Nothing
## ----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
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