removed SimData class

R/simulation-classes.R

@@ -49,29 +49,3 @@ setClass("SimList",
          slots=list(.loaded="list", modules="list", params="list",
                     events="data.table", simtime="numeric", debug="logical"
 ))
-
-
-
-#' The \code{SimData} class
-#'
-#' This class store data used by and generated in a simulation.
-#'
-#' An object of class SimData contains: 
-#'      agents: custom list of agents used in the simulation;
-#'      maps: custom list of maps loaded or generated by the simulation;
-#'      stats: custom list of stats collected during the simulation.
-#'
-#' @slot agents The list of agents, as an agent class (or subclass).
-#' 
-#' @slot maps   The list(s) of maps, as raster class (raster package) or Spatial class (sp package).
-#' 
-#' @slot stats  The list(s) of statistics.
-#'
-#' @note add additional notes here.
-#' 
-#' @name SimData 
-#' @rdname SimData-class
-#' @aliases SimData-class
-#' @exportClass SimData
-setClass("SimData", slots=list(agents="list", maps="list", stats="list"))
-# setClass("SimData", slots=list(agents="AgentsList", maps="MapsList", stats="StatsList"))

R/simulation-methods.R

@@ -216,74 +216,6 @@ setReplaceMethod("sim.debug",
 
 
 
-setGeneric("sim.agents", function(object) {
-    standardGeneric("sim.agents")
-})
-
-setMethod("sim.agents",
-          signature = "SimData",
-          definition = function(object) {
-              return(object@agents)
-})
-
-setGeneric("sim.agents<-",
-           function(object, value) {
-               standardGeneric("sim.agents<-")
-})
-
-setReplaceMethod("sim.agents",
-                 signature="SimData",
-                 function(object, value) {
-                     object@agents <- value
-                     validObject(object)
-                     return(object)
-})
-
-setGeneric("sim.maps", function(object) {
-    standardGeneric("sim.maps")
-})
-
-setMethod("sim.maps",
-          signature = "SimData",
-          definition = function(object) {
-              return(object@maps)
-})
-
-setGeneric("sim.maps<-",
-           function(object, value) {
-               standardGeneric("sim.maps<-")
-})
-
-setReplaceMethod("sim.maps",
-                 signature="SimData",
-                 function(object, value) {
-                     object@maps <- value
-                     validObject(object)
-                     return(object)
-})
-
-setGeneric("sim.stats", function(object) {
-    standardGeneric("sim.stats")
-})
-
-setMethod("sim.stats",
-          signature = "SimData",
-          definition = function(object) {
-              return(object@stats)
-})
-
-setGeneric("sim.stats<-",
-           function(object, value) {
-               standardGeneric("sim.stats<-")
-})
-
-setReplaceMethod("sim.stats",
-                 signature="SimData",
-                 function(object, value) {
-                     object@stats <- value
-                     validObject(object)
-                     return(object)
-})
 
 
 
@@ -317,7 +249,6 @@ sim.init <- function(params, modules, path) {
     path <- check.path(path)
 
     sim <<- new("SimList")
-    sim.data <<- new("SimData")
 
     # load simulation parameters and modules
     sim.params(sim) <<- params
@@ -328,7 +259,6 @@ sim.init <- function(params, modules, path) {
     }
     # set up first event(s): all first events should be initialization events e.g. from modules
     #    schedule.event(EVENT.TIME, "MODULE.NAME", "EVENT.TYPE", list(OPTIONAL.ITEMS))
-    schedule.event(0.00, "observer", "init") # needs optional flags for plotting, etc.
     for (m in modules) {
         schedule.event(0.00, m, "init")
     }

SAMPLE/caribou.R

@@ -51,7 +51,6 @@ caribou.init = function() {
     pkgs = list("raster") # list required packages here
     load.packages(pkgs)
 
-    hab = get.habitat.map() # from habitat module
     best = max(hab@data@values)
     worst = min(hab@data@values)
     good = Which(hab>0.8*best)
@@ -61,24 +60,14 @@ caribou.init = function() {
     na = NumAgents(100)         # could be specified globally in params
 
     # initialize caribou agents
-    caribou = new("mobileAgent", agentlocation=al, numagents= na, probinit=pri)
+    caribou <<- new("mobileAgent", agentlocation=al, numagents= na, probinit=pri)
     points(caribou, pch=19, cex=0.1)
 
-    ### module parameters
-    #   - export module params to global list
-    sim.agents(sim.data) <<- list(caribou=caribou)
-
-    #   -  export data structure for module stats
-#    sim.stats(sim.data)[["caribou"]] <<- list()
-
     # last thing to do is add module name to the loaded list
     sim.loaded(sim) <<- append(sim.loaded(sim), "caribou")
 }
 
 caribou.move = function() {
-    hab = get.habitat.map() # from habitat module
-    caribou = get.caribou.population() # see below
-
     ex =  hab[position(caribou)] # find out what pixels the individuals are on now
     wh = which(!is.na(ex))
     if (length(wh)==0) stop(paste("all agents off map at time", sim.time(sim)))
@@ -88,20 +77,13 @@ caribou.move = function() {
     ln = rlnorm(length(ex), sl, 0.02) # log normal step length
     dir.sd = 30 # could be specified globally in params
 
-    caribou = crw(caribou, step.len=ln , dir.sd=dir.sd)
+    caribou <<- crw(caribou, step.len=ln , dir.sd=dir.sd)
     points(caribou, pch=19, cex = 0.1)
 
     rads = sample(10:30, length(caribou), replace=TRUE)
     rings = cir(caribou, radiuses=rads, hab, 1)
     points(rings$x, rings$y, col=rings$ids, pch=19, cex=0.1)
     dev.flush()
-
-    sim.agents(sim.data)["caribou"] <<- caribou
 }
 
 ### user-defined subroutines
-
-get.caribou.population = function() {
-    pop = sim.agents(sim.data)$caribou
-    return(pop)
-}

SAMPLE/habitat.R

@@ -45,26 +45,14 @@ habitat.init = function() {
     ### initialize habitat
     nx = 5e2 # could be specified globally in params
     ny = 5e2 # could be specified globally in params
-    hab <- raster(nrows=ny, ncols=nx, xmn=-nx/2, xmx=nx/2, ymn = -ny/2, ymx = ny/2)
-    hab <- round(GaussMap(extent(hab), speedup=10), 1)
+    hab <<- raster(nrows=ny, ncols=nx, xmn=-nx/2, xmx=nx/2, ymn = -ny/2, ymx = ny/2)
+    hab <<- round(GaussMap(extent(hab), speedup=10), 1)
     plot(hab)
     dev.flush()
 
-    ### module parameters
-    #   - export module params to global list
-    sim.maps(sim.data)[["habitat"]] <<- list(quality=hab)
-
-    #   -  export data structure for module stats
-#    sim.stats(sim.data)[["habitat"]] <<- list()
-
     # last thing to do is add module name to the loaded list
     sim.loaded(sim) <<- append(sim.loaded(sim), "habitat")
 }
 
 
 ### user-defined subroutines
-
-get.habitat.map = function() {
-    map = sim.maps(sim.data)$habitat$quality
-    return(map)
-}