Updating news file and correcting how seeds are set

NEWS.md

@@ -1,3 +1,21 @@
+# epiworldR 0.4-3 (development version)
+
+## New features
+
+* The package now includes the `LFMCMC` module that implements
+  the likelihood-free Markov Chain Monte Carlo algorithm. This
+  module is used to estimate the parameters of the models.
+
+* The new function `add_param()` allows the user to add parameters
+  to the model.
+
+* The new function `rm_globalevent()` allows the user to remove
+  global events from the model.
+
+* The function `today()` returns the current day (step) of the
+  simulation.
+
+
 # epiworldR 0.3-2
 
 * Starting version 0.3-0, `epiworldR` is versioned using the same version as the C++ library, `epiworld`.

R/LFMCMC.R

@@ -1,10 +1,12 @@
 #' Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
 #'
-#'
 #' @aliases epiworld_lfmcmc
+#' @param model A model of class [epiworld_model] or `NULL` (see details).
 #' @details
-#' Performs a Likelihood-Free Markhov Chain Monte Carlo simulation
-#' @param model A model of class [epiworld_model]
+#' Performs a Likelihood-Free Markhov Chain Monte Carlo simulation. When
+#' `model` is not `NULL`, the model uses the same random-number generator
+#' engine as the model. Otherwise, when `model` is `NULL`, a new random-number
+#' generator engine is created.
 #' @returns
 #' The `LFMCMC` function returns a model of class [epiworld_lfmcmc].
 #' @examples
@@ -73,14 +75,19 @@
 #' get_params_mean(lfmcmc_model)
 #'
 #' @export
-LFMCMC <- function(model) {
-  if (!inherits(model, "epiworld_model"))
-    stop("model should be of class 'epiworld_model'. It is of class ", class(model))
+LFMCMC <- function(model = NULL) {
+
+  if ((length(model) > 0) && !inherits(model, "epiworld_model"))
+    stop(
+      "model should be of class 'epiworld_model'. It is of class ",
+      paste(class(model), collapse = "\", ")
+    )
 
   structure(
     LFMCMC_cpp(model),
     class = c("epiworld_lfmcmc")
   )
+
 }
 
 #' @rdname LFMCMC
@@ -91,21 +98,40 @@ LFMCMC <- function(model) {
 #' @param seed Random engine seed
 #' @returns The simulated model of class [epiworld_lfmcmc].
 #' @export
-run_lfmcmc <- function(lfmcmc, params_init_, n_samples_, epsilon_, seed = NULL) UseMethod("run_lfmcmc")
+run_lfmcmc <- function(
+    lfmcmc, params_init_, n_samples_, epsilon_,
+    seed = NULL
+    ) {
+  UseMethod("run_lfmcmc")
+}
 
 #' @export
-run_lfmcmc.epiworld_lfmcmc <- function(lfmcmc, params_init_, n_samples_, epsilon_, seed = NULL) {
-  if (length(seed)) set.seed(seed)
-  run_lfmcmc_cpp(lfmcmc, params_init_, n_samples_, epsilon_, sample.int(1e4, 1))
+run_lfmcmc.epiworld_lfmcmc <- function(
+    lfmcmc, params_init_, n_samples_, epsilon_,
+    seed = NULL
+    ) {
+
+  if (length(seed))
+    set.seed(seed)
+
+  run_lfmcmc_cpp(
+    lfmcmc, params_init_, n_samples_, epsilon_, sample.int(1e4, 1)
+  )
+
   invisible(lfmcmc)
+
 }
 
 #' @rdname LFMCMC
 #' @param lfmcmc LFMCMC model
 #' @param observed_data_ Observed data
 #' @returns The lfmcmc model with the observed data added
 #' @export
-set_observed_data <- function(lfmcmc, observed_data_) UseMethod("set_observed_data")
+set_observed_data <- function(
+    lfmcmc, observed_data_
+    ) {
+  UseMethod("set_observed_data")
+}
 
 #' @export
 set_observed_data.epiworld_lfmcmc <- function(lfmcmc, observed_data_) {

src/lfmcmc.cpp

@@ -29,8 +29,13 @@ SEXP LFMCMC_cpp(
         new LFMCMC<TData_default>()
     );
 
-    cpp11::external_pointer<Model<int>> modelptr(model);
-    lfmcmc_ptr->set_rand_engine(modelptr->get_rand_endgine());
+    if (Rf_inherits(model, "epiworld_model")) {
+        cpp11::external_pointer<Model<int>> modelptr(model);
+        lfmcmc_ptr->set_rand_engine(modelptr->get_rand_endgine());
+    } else {
+        auto new_ptr = std::make_shared<std::mt19937>(std::mt19937());
+        lfmcmc_ptr->set_rand_engine(new_ptr);
+    }
 
     return lfmcmc_ptr;
 }