Removing dangling calls

R/agents.R

@@ -19,7 +19,6 @@ stopifnot_agent <- function(x) {
 #' @param d,directed Logical scalar. Whether the graph is directed or not.
 #' @param p Probability of rewiring.
 #' @export
-#' @aliases agents
 #' @return
 #' - The 'agents_smallworld' function returns a model with the agents 
 #' loaded.

R/cpp11.R

@@ -416,8 +416,8 @@ print_agent_tools_cpp <- function(tools) {
   .Call(`_epiworldR_print_agent_tools_cpp`, tools)
 }
 
-set_distribution_tool_cpp <- function(tool, model, tfun) {
-  .Call(`_epiworldR_set_distribution_tool_cpp`, tool, model, tfun)
+set_distribution_tool_cpp <- function(tool, distfun) {
+  .Call(`_epiworldR_set_distribution_tool_cpp`, tool, distfun)
 }
 
 distribute_tool_randomly_cpp <- function(prevalence, as_proportion) {

R/entity.R

@@ -5,9 +5,9 @@ stopifnot_entity <- function(entity) {
   }
 }
 
-stopifnot_entity_distfun <- function(dist_fun) {
-  if (!inherits(dist_fun, "epiworld_distribution_entity")) {
-    stop("Argument 'dist_fun' must be a distribution function.")
+stopifnot_entity_distfun <- function(distfun) {
+  if (!inherits(distfun, "epiworld_distribution_entity")) {
+    stop("Argument 'distfun' must be a distribution function.")
   }
 }
 
@@ -92,6 +92,8 @@ print.epiworld_entities <- function(x, ...) {
 #' @param prevalence Numeric scalar. Prevalence of the entity.
 #' @param as_proportion Logical scalar. If `TRUE`, `prevalence` is interpreted
 #' as a proportion.
+#' @param to_unassigned Logical scalar. If `TRUE`, the entity is added to the
+#' unassigned pool.
 #' @return 
 #' - The function `entity` creates an entity object.
 #' @rdname entities
@@ -280,14 +282,14 @@ distribute_entity_to_set <- function(
 
 #' @export 
 #' @rdname entities
-#' @param dist_fun Distribution function object of class `epiworld_distribution_entity`.
+#' @param distfun Distribution function object of class `epiworld_distribution_entity`.
 set_distribution_entity <- function(
   entity,
-  dist_fun
+  distfun
 ) {
 
   stopifnot_entity(entity)
-  stopifnot_entity_distfun(dist_fun)
+  stopifnot_entity_distfun(distfun)
   set_distribution_entity_cpp(entity, distribution)
 
   invisible(entity)

R/functions-renamed.R

@@ -10,15 +10,21 @@
 #' @name epiworldR-deprecated
 NULL
 
-#' @param n Deprecated. Either set the prevalence during the tool/virus
-#' initialization or use `set_prevalence_tool`/`set_prevalence_virus`.
+#' @param n Deprecated. 
 #' @export 
 #' @rdname epiworldR-deprecated
 add_tool_n <- function(model, tool, n) {
 
   .Deprecated(new = "add_tool")
 
-  set_prevalence_tool(tool, n, as_proportion = FALSE)
+  set_distribution_tool(
+    tool,
+    distfun = distribute_tool_randomly(
+      prevalence = n,
+      as_proportion = TRUE
+    )
+  )
+
   add_tool(model, tool)
 
 }
@@ -28,7 +34,15 @@ add_tool_n <- function(model, tool, n) {
 add_virus_n <- function(model, virus, n) {
 
   .Deprecated(new = "add_virus")
-  set_prevalence_virus(virus, n, as_proportion = FALSE)
+
+  set_distribution_virus(
+    virus = virus,
+    distfun = distribute_virus_randomly(
+      prevalence = n,
+      as_proportion = TRUE
+      )
+  )
+
   add_virus(model, virus)
 
 }

R/tool.R

@@ -47,7 +47,8 @@
 #' 
 #' # To declare a certain number of individuals with the tool
 #' rm_tool(model_sirconn, 0) # Removing epitool from the model
-#' set_prevalence_tool(epitool, 0.1, TRUE) # Setting prevalence to 0.1
+#' # Setting prevalence to 0.1
+#' set_distribution_tool(epitool, distribute_tool_randomly(0.1, TRUE))
 #' add_tool(model_sirconn, epitool)
 #' run(model_sirconn, ndays = 100, seed = 1912)
 #' 
@@ -152,8 +153,7 @@ get_name_tool <- function(tool) {
 
 #' @export
 #' @param tool An object of class `epiworld_tool`
-#' @param proportion Deprecated. Either set the prevalence during the tool
-#' initialization or use `set_prevalence_tool`.
+#' @param proportion Deprecated.
 #' @details 
 #' The `add_tool` function adds the specified tool to the model of class 
 #' [epiworld_model] with specified proportion.
@@ -164,10 +164,13 @@ add_tool <- function(model, tool, proportion) {
 
     warning(
       "The 'proportion' argument is deprecated. ",
-      "Use 'set_prevalence_tool' instead."
+      "Use 'set_distribution_tool' instead."
       )
 
