inst/doc/simdesign-examples.R

In nlrx: Setup, Run and Analyze 'NetLogo' Model Simulations from 'R' via 'XML'

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval=FALSE---------------------------------------------------------------
# library(nlrx)
# # Windows default NetLogo installation path (adjust to your needs!):
# netlogopath <- file.path("C:/Program Files/NetLogo 6.0.3")
# modelpath <- file.path(netlogopath, "app/models/Sample Models/Biology/Wolf Sheep Predation.nlogo")
# outpath <- file.path("C:/out")
# # Unix default NetLogo installation path (adjust to your needs!):
# netlogopath <- file.path("/home/NetLogo 6.0.3")
# modelpath <- file.path(netlogopath, "app/models/Sample Models/Biology/Wolf Sheep Predation.nlogo")
# outpath <- file.path("/home/out")
# 
# nl <- nl(nlversion = "6.0.3",
#          nlpath = netlogopath,
#          modelpath = modelpath,
#          jvmmem = 1024)

## ----eval=FALSE---------------------------------------------------------------
# nl@experiment <- experiment(expname="wolf-sheep",
#                             outpath="C:/out/",
#                             repetition=1,
#                             tickmetrics="true",
#                             idsetup="setup",
#                             idgo="go",
#                             idfinal=NA_character_,
#                             idrunnum=NA_character_,
#                             runtime=50,
#                             evalticks=seq(40,50),
#                             metrics=c("count sheep", "count wolves", "count patches with [pcolor = green]"),
#                             variables = list(),
#                             constants = list("initial-number-sheep" = 20,
#                                              "initial-number-wolves" = 20,
#                                              "model-version" = "\"sheep-wolves-grass\"",
#                                              "grass-regrowth-time" = 30,
#                                              "sheep-gain-from-food" = 4,
#                                              "wolf-gain-from-food" = 20,
#                                              "sheep-reproduce" = 4,
#                                              "wolf-reproduce" = 5,
#                                              "show-energy?" = "false"))
# 
# nl@simdesign <- simdesign_simple(nl=nl,
#                                  nseeds=3)

## ----eval=FALSE---------------------------------------------------------------
# nl@experiment <- experiment(expname="wolf-sheep",
#                             outpath="C:/out/",
#                             repetition=1,
#                             tickmetrics="true",
#                             idsetup="setup",
#                             idgo="go",
#                             idfinal=NA_character_,
#                             idrunnum=NA_character_,
#                             runtime=50,
#                             evalticks=seq(40,50),
#                             metrics=c("count sheep", "count wolves", "count patches with [pcolor = green]"),
#                             variables = list('initial-number-sheep' = list(values=c(10, 20, 30, 40)),
#                                              'initial-number-wolves' = list(values=c(30, 40, 50, 60))),
#                             constants = list("model-version" = "\"sheep-wolves-grass\"",
#                                              "grass-regrowth-time" = 30,
#                                              "sheep-gain-from-food" = 4,
#                                              "wolf-gain-from-food" = 20,
#                                              "sheep-reproduce" = 4,
#                                              "wolf-reproduce" = 5,
#                                              "show-energy?" = "false"))
# 
# nl@simdesign <- simdesign_distinct(nl=nl,
#                                    nseeds=3)

## ----eval=FALSE---------------------------------------------------------------
# nl@experiment <- experiment(expname="wolf-sheep",
#                             outpath="C:/out/",
#                             repetition=1,
#                             tickmetrics="true",
#                             idsetup="setup",
#                             idgo="go",
#                             idfinal=NA_character_,
#                             idrunnum=NA_character_,
#                             runtime=50,
#                             evalticks=seq(40,50),
#                             metrics=c("count sheep", "count wolves", "count patches with [pcolor = green]"),
#                             variables = list('initial-number-sheep' = list(values=c(10, 20, 30, 40)),
#                                              'initial-number-wolves' = list(min=0, max=50, step=10)),
#                             constants = list("model-version" = "\"sheep-wolves-grass\"",
#                                              "grass-regrowth-time" = 30,
#                                              "sheep-gain-from-food" = 4,
#                                              "wolf-gain-from-food" = 20,
#                                              "sheep-reproduce" = 4,
#                                              "wolf-reproduce" = 5,
#                                              "show-energy?" = "false"))
# 
# nl@simdesign <- simdesign_ff(nl=nl,
#                              nseeds=3)

## ----eval=FALSE---------------------------------------------------------------
# nl@experiment <- experiment(expname="wolf-sheep",
#                             outpath="C:/out/",
#                             repetition=1,
#                             tickmetrics="true",
#                             idsetup="setup",
#                             idgo="go",
#                             idfinal=NA_character_,
#                             idrunnum=NA_character_,
#                             runtime=50,
#                             evalticks=seq(40,50),
#                             metrics=c("count sheep", "count wolves", "count patches with [pcolor = green]"),
#                             variables = list('initial-number-sheep' = list(min=50, max=150, qfun="qunif"),
#                                              'initial-number-wolves' = list(min=50, max=150, qfun="qunif")),
#                             constants = list("model-version" = "\"sheep-wolves-grass\"",
#                                              "grass-regrowth-time" = 30,
#                                              "sheep-gain-from-food" = 4,
#                                              "wolf-gain-from-food" = 20,
#                                              "sheep-reproduce" = 4,
#                                              "wolf-reproduce" = 5,
#                                              "show-energy?" = "false"))
# 
# nl@simdesign <- simdesign_lhs(nl=nl,
#                                samples=100,
#                                nseeds=3,
#                                precision=3)
# 

