Package: nlrx 0.4.5

Sebastian Hanss

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

Setup, run and analyze 'NetLogo' (<https://ccl.northwestern.edu/netlogo/>) model simulations in 'R'. 'nlrx' experiments use a similar structure as 'NetLogos' Behavior Space experiments. However, 'nlrx' offers more flexibility and additional tools for running and analyzing complex simulation designs and sensitivity analyses. The user defines all information that is needed in an intuitive framework, using class objects. Experiments are submitted from 'R' to 'NetLogo' via 'XML' files that are dynamically written, based on specifications defined by the user. By nesting model calls in future environments, large simulation design with many runs can be executed in parallel. This also enables simulating 'NetLogo' experiments on remote high performance computing machines. In order to use this package, 'Java' and 'NetLogo' (>= 5.3.1) need to be available on the executing system.

Authors:Jan Salecker [aut], Marco Sciaini [aut], Marina Papadopoulou [rev], Sebastian Hanss [cre]

nlrx_0.4.5.tar.gz
nlrx_0.4.5.zip(r-4.5)nlrx_0.4.5.zip(r-4.4)nlrx_0.4.5.zip(r-4.3)
nlrx_0.4.5.tgz(r-4.4-any)nlrx_0.4.5.tgz(r-4.3-any)
nlrx_0.4.5.tar.gz(r-4.5-noble)nlrx_0.4.5.tar.gz(r-4.4-noble)
nlrx_0.4.5.tgz(r-4.4-emscripten)nlrx_0.4.5.tgz(r-4.3-emscripten)
nlrx.pdf |nlrx.html
nlrx/json (API)
NEWS

# Install nlrx in R:
install.packages('nlrx', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/nlrx/issues

Datasets:
  • nl_distinct - Wolf Sheep model sample data: simdesign distinct
  • nl_eFast - Wolf Sheep model sample data: simdesign eFast
  • nl_ff - Wolf Sheep model sample data: simdesign ff
  • nl_gensa - Wolf Sheep model sample data: gensa
  • nl_lhs - Wolf Sheep model sample data: simdesign lhs
  • nl_morris - Wolf Sheep model sample data: simdesign morris
  • nl_simple - Wolf Sheep model sample data: simdesign simple
  • nl_sobol - Wolf Sheep model sample data: simdesign sobol
  • nl_sobol2007 - Wolf Sheep model sample data: simdesign sobol2007
  • nl_soboljansen - Wolf Sheep model sample data: simdesign soboljansen
  • nl_spatial - Wolf Sheep model sample data: spatial

On CRAN:

agent-based-modelingindividual-based-modellingnetlogopeer-reviewed

44 exports 75 stars 3.82 score 126 dependencies 285 downloads

Last updated 5 months agofrom:7f0d6c6d922ee4121a7735d3ec1f18dba3ce6994 (via master)

Exports:%>%analyze_nlcheck_netlogo_versiondownload_netlogoeval_simoutputeval_variables_constantsexperimentexport_nlgetexpgetnlgetsimimport_nlnlnl_to_graphnl_to_pointsnl_to_rasternldocnldoc_networkreport_model_parametersrun_nl_allrun_nl_dynrun_nl_onesetexp<-setnl<-setsim<-simdesignsimdesign_ABCmcmc_Marjoramsimdesign_ABCmcmc_Marjoram_originalsimdesign_ABCmcmc_Wegmannsimdesign_distinctsimdesign_eFastsimdesign_ffsimdesign_GenAlgsimdesign_GenSAsimdesign_lhssimdesign_morrissimdesign_simplesimdesign_sobolsimdesign_sobol2007simdesign_soboljansensupported_netlogo_versionstest_nlrxunnest_simoutputwrite_simoutput

Dependencies:abcabc.database64encbitbit64bootbslibcachemclassclassIntclicliprclueclustercodetoolscolorspacecommonmarkcpp11crayonDBIdigestdplyrdtwdtwcluste1071EasyABCfansifarverfastmapflexclustfontawesomeforeachfsfurrrfuturegenalggenericsGenSAggplot2ggrepelglobalsgluegtablehmshtmltoolshttpuvigraphisobanditeratorsjquerylibjsonliteKernSmoothlabelinglaterlatticelhslifecyclelistenvlocfitmagrittrMASSMatrixMatrixModelsmemoisemgcvmimemnormtmodeltoolsmunsellnlmennetnumbersparallellypillarpkgconfigplsplyrprettyunitsprogressprogressrpromisesproxypurrrquantregR6rappdirsrasterRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppThreadreadrreshape2rlangRSpectrarstudioapis2sassscalessensitivitysfshinyshinyjssourcetoolsspSparseMstringistringrsurvivaltensorAterratibbletidyrtidyselecttzdbunitsutf8vctrsviridisLitevroomwithrwkXMLxtable

Advanced configuration

Rendered fromfurthernotes.Rmdusingknitr::rmarkdownon Jun 08 2024.

