From 7e638ac963e72906657a19587107a443ae274739 Mon Sep 17 00:00:00 2001
From: "George G. Vega Yon" <g.vegayon@gmail.com>
Date: Sun, 3 Dec 2023 10:51:06 -0700
Subject: [PATCH] Adding clone method

---
 NAMESPACE               |  1 +
 R/cpp11.R               |  4 ++++
 R/model-methods.R       | 15 +++++++++++++++
 man/epiworld-methods.Rd | 11 +++++++++++
 src/cpp11.cpp           |  8 ++++++++
 src/model.cpp           | 13 +++++++++++++
 6 files changed, 52 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 8acbfbe6..2e23cdec 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -102,6 +102,7 @@ export(add_virus_n)
 export(agents_from_edgelist)
 export(agents_smallworld)
 export(change_state)
+export(clone_model)
 export(get_agents)
 export(get_agents_data_ncols)
 export(get_agents_states)
diff --git a/R/cpp11.R b/R/cpp11.R
index ee345e3c..d799599d 100644
--- a/R/cpp11.R
+++ b/R/cpp11.R
@@ -260,6 +260,10 @@ initial_states_cpp <- function(model, proportions) {
   .Call(`_epiworldR_initial_states_cpp`, model, proportions)
 }
 
+clone_model_cpp <- function(model) {
+  .Call(`_epiworldR_clone_model_cpp`, model)
+}
+
 tool_cpp <- function(name, susceptibility_reduction, transmission_reduction, recovery_enhancer, death_reduction) {
   .Call(`_epiworldR_tool_cpp`, name, susceptibility_reduction, transmission_reduction, recovery_enhancer, death_reduction)
 }
diff --git a/R/model-methods.R b/R/model-methods.R
index a4f27bbd..19991701 100644
--- a/R/model-methods.R
+++ b/R/model-methods.R
@@ -365,3 +365,18 @@ initial_states <- function(model, proportions) {
 
 }
 
+#' @rdname epiworld-methods
+#' @export
+#' @details `epiworld_model` objects are pointers to an underlying C++ class
+#' in `epiworld`. To generate a copy of a model, use `clone_model`, otherwise,
+#' the assignment operator will only copy the pointer.
+#' @return
+#' - `clone_model` returns a copy of the model.
+clone_model <- function(model) {
+  stopifnot_model(model)
+  structure(
+    clone_model_cpp(model),
+    class = class(model)
+  )
+}
+
diff --git a/man/epiworld-methods.Rd b/man/epiworld-methods.Rd
index f0be4980..0f175377 100644
--- a/man/epiworld-methods.Rd
+++ b/man/epiworld-methods.Rd
@@ -24,6 +24,7 @@
 \alias{get_virus}
 \alias{get_tool}
 \alias{initial_states}
+\alias{clone_model}
 \title{Methods for epiworldR objects}
 \usage{
 queuing_on(x)
@@ -67,6 +68,8 @@ get_virus(model, virus_pos)
 get_tool(model, tool_pos)
 
 initial_states(model, proportions)
+
+clone_model(model)
 }
 \arguments{
 \item{x}{An object of class \code{epiworld_model}.}
@@ -174,6 +177,10 @@ of \code{epiworld_model}.
 \itemize{
 \item \code{inital_states} returns the model with an updated initial state.
 }
+
+\itemize{
+\item \code{clone_model} returns a copy of the model.
+}
 }
 \description{
 The functions described in this section are methods for objects of class
@@ -184,6 +191,10 @@ and running the simulation.
 \details{
 The \code{verbose_on} and \code{verbose_off} functions activate and deactivate printing
 progress on screen, respectively. Both functions return the model (\code{x}) invisibly.
+
+\code{epiworld_model} objects are pointers to an underlying C++ class
+in \code{epiworld}. To generate a copy of a model, use \code{clone_model}, otherwise,
+the assignment operator will only copy the pointer.
 }
 \examples{
 
diff --git a/src/cpp11.cpp b/src/cpp11.cpp
index 2fe6ced3..fdf878a5 100644
--- a/src/cpp11.cpp
+++ b/src/cpp11.cpp
@@ -460,6 +460,13 @@ extern "C" SEXP _epiworldR_initial_states_cpp(SEXP model, SEXP proportions) {
     return cpp11::as_sexp(initial_states_cpp(cpp11::as_cpp<cpp11::decay_t<SEXP>>(model), cpp11::as_cpp<cpp11::decay_t<cpp11::doubles>>(proportions)));
   END_CPP11
 }
+// model.cpp
+SEXP clone_model_cpp(const SEXP & model);
+extern "C" SEXP _epiworldR_clone_model_cpp(SEXP model) {
+  BEGIN_CPP11
+    return cpp11::as_sexp(clone_model_cpp(cpp11::as_cpp<cpp11::decay_t<const SEXP &>>(model)));
+  END_CPP11
+}
 // tool.cpp
 SEXP tool_cpp(std::string name, double susceptibility_reduction, double transmission_reduction, double recovery_enhancer, double death_reduction);
 extern "C" SEXP _epiworldR_tool_cpp(SEXP name, SEXP susceptibility_reduction, SEXP transmission_reduction, SEXP recovery_enhancer, SEXP death_reduction) {
@@ -787,6 +794,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_epiworldR_agents_from_edgelist_cpp",             (DL_FUNC) &_epiworldR_agents_from_edgelist_cpp,              5},
     {"_epiworldR_agents_smallworld_cpp",                (DL_FUNC) &_epiworldR_agents_smallworld_cpp,                 5},
     {"_epiworldR_change_state_cpp",                     (DL_FUNC) &_epiworldR_change_state_cpp,                      4},
+    {"_epiworldR_clone_model_cpp",                      (DL_FUNC) &_epiworldR_clone_model_cpp,                       1},
     {"_epiworldR_get_agent_cpp",                        (DL_FUNC) &_epiworldR_get_agent_cpp,                         2},
     {"_epiworldR_get_agents_cpp",                       (DL_FUNC) &_epiworldR_get_agents_cpp,                        1},
     {"_epiworldR_get_agents_data_ncols_cpp",            (DL_FUNC) &_epiworldR_get_agents_data_ncols_cpp,             1},
diff --git a/src/model.cpp b/src/model.cpp
index 80e80fe1..3a054d04 100644
--- a/src/model.cpp
+++ b/src/model.cpp
@@ -315,3 +315,16 @@ SEXP initial_states_cpp(SEXP model, cpp11::doubles proportions) {
   return model;
  
 }
+
+// Function for cloning a model
+[[cpp11::register]]
+SEXP clone_model_cpp(const SEXP & model) {
+  
+  external_pointer<const Model<>> modelptr(model);
+  
+  return external_pointer<Model<>>(
+    new Model<>(*modelptr)
+  );
+  
+}
+