Merge pull request #12 from UofUEpiBio/rename-actions-to-events

Rename actions to events

Makefile

@@ -34,7 +34,7 @@ local-update:
 	rsync -avz ../epiworld/include/epiworld inst/include/.
 
 check: build
-	R CMD check epiworldR_*.tar.gz
+	cd .. && R CMD check epiworldR_*.tar.gz
 
 clean: 
 	Rscript --vanilla -e 'devtools::clean_dll()'

NAMESPACE

@@ -58,7 +58,7 @@ S3method(plot,epiworld_surv)
 S3method(print,epiworld_agent)
 S3method(print,epiworld_agents)
 S3method(print,epiworld_agents_tools)
-S3method(print,epiworld_globalaction)
+S3method(print,epiworld_globalevent)
 S3method(print,epiworld_model)
 S3method(print,epiworld_saver)
 S3method(print,epiworld_tool)
@@ -90,7 +90,7 @@ export(ModelSIRLogit)
 export(ModelSIS)
 export(ModelSISD)
 export(ModelSURV)
-export(add_global_action)
+export(add_globalevent)
 export(add_tool)
 export(add_tool_agent)
 export(add_tool_n)
@@ -131,6 +131,10 @@ export(globalaction_fun)
 export(globalaction_set_params)
 export(globalaction_tool)
 export(globalaction_tool_logit)
+export(globalevent_fun)
+export(globalevent_set_params)
+export(globalevent_tool)
+export(globalevent_tool_logit)
 export(has_tool)
 export(has_virus)
 export(initial_states)

R/cpp11.R

@@ -1,31 +1,31 @@
 # Generated by cpp11: do not edit by hand
 
-globalaction_tool_logit_cpp <- function(tool, vars, coefs, name, day) {
-  .Call(`_epiworldR_globalaction_tool_logit_cpp`, tool, vars, coefs, name, day)
+globalevent_tool_logit_cpp <- function(tool, vars, coefs, name, day) {
+  .Call(`_epiworldR_globalevent_tool_logit_cpp`, tool, vars, coefs, name, day)
 }
 
-globalaction_tool_cpp <- function(tool, prob, name, day) {
-  .Call(`_epiworldR_globalaction_tool_cpp`, tool, prob, name, day)
+globalevent_tool_cpp <- function(tool, prob, name, day) {
+  .Call(`_epiworldR_globalevent_tool_cpp`, tool, prob, name, day)
 }
 
-globalaction_set_param_cpp <- function(param, value, name, day) {
-  .Call(`_epiworldR_globalaction_set_param_cpp`, param, value, name, day)
+globalevent_set_param_cpp <- function(param, value, name, day) {
+  .Call(`_epiworldR_globalevent_set_param_cpp`, param, value, name, day)
 }
 
 print_global_action_cpp <- function(action) {
   .Call(`_epiworldR_print_global_action_cpp`, action)
 }
 
-add_global_action_cpp <- function(model, action) {
-  .Call(`_epiworldR_add_global_action_cpp`, model, action)
+add_globalevent_cpp <- function(model, action) {
+  .Call(`_epiworldR_add_globalevent_cpp`, model, action)
 }
 
-rm_global_action_cpp <- function(model, name) {
-  .Call(`_epiworldR_rm_global_action_cpp`, model, name)
+rm_globalevent_cpp <- function(model, name) {
+  .Call(`_epiworldR_rm_globalevent_cpp`, model, name)
 }
 
-globalaction_fun_cpp <- function(fun, name, day) {
-  .Call(`_epiworldR_globalaction_fun_cpp`, fun, name, day)
+globalevent_fun_cpp <- function(fun, name, day) {
+  .Call(`_epiworldR_globalevent_fun_cpp`, fun, name, day)
 }
 
 get_agents_cpp <- function(model) {

R/functions-renamed.R

@@ -0,0 +1,7 @@
+#' Deprecated functions in epiworldR
+#' @description
+#' Starting version 0.0-4, epiworld changed how it refered to "actions."
+#' Following more traditional ABMs, actions are now called "events."
+#' @param ... Arguments to be passed to the new function.
+#' @name epiworldR-deprecated
+NULL

