Cross village interaction

.github/workflows/R-CMD-check.yaml

@@ -27,7 +27,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v1
 
@@ -37,11 +37,11 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
 
       - name: Show testthat output
         if: always()

.gitignore

@@ -45,3 +45,8 @@ docs/
 
 # translation temp files
 po/*~
+
+results/*
+tests/testthat/test_results/
+tests/testthat/results*
+vignettes/results/*

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: villager
 Title: A Framework for Designing and Running Agent Based Models
-Version: 1.2.2
+Version: 2.0.0
 Authors@R: c(
   person(
     given = "Thomas",
     family = "Thelen",
     role = c("aut", "cre"),
-    email = "[email protected]"
+    email = "[email protected]"
   ),
   person(
     given = "Gerardo",
@@ -31,7 +31,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: false
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.1
 Depends: R (>= 3.5.0)
 Imports:
     readr,
@@ -46,7 +46,8 @@ Suggests:
     remotes,
     rmarkdown,
     testthat,
+    roxygen2,
+    pandoc,
 URL: https://github.com/zizroc/villager/
 BugReports: https://github.com/zizroc/villager/issues/
 VignetteBuilder: knitr
-

NAMESPACE

@@ -8,6 +8,7 @@ export(resource)
 export(resource_manager)
 export(simulation)
 export(village)
+export(village_manager)
 export(village_state)
 importFrom(R6,R6Class)
 importFrom(readr,write_csv)

R/simulation.R

@@ -12,7 +12,7 @@
 simulation <- R6::R6Class("simulation",
   public = list(
     length = NA,
-    villages = NA,
+    village_mgr = NA,
     writer = NA,
 
     #' Creates a new Simulation instance
@@ -24,7 +24,7 @@ simulation <- R6::R6Class("simulation",
     initialize = function(length,
                           villages,
                           writer = villager::data_writer$new()) {
-      self$villages <- villages
+      self$village_mgr <- village_manager$new(villages)
       self$length <- length
       self$writer <- writer
     },
@@ -33,16 +33,16 @@ simulation <- R6::R6Class("simulation",
     #'
     #' @return None
     run_model = function() {
-      for (village in self$villages) {
+      for (village in self$village_mgr$get_villages()) {
         village$set_initial_state()
       }
       # Loop over each village and run the user defined initial condition function. Index off of 1 because the
       # initial condition is set at 0
       current_step <- 1
       while (current_step <= self$length) {
         # Iterate the villages a single time step
-        for (village in self$villages) {
-          village$propagate(current_step)
+        for (village in self$village_mgr$get_villages()) {
+          village$propagate(current_step, self$village_mgr)
           self$writer$write(village$current_state, village$name)
         }
         current_step <- current_step + 1

R/village.R

@@ -13,6 +13,8 @@
 #'   }
 village <- R6::R6Class("village",
   public = list(
+    #' @field name Unique identifier for the village
+    identifier = NA,
     #' @field name An optional name for the village
     name = NA,
     #' @field initial_condition A function that sets the initial state of the village
@@ -47,7 +49,7 @@ village <- R6::R6Class("village",
       self$initial_condition <- initial_condition
       self$agent_mgr <- agent_manager$new(agent_class)
       self$resource_mgr <- resource_manager$new(resource_class)
-
+      self$identifier <- uuid::UUIDgenerate()
       # Check to see if the user supplied a single model, outside of a list
       # If so, put it in a vector because other code expects 'models' to be a list
       if (!is.list(models) && !is.null(models)) {
@@ -69,7 +71,7 @@ village <- R6::R6Class("village",
     #' to set initial conditions. See the set_initial_state method.
     #' @param current_step The current time step
     #' @return None
-    propagate = function(current_step) {
+    propagate = function(current_step, village_mgr) {
       # Create a new state representing this slice in time. Since many of the
       # values will be the same as the previous state, clone the previous state
       self$current_state <- self$previous_state$clone(deep = TRUE)
@@ -79,7 +81,7 @@ village <- R6::R6Class("village",
       for (model in self$models) {
         # Create a read only copy of the last state so that users can make decisions off of it
         self$previous_state <- self$current_state$clone(deep = TRUE)
-        model(self$current_state, self$previous_state, self$model_data, self$agent_mgr, self$resource_mgr
+        model(self$current_state, self$previous_state, self$model_data, self$agent_mgr, self$resource_mgr, village_mgr
         )
       }
       self$current_state$agent_states <- self$agent_mgr$get_states()

