knitr::opts_chunk$set(cache = TRUE, echo = TRUE, eval = FALSE)
SpaDES
packageLoad the following packages:
igraph
rgdal
SpaDES
library(igraph) library(rgdal) library(SpaDES) if (packageVersion("SpaDES") < "1.3.1.9016") stop("Please update your version of SpaDES to the latest development version.")
simList
objectemptySim <- simInit()
simList
object?'.simList-class'
.str(emptySim) slotNames(emptySim) getSlots('simList') ?'.simList-class'
This code is based on the SpaDES
package demo.
set.seed(42) filelist <- data.frame( files = dir(system.file("maps", package = "quickPlot"), full.names = TRUE, pattern = "tif"), functions = "rasterToMemory", packages = "SpaDES.core", stringsAsFactors = FALSE ) # create the simList object 'mySim' mySim <- simInit( times = list(start = 0.0, end = 100.00), params = list( .progress = list(type = NA, interval = NA), .globals = list(burnStats = "nPixelsBurned"), randomLandscapes = list( nx = 1e2, ny = 1e2, .saveObjects = "landscape", .plotInitialTime = NA, .plotInterval = NA, inRAM = TRUE ), caribouMovement = list( N = 1e2, .saveObjects = c("caribou"), .plotInitialTime = 1, .plotInterval = 1, moveInterval = 1 ), fireSpread = list( nFires = 1e1, spreadprob = 0.235, persistprob = 0, its = 1e6, returnInterval = 10, startTime = 0, .plotInitialTime = 0, .plotInterval = 10 ) ), modules = list("randomLandscapes", "fireSpread", "caribouMovement"), inputs = filelist, paths = list(modulePath = system.file("sampleModules", package = "SpaDES.core")) ) mySim$landscape <- stack(mySim$DEM, mySim$forestAge, mySim$habitatQuality, mySim$percentPine)
simList
objectUse the simList accessor functions to determine the following:
# list modules used in the simulation modules(mySim) # list module dependencies and packages used depends(mySim) packages(mySim) # list global and module-specific param values globals(mySim) params(mySim) P(mySim) ## bonus: how do params() and P() differ? # list start and end times times(mySim) start(mySim) end(mySim) # get the simulation and module timeunits timeunit(mySim) timeunits(mySim) # get the scheduled and completed event queues events(mySim) completed(mySim) # list the objects (functions, data, etc.) stored in the simList objects(mySim) # list the file paths used in the simulation paths(mySim) inputPath(mySim) outputPath(mySim)
dev() mySimOut <- Copy(mySim) ## make a deep copy of the simList mySimOut <- spades(mySimOut)
times(mySim) times(mySimOut) objects(mySim) objects(mySimOut)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.