Last update: 2023-05-15
Started: 2018-12-19

Approximate Bayesian Computation (ABC)

Rendered fromabc.Rmdusingknitr::rmarkdownon Jun 08 2024.

Last update: 2020-12-17
Started: 2019-10-30

Get Started

Rendered fromgetstarted.Rmdusingknitr::rmarkdownon Jun 08 2024.

Last update: 2023-05-11
Started: 2018-08-14

Optimization

Rendered fromoptimization.Rmdusingknitr::rmarkdownon Jun 08 2024.

Last update: 2020-12-17
Started: 2019-09-23

Sensitivity Analysis

Rendered fromsensitivity.Rmdusingknitr::rmarkdownon Jun 08 2024.

Last update: 2020-12-17
Started: 2019-09-23

Simdesign examples

Rendered fromsimdesign-examples.Rmdusingknitr::rmarkdownon Jun 08 2024.

Last update: 2023-05-15
Started: 2018-08-22

Readme and manuals

Help Manual

Help pageTopics
nlrx: A package for running NetLogo simulations from R.nlrx-package nlrx
Analyze NetLogo simulation outputanalyze_nl
Check supported NetLogo versionscheck_netlogo_version
Download NetLogodownload_netlogo
Evaluate input/output integrityeval_simoutput
Evaluate variable validityeval_variables_constants
Construct a new experiment objectexperiment
Export NetLogo Experimentexport_nl
Getter function to get a variable of an experiment objectgetexp
Getter function to get a variable of a nl objectgetnl
Getter function to get a variable of a simdesign objectgetsim
Import NetLogo Experimentimport_nl
Construct a new nl objectnl
Wolf Sheep model sample data: simdesign distinctnl_distinct
Wolf Sheep model sample data: simdesign eFastnl_eFast
Wolf Sheep model sample data: simdesign ffnl_ff
Wolf Sheep model sample data: gensanl_gensa
Wolf Sheep model sample data: simdesign lhsnl_lhs
Wolf Sheep model sample data: simdesign morrisnl_morris
Wolf Sheep model sample data: simdesign simplenl_simple
Wolf Sheep model sample data: simdesign sobolnl_sobol
Wolf Sheep model sample data: simdesign sobol2007nl_sobol2007
Wolf Sheep model sample data: simdesign soboljansennl_soboljansen
Wolf Sheep model sample data: spatialnl_spatial
Generate igraph objects from measured turtles and links metricsnl_to_graph
Get spatial data from metrics.turtles outputnl_to_points
Get spatial data from metrics.patches outputnl_to_raster
Create NetLogo documentationnldoc
Create NetLogo procedure networknldoc_network
Print content of nl objectprint.nl
Report globals from a NetLogo model that is defined within a nl objectreport_model_parameters
Execute all NetLogo simulations from a nl objectrun_nl_all
Execute NetLogo simulation without pregenerated parametersetsrun_nl_dyn
Execute one NetLogo simulation from a nl objectrun_nl_one
Setter function to set a variable of an experiment objectsetexp setexp<-
Setter function to set a variable of a nl objectsetnl setnl<-
Setter function to set a variable of a simdesign objectsetsim setsim<-
Construct a new simdesign objectsimdesign
Add an Approximate Bayesian Computation (Monte-Carlo Markov-Chain) simdesign using the Majoram algorithm to a nl objectsimdesign_ABCmcmc_Marjoram
Add an Approximate Bayesian Computation (Monte-Carlo Markov-Chain) simdesign using the Majoram Original algorithm to a nl objectsimdesign_ABCmcmc_Marjoram_original
Add an Approximate Bayesian Computation (Monte-Carlo Markov-Chain) simdesign using the Wegmann algorithm to a nl objectsimdesign_ABCmcmc_Wegmann
Add a distinct simdesign to a nl objectsimdesign_distinct
Add an eFast simdesign to a nl objectsimdesign_eFast
Add a