R/village_manager.R

@@ -0,0 +1,52 @@
+#' @export
+#' @title Village Manager
+#' @docType class
+#' @description This object manages all of the villages. It acts as an interface to them
+#' @section Methods:
+#' \describe{
+#'   \item{\code{initialize()}}{Creates a new manager}
+#'   \item{\code{get_villages()}}{Gets all of the villages that the manager has}
+#'   \item{\code{get_village()}}{Retrieves a specific village from the manager, by name}
+#'   \item{\code{add_village()}}{Adds a village to the manager}
+#'   }
+village_manager <- R6::R6Class(
+  "village_manager",
+  public = list(
+    #' @field villages A list of village objects
+    villages = NULL,
+    #' Creates a new, village manager
+    #' @description Get a new instance of a village_manager
+    initialize = function(villages) {
+      self$villages <- villages
+    },
+
+    #' Gets all of the managed villages
+    #'
+    #' @return A list of resources
+    get_villages = function() {
+      return(self$villages)
+    },
+
+    #' Gets a village given a village name
+    #'
+    #' @param name The name of the requested village
+    #' @return A village object
+    get_village = function(name) {
+      for (village in self$villages) {
+        if (village$name == name) {
+          return(village)
+        }
+      }
+    },
+
+    #' Adds a village to the manager.
+    #'
+    #' @param ... The villages to add
+    #' @return None
+    add_resource = function(...) {
+      for (new_village in list(...)) {
+        self$villages <- append(self$villages, new_village)
+      }
+    }
+  )
+)

README.md

@@ -46,7 +46,7 @@ test_model <- function(current_state, previous_state, model_data, agent_mgr, res
 Agents are created by instantiating the `agent` class. There are a number of agent properties that can be passed to the constructor.
 
 ```{r}
-test_model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr) {
+test_model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr, village_mgr) {
   mother <- agent$new(first_name="Kirsten", last_name="Taylor", age=9125)
   father <- agent$new(first_name="Joshua", last_name="Thompson", age=7300)
   daughter <- agent$new(first_name="Mariylyyn", last_name="Thompson", age=10220)
@@ -56,7 +56,7 @@ test_model <- function(current_state, previous_state, model_data, agent_mgr, res
 To add agents to the simulation, use the provided `agent_mgr` object to call `add_agent`. Because the classes are R6, the object can be modified after being added to the manager and the changes will be persisted without needing to re-add the villager. For example, setting a daughter's mother and her father below. Note that the standard way is to modify the properties _beforehand_, although not strictly necessary.
 
 ```{r}
-test_model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr) {
+test_model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr, village_mgr) {
   agent_mgr <- agent_manager$new()
   agent_mgr$add_agent(mother, father, daughter)
   daughter$mother_id <- mother$identifier
@@ -74,7 +74,7 @@ agent_mgr$agent_mgr$connect_agents(mother, father)
 Resources are similar to agents in that they're both R6 classes, are instantiated similarly, and are also managed by an object passed into the model. An example of creating resources and adding them to the simulation is given below.
 
 ```
-test_model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr) {
+test_model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr, village_mgr) {
   corn_resource <- resource$new(name="corn", quantity = 10)
   fish_resource <- resource$new(name="fish", quantity = 15)
   corn_resource$quantity=5
@@ -161,7 +161,7 @@ initial_condition <- function(current_state, model_data, agent_mgr, resource_mgr
   resource_mgr$add_resource(corn_resource, fish_resource)
 }
 
-test_model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr) {
+test_model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr, village_mgr) {
 print(paste("Step:", current_state$step))
   for (agent in agent_mgr$get_living_agents()) {
     agent$age <- agent$age+1
@@ -185,9 +185,16 @@ To demonstrate programatically creating villagers, consider the model below that
 - Every odd day, one villager dies
 
 ```
-library(villager)
+  initial_condition <- function(current_state, model_data, agent_mgr, resource_mgr) {
+    for (i in 1:10) {
+      name <- runif(1, 0.0, 100)
+      new_agent <- agent$new(first_name <- name, last_name <- "Smith")
+      agent_mgr$add_agent(new_agent)
+    }
+  }
+
+  model <- function(current_state, previous_state, model_data, agent_mgr, resource_mgr, village_mgr) {
     current_day <- current_state$step
-    print(current_day)
     if((current_day%%2) == 0) {
       # Then it's an even day
       # Create two new agents whose first names are random numbers
@@ -206,7 +213,6 @@ library(villager)
   coastal_village <- village$new("Test village", initial_condition, model)
   simulator <- simulation$new(4, villages = list(coastal_village))
   simulator$run_model()
-  mgr <- simulator$villages[[1]]$agent_mgr
 ```
 
 ## Advanced Usage