R/global-actions.R

@@ -31,8 +31,8 @@
 #' 
 #' 
 #' # Adding a global action
-#' vaccine_day_20 <- globalaction_tool(epitool, .2, day = 20)
-#' add_global_action(model_sirconn, vaccine_day_20)
+#' vaccine_day_20 <- globalevent_tool(epitool, .2, day = 20)
+#' add_globalevent(model_sirconn, vaccine_day_20)
 #' 
 #' # Running and printing
 #' run(model_sirconn, ndays = 40, seed = 1912)
@@ -49,107 +49,143 @@
 #'   recovery_rate       = 0.95
 #' )
 #' 
-#' closure_day_10 <- globalaction_set_params("Contact rate", 0, day = 10)
-#' add_global_action(model_sirconn2, closure_day_10)
+#' closure_day_10 <- globalevent_set_params("Contact rate", 0, day = 10)
+#' add_globalevent(model_sirconn2, closure_day_10)
 #' 
 #' # Running and printing
 #' run(model_sirconn2, ndays = 40, seed = 1912)
 #' model_sirconn2
 #' plot_incidence(model_sirconn2)
 #' @returns
-#' - The `globalaction_set_params` function returns an object of class
-#' [epiworld_globalaction_set_param] and [epiworld_globalaction].
+#' - The `globalevent_set_params` function returns an object of class
+#' [epiworld_globalevent_set_param] and [epiworld_globalevent].
 #' 
-#' - `globalaction_tool` returns an object of class 
-#' [epiworld_globalaction_tool] and [epiworld_globalaction].
+#' - `globalevent_tool` returns an object of class 
+#' [epiworld_globalevent_tool] and [epiworld_globalevent].
 #' 
-#' - `globalaction_tool_logit` returns an object of class
-#' [epiworld_globalaction_tool_logit] and [epiworld_globalaction].
+#' - `globalevent_tool_logit` returns an object of class
+#' [epiworld_globalevent_tool_logit] and [epiworld_globalevent].
 #' @aliases 
-#' epiworld_globalaction_set_param
-#' epiworld_globalaction_tool
-#' epiworld_globalaction_tool_logit
-#' epiworld_globalaction
+#' epiworld_globalevent_set_param
+#' epiworld_globalevent_tool
+#' epiworld_globalevent_tool_logit
+#' epiworld_globalevent
 #' actions
 #' 
-globalaction_tool <- function(
+globalevent_tool <- function(
   tool, prob,
   name = get_name_tool(tool), day = -99
   ) {
 
   structure(
-    globalaction_tool_cpp(tool, prob, name, day),
-    class = c("epiworld_globalaction_tool", "epiworld_globalaction"),
+    globalevent_tool_cpp(tool, prob, name, day),
+    class = c("epiworld_globalevent_tool", "epiworld_globalevent"),
     tool = tool,
     call = match.call()
   )
 }
 
+#' @export
+#' @rdname epiworldR-deprecated
+globalaction_tool <- function(...) {
+
+  .Deprecated(
+    new = "globalevent_tool"
+    )  
+
+  globalevent_tool(...)
+
+}
+
 #' @export
 #' @rdname global-actions
 #' @param vars Integer vector. The position of the variables in the model.
 #' @param coefs Numeric vector. The coefficients of the logistic regression.
-#' @details The function `globalaction_tool_logit` allows to specify a logistic
+#' @details The function `globalevent_tool_logit` allows to specify a logistic
 #' regression model for the probability of using a tool. The model is specified
 #' by the vector of coefficients `coefs` and the vector of variables `vars`.
 #' `vars` is an integer vector indicating the position of the variables in the
 #' model.
-globalaction_tool_logit <- function(
+globalevent_tool_logit <- function(
   tool, vars, coefs,
   name = get_name_tool(tool), day = -99
   ) {
 
   stopifnot_tool(tool)
 
   structure(
-    globalaction_tool_logit_cpp(
+    globalevent_tool_logit_cpp(
       tool,
       as.integer(vars),
       as.double(coefs),
       name,
       as.integer(day)
       ),
-    class = c("epiworld_globalaction_tool_logit", "epiworld_globalaction"),
+    class = c("epiworld_globalevent_tool_logit", "epiworld_globalevent"),
     tool = tool,
     call = match.call()
   )
 