## ----eval=FALSE---------------------------------------------------------------
# nl@experiment <- experiment(expname="wolf-sheep",
#                             outpath="C:/out/",
#                             repetition=1,
#                             tickmetrics="true",
#                             idsetup="setup",
#                             idgo="go",
#                             idfinal=NA_character_,
#                             idrunnum=NA_character_,
#                             runtime=50,
#                             evalticks=seq(40,50),
#                             metrics=c("count sheep", "count wolves", "count patches with [pcolor = green]"),
#                             variables = list('initial-number-sheep' = list(min=50, max=150, qfun="qunif"),
#                                              'initial-number-wolves' = list(min=50, max=150, qfun="qunif")),
#                             constants = list("model-version" = "\"sheep-wolves-grass\"",
#                                              "grass-regrowth-time" = 30,
#                                              "sheep-gain-from-food" = 4,
#                                              "wolf-gain-from-food" = 20,
#                                              "sheep-reproduce" = 4,
#                                              "wolf-reproduce" = 5,
#                                              "show-energy?" = "false"))
# 
# nl@simdesign <- simdesign_lhs(nl=nl,
#                                samples=100,
#                                nseeds=3,
#                                precision=3)
# 
# 
# nl@simdesign <- simdesign_sobol(nl=nl,
#                                  samples=200,
#                                  sobolorder=2,
#                                  sobolnboot=20,
#                                  sobolconf=0.95,
#                                  nseeds=3,
#                                  precision=3)
# 
# nl@simdesign <- simdesign_sobol2007(nl=nl,
#                                      samples=200,
#                                      sobolnboot=20,
#                                      sobolconf=0.95,
#                                      nseeds=3,
#                                      precision=3)
# 
# nl@simdesign <- simdesign_soboljansen(nl=nl,
#                                        samples=200,
#                                        sobolnboot=20,
#                                        sobolconf=0.95,
#                                        nseeds=3,
#                                        precision=3)
# 
# 
# nl@simdesign <- simdesign_morris(nl=nl,
#                                   morristype="oat",
#                                   morrislevels=4,
#                                   morrisr=100,
#                                   morrisgridjump=2,
#                                   nseeds=3)
# 
# nl@simdesign <- simdesign_eFast(nl=nl,
#                                  samples=100,
#                                  nseeds=3)

## ----eval=FALSE---------------------------------------------------------------
# nl@experiment <- experiment(expname="wolf-sheep",
#                             outpath="C:/out/",
#                             repetition=1,
#                             tickmetrics="true",
#                             idsetup="setup",
#                             idgo="go",
#                             idfinal=NA_character_,
#                             idrunnum=NA_character_,
#                             runtime=50,
#                             evalticks=seq(40,50),
#                             metrics=c("count sheep", "count wolves", "count patches with [pcolor = green]"),
#                             variables = list('initial-number-sheep' = list(min=50, max=150),
#                                              'initial-number-wolves' = list(min=50, max=150)),
#                             constants = list("model-version" = "\"sheep-wolves-grass\"",
#                                              "grass-regrowth-time" = 30,
#                                              "sheep-gain-from-food" = 4,
#                                              "wolf-gain-from-food" = 20,
#                                              "sheep-reproduce" = 4,
#                                              "wolf-reproduce" = 5,
#                                              "show-energy?" = "false"))
# 
# nl@simdesign <- simdesign_GenAlg(nl=nl,
#                                  popSize = 200,
#                                  iters = 100,
#                                  evalcrit = 1,
#                                  elitism = NA,
#                                  mutationChance = NA,
#                                  nseeds = 1)
# 
# nl@simdesign <- simdesign_GenSA(nl=nl,
#                                 par=NULL,
#                                 evalcrit=1,
#                                 control=list(max.time = 600),
#                                 nseeds=1)
# 

## ----eval=FALSE---------------------------------------------------------------
# nl@experiment <- experiment(expname="wolf-sheep",
#                             outpath="C:/out/",
#                             repetition=1,
#                             tickmetrics="true",
#                             idsetup="setup",
#                             idgo="go",
#                             idfinal=NA_character_,
#                             idrunnum=NA_character_,
#                             runtime=50,
#                             evalticks=seq(40,50),
#                             metrics=c("count sheep", "count wolves", "count patches with [pcolor = green]"),
#                             variables = list('initial-number-sheep' = list(min=50, max=150),
#                                              'initial-number-wolves' = list(min=50, max=150)),
#                             constants = list("model-version" = "\"sheep-wolves-grass\"",
#                                              "grass-regrowth-time" = 30,
#                                              "sheep-gain-from-food" = 4,
#                                              "wolf-gain-from-food" = 20,
#                                              "sheep-reproduce" = 4,
#                                              "wolf-reproduce" = 5,
#                                              "show-energy?" = "false"))
# 
# nl@simdesign <- simdesign_ABCmcmc_Marjoram(nl=nl,
#                                            summary_stat_target = c(100, 80),
#                                            n_rec = 100,
#                                            n_calibration=200,
#                                            use_seed = TRUE,
#                                            progress_bar = TRUE,
#                                            nseeds = 1)
# 
# nl@simdesign <- simdesign_ABCmcmc_Marjoram_original(nl=nl,
#                                            summary_stat_target = c(100, 80),
#                                            n_rec = 10,
#                                            use_seed = TRUE,
#                                            progress_bar = TRUE,
#                                            nseeds = 1)
# 
# nl@simdesign <- simdesign_ABCmcmc_Wegmann(nl=nl,
#                                           summary_stat_target = c(100, 80),
#                                           n_rec = 10,
#                                           n_calibration=200,
#                                           use_seed = TRUE,
#                                           progress_bar = TRUE,
#                                           nseeds = 1)
#