vignettes/i-introduction.R

In PredictiveEcology/SpaDES.core: Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

## ----setup, include=FALSE-----------------------------------------------------
SuggestedPkgsNeeded <- c("knitr", "NLMR", "SpaDES.tools")
hasSuggests <- all(sapply(SuggestedPkgsNeeded, require, character.only = TRUE, quietly = TRUE))
useSuggests <- !(tolower(Sys.getenv("_R_CHECK_DEPENDS_ONLY_")) == "true")

knitr::opts_chunk$set(eval = hasSuggests && useSuggests)

options(spades.moduleCodeChecks = FALSE,
        spades.useRequire = FALSE)

## ----SpaDES-demo, eval=FALSE, echo=TRUE---------------------------------------
#  ## NOTE: Suggested packages SpaDES.tools and NLMR packages must be installed
#  #install.packages("SpaDES.taols")
#  #install.packages("NLMR", repos = "https://predictiveecology.r-universe.dev/")
#  
#  knitr::opts_chunk$set(eval = requireNamespace("SpaDES.tools") && !requireNamespace("NLMR"))
#  
#  library(SpaDES.core)
#  
#  demoSim <- suppressMessages(simInit(
#    times = list(start = 0, end = 100),
#    modules = "SpaDES_sampleModules",
#    params = list(
#      .globals = list(burnStats = "nPixelsBurned"),
#      randomLandscapes = list(
#        nx = 1e2, ny = 1e2, .saveObjects = "landscape",
#        .plotInitialTime = NA, .plotInterval = NA, inRAM = TRUE
#      ),
#      caribouMovement = list(
#        N = 1e2, .saveObjects = "caribou",
#        .plotInitialTime = 1, .plotInterval = 1, moveInterval = 1
#      ),
#      fireSpread = list(
#        nFires = 1e1, spreadprob = 0.235, persistprob = 0, its = 1e6,
#        returnInterval = 10, startTime = 0,
#        .plotInitialTime = 0, .plotInterval = 10
#      )
#    ),
#    path = list(modulePath = getSampleModules(tempdir()))
#  ))
#  spades(demoSim)

## ----SpaDES-modules, eval=FALSE, echo=TRUE------------------------------------
#  downloadModule(name = "moduleName")

## ----view-sim, eval=FALSE, echo=TRUE------------------------------------------
#  # full simulation details:
#  #  simList object info + simulation data
#  mySim
#  
#  # less detail:
#  # simList object isn't shown; object details are
#  ls.str(mySim)
#  
#  # least detail:
#  # simList object isn't shown; object names only
#  ls(mySim)

## ----view-dependencies, eval=FALSE, echo=TRUE---------------------------------
#  library(igraph)
#  library(DiagrammeR)
#  depsEdgeList(mySim, FALSE)  # data.frame of all object dependencies
#  moduleDiagram(mySim)        # plots simplified module (object) dependency graph
#  objectDiagram(mySim)        # plots object dependency diagram

## ----view-event-sequences, eval=FALSE, echo=TRUE------------------------------
#  options(spades.nCompleted = 50)   # default: store 1000 events in the completed event list
#  mySim <- simInit(...)             # initialize a simulation using valid parameters
#  mySim <- spades(mySim)            # run the simulation, returning the completed sim object
#  eventDiagram(mySim)               # visualize the sequence of events for all modules