 }
 
+#' @export
+#' @rdname epiworldR-deprecated
+globalaction_tool_logit <- function(...) {
+
+  .Deprecated(
+    new = "globalevent_tool_logit"
+    )  
+
+  globalevent_tool_logit(...)
+
+}
+
 #' @export 
 #' @param param Character scalar. The name of the parameter to be set.
 #' @param value Numeric scalar. The value of the parameter.
 #' @rdname global-actions
-#' @details The function `globalaction_set_param` allows to set a parameter of
+#' @details The function `globalevent_set_param` allows to set a parameter of
 #' the model. The parameter is specified by its name `param` and the value by
 #' `value`.
-globalaction_set_params <- function(
+globalevent_set_params <- function(
   param, value,
   name = paste0("Set ", param, " to ", value), day = -99
   ) {
 
   structure(
-    globalaction_set_param_cpp(
+    globalevent_set_param_cpp(
       param,
       as.double(value),
       name,
       as.integer(day)
       ),
-    class = c("epiworld_globalaction_set_param", "epiworld_globalaction"),
+    class = c("epiworld_globalevent_set_param", "epiworld_globalevent"),
     param = param,
     value = as.double(value),
     call = match.call()
   )
 }
 
+#' @export
+#' @rdname epiworldR-deprecated
+globalaction_set_params <- function(...) {
+
+  .Deprecated(
+    new = "globalevent_set_params"
+    )  
+
+  globalevent_set_params(...)
+
+}
+
 #' @export 
 #' @rdname global-actions
 #' @param fun Function. The function to be executed.
-#' @details The function `globalaction_fun` allows to specify a function to be
+#' @details The function `globalevent_fun` allows to specify a function to be
 #' executed at a given day. The function object must receive an object of class
 #' [epiworld_model] as only argument.
 #' @examples 
-#' # Example using `globalaction_fun` to record the state of the
+#' # Example using `globalevent_fun` to record the state of the
 #' # agents at each time step.
 #' 
 #' # We start by creating an SIR connected model
@@ -179,27 +215,39 @@ globalaction_set_params <- function(
 #'     )
 #'     
 #' }
-globalaction_fun <- function(
+globalevent_fun <- function(
   fun, name = deparse(substitute(fun)), day = -99
   ) {
 
   structure(
-    globalaction_fun_cpp(fun, name, as.integer(day)),
-    class = c("epiworld_globalaction_fun", "epiworld_globalaction"),
+    globalevent_fun_cpp(fun, name, as.integer(day)),
+    class = c("epiworld_globalevent_fun", "epiworld_globalevent"),
     fun = fun,
     call = match.call()
   )
 
 }
 
 #' @export
-print.epiworld_globalaction <- function(x, ...) {
+#' @rdname epiworldR-deprecated
+globalaction_fun <- function(...) {
+
+  .Deprecated(
+    new = "globalevent_fun"
+    )  
+
+  globalevent_fun(...)
+
+}
+
+#' @export
+print.epiworld_globalevent <- function(x, ...) {
 
   print_global_action_cpp(x)
   cat("Call: ", deparse(attr(x, "call")), "\n")
   if (length(attr(x, "tool"))) {
     cat("Tool: ", get_name_tool(attr(x, "tool")), "\n")
-  } else if (inherits(x, "epiworld_globalaction_set_param")) {
+  } else if (inherits(x, "epiworld_globalevent_set_param")) {
     cat("Parameter: ", attr(x, "param"), "\n")
     cat("Value: ", attr(x, "value"), "\n")
   }
@@ -215,20 +263,20 @@ print.epiworld_globalaction <- function(x, ...) {
 #' @param name Character scalar. The name of the action.
 #' @rdname global-actions
 #' @seealso epiworld-model
-#' @details The function `add_global_action` adds a global action to a model.
+#' @details The function `add_globalevent` adds a global action to a model.
 #' The model checks for actions to be executed at each time step. If the added
 #' action matches the current time step, the action is executed. When `day` is
 #' negative, the action is executed at each time step. When `day` is positive,
 #' the action is executed at the specified time step.
 #' @returns
-#' - The function `add_global_action` returns the model with the added
+#' - The function `add_globalevent` returns the model with the added
 #' action.
-add_global_action <- function(model, action) {
+add_globalevent <- function(model, action) {
 
   if (length(attr(action, "tool")))
     add_tool_n(model, attr(action, "tool"), 0)
 
-  invisible(add_global_action_cpp(model, action))
+  invisible(add_globalevent_cpp(model, action))
 
 }
 

README.Rmd

@@ -205,7 +205,7 @@ net <- get_transmissions(sir)
 
 # Plotting
 library(epiworldR)
-library(netplot)
+library(epiworldR)
 x <- igraph::graph_from_edgelist(
   as.matrix(net[,2:3]) + 1
   )

README.md

@@ -346,7 +346,7 @@ net <- get_transmissions(sir)
 
 # Plotting
 library(epiworldR)
-library(netplot)
+library(epiworldR)
 #> Loading required package: grid
 x <- igraph::graph_from_edgelist(
   as.matrix(net[,2:3]) + 1