::as_sexp(set_stat_names_cpp(cpp11::as_cpp<cpp11::decay_t<SEXP>>(lfmcmc), cpp11::as_cpp<cpp11::decay_t<std::vector< std::string >>>(names)));
+    return cpp11::as_sexp(set_stats_names_cpp(cpp11::as_cpp<cpp11::decay_t<SEXP>>(lfmcmc), cpp11::as_cpp<cpp11::decay_t<std::vector< std::string >>>(names)));
   END_CPP11
 }
 // lfmcmc.cpp
@@ -1182,7 +1182,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_epiworldR_set_name_virus_cpp",                   (DL_FUNC) &_epiworldR_set_name_virus_cpp,                    2},
     {"_epiworldR_set_observed_data_cpp",                (DL_FUNC) &_epiworldR_set_observed_data_cpp,                 2},
     {"_epiworldR_set_param_cpp",                        (DL_FUNC) &_epiworldR_set_param_cpp,                         3},
-    {"_epiworldR_set_param_names_cpp",                  (DL_FUNC) &_epiworldR_set_param_names_cpp,                   2},
+    {"_epiworldR_set_params_names_cpp",                 (DL_FUNC) &_epiworldR_set_params_names_cpp,                  2},
     {"_epiworldR_set_prob_death_cpp",                   (DL_FUNC) &_epiworldR_set_prob_death_cpp,                    2},
     {"_epiworldR_set_prob_death_fun_cpp",               (DL_FUNC) &_epiworldR_set_prob_death_fun_cpp,                3},
     {"_epiworldR_set_prob_death_ptr_cpp",               (DL_FUNC) &_epiworldR_set_prob_death_ptr_cpp,                3},
@@ -1197,7 +1197,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_epiworldR_set_recovery_enhancer_fun_cpp",        (DL_FUNC) &_epiworldR_set_recovery_enhancer_fun_cpp,         3},
     {"_epiworldR_set_recovery_enhancer_ptr_cpp",        (DL_FUNC) &_epiworldR_set_recovery_enhancer_ptr_cpp,         3},
     {"_epiworldR_set_simulation_fun_cpp",               (DL_FUNC) &_epiworldR_set_simulation_fun_cpp,                2},
-    {"_epiworldR_set_stat_names_cpp",                   (DL_FUNC) &_epiworldR_set_stat_names_cpp,                    2},
+    {"_epiworldR_set_stats_names_cpp",                  (DL_FUNC) &_epiworldR_set_stats_names_cpp,                   2},
     {"_epiworldR_set_summary_fun_cpp",                  (DL_FUNC) &_epiworldR_set_summary_fun_cpp,                   2},
     {"_epiworldR_set_susceptibility_reduction_cpp",     (DL_FUNC) &_epiworldR_set_susceptibility_reduction_cpp,      2},
     {"_epiworldR_set_susceptibility_reduction_fun_cpp", (DL_FUNC) &_epiworldR_set_susceptibility_reduction_fun_cpp,  3},

diff --git a/src/lfmcmc.cpp b/src/lfmcmc.cpp
@@ -212,22 +212,22 @@ SEXP use_kernel_fun_gaussian_cpp(
 // *************************************
 
 [[cpp11::register]]
-SEXP set_param_names_cpp(
+SEXP set_params_names_cpp(
     SEXP lfmcmc,
     std::vector< std::string > names
 ) {
     WrapLFMCMC(lfmcmc_ptr)(lfmcmc);
-    lfmcmc_ptr->set_param_names(names);
+    lfmcmc_ptr->set_params_names(names);
     return lfmcmc;
 }
 
 [[cpp11::register]]
-SEXP set_stat_names_cpp(
+SEXP set_stats_names_cpp(
     SEXP lfmcmc,
     std::vector< std::string > names
 ) {
     WrapLFMCMC(lfmcmc_ptr)(lfmcmc);
-    lfmcmc_ptr->set_stat_names(names);
+    lfmcmc_ptr->set_stats_names(names);
     return lfmcmc;
 }
 

diff --git a/vignettes/likelihood-free-mcmc.Rmd b/vignettes/likelihood-free-mcmc.Rmd
@@ -117,8 +117,8 @@ run_lfmcmc(
 )
 
 # Print the results
-set_stat_names(lfmcmc_model, get_states(model_sir))
-set_param_names(lfmcmc_model, c("Immune recovery", "Infectiousness"))
+set_stats_names(lfmcmc_model, get_states(model_sir))
+set_params_names(lfmcmc_model, c("Immune recovery", "Infectiousness"))
 
 print(lfmcmc_model)
 ```