-    set_prevalence_tool(tool, proportion, TRUE)
+    set_distribution_tool(
+      tool,
+      distribute_tool_randomly(proportion, TRUE)
+    )
 
   }
 
@@ -502,12 +505,13 @@ print.epiworld_agents_tools <- function(x, max_print = 10, ...) {
 #' specified tool of class [epiworld_tool]. The distribution function can be
 #' created using the functions [distribute_tool_randomly()] and
 #' [distribute_tool_to_set()].
+#' @param distfun An object of class `epiworld_tool_distfun`.
 #' @rdname tool
 set_distribution_tool <- function(tool, distfun) {
 
   stopifnot_tool(tool)
   stopifnot_tool_distfun(distfun)
-  invisible(set_distribution_tool_cpp(tool, distfun))
+  invisible(set_distribution_tool_cpp(tool = tool, distfun = distfun))
 
 }
 
@@ -516,6 +520,9 @@ set_distribution_tool <- function(tool, distfun) {
 #' @details 
 #' The `distribute_tool_randomly` function creates a distribution function that
 #' randomly assigns the tool to a proportion of the population.
+#' @param as_proportion Logical scalar. If `TRUE`, `prevalence` is interpreted
+#' as a proportion of the total number of agents in the model.
+#' @param prevalence Numeric scalar. Prevalence of the tool.
 #' @return 
 #' - The `distribute_tool_randomly` function returns a distribution function of
 #' class `epiworld_tool_distfun`.

R/virus.R

@@ -43,7 +43,7 @@
 #' mseirconn
 #' 
 #' rm_virus(mseirconn, 0) # Removing the first virus from the model object
-#' set_prevalence_virus(delta, 100, as_proportion = FALSE)
+#' set_distribution_virus(delta, distribute_virus_randomly(100, as_proportion = FALSE))
 #' add_virus(mseirconn, delta) 
 #' 
 #' # Setting parameters for the delta virus manually
@@ -154,8 +154,7 @@ get_name_virus <- function(virus) {
 #' @rdname virus
 #' @param model An object of class `epiworld_model`.
 #' @param virus An object of class `epiworld_virus`
-#' @param proportion Deprecated. Either set the prevalence during the virus
-#' initialization or use `set_prevalence_virus`.
+#' @param proportion Deprecated. 
 #' @returns 
 #' - The `add_virus` function does not return a value, instead it adds the 
 #' virus of choice to the model object of class [epiworld_model].
@@ -168,7 +167,10 @@ add_virus <- function(model, virus, proportion) {
       "the next version."
       )
 
-    set_prevalence_virus(virus, proportion, as_proportion = TRUE)
+    set_distribution_virus(
+      virus=virus,
+      distfun=distribute_virus_randomly(proportion, as_proportion = TRUE)
+    )
 
   }
 
@@ -521,12 +523,12 @@ set_incubation_fun <- function(virus, model, vfun) {
 
 #' @export
 #' @rdname virus
-#' @param dist_fun An object of class `epiworld_distribution_virus`.
-set_distribution_virus <- function(virus, dist_fun) {
+#' @param distfun An object of class `epiworld_distribution_virus`.
+set_distribution_virus <- function(virus, distfun) {
 
   stopifnot_virus(virus)
-  stopifnot_virus_distfun(dist_fun)
-  invisible(set_distribution_virus_cpp(virus, dist_fun))
+  stopifnot_virus_distfun(distfun)
+  invisible(set_distribution_virus_cpp(virus, distfun))
 
 }
 
@@ -552,20 +554,20 @@ distribute_virus_randomly <- function(
       as.double(prevalence),
       as.logical(as_proportion)
     ),
-    class = "epiworld_distribution_virus"
+    class = "epiworld_virus_distfun"
   )
 
 }
 
 #' @export
 #' @rdname virus
-#' @param agents_id Integer vector. Indices of the agents that will receive the
+#' @param agents_ids Integer vector. Indices of the agents that will receive the
 #' virus.
 distribute_virus_set <- function(agents_ids) {
 
   structure(
     distribute_virus_set_cpp(as.vector(agents_id)),
-    class = "epiworld_distribution_virus"
+    class = "epiworld_virus_distfun"
   )
 
 }

inst/tinytest/test-mixing.R

@@ -26,9 +26,9 @@ flu_model <- ModelSEIRMixing(
 
 # Adding the entities 
 flu_model |>
-  add_entity_n(e1) |>
-  add_entity_n(e2) |>
-  add_entity_n(e3)
+  add_entity(e1) |>
+  add_entity(e2) |>
+  add_entity(e3)
 
 run(flu_model, ndays = 100, seed = 1233)
 summary(flu_model)

playground/.gitignore

@@ -1,2 +1,4 @@
 *_files/
 *_cache/
+
+/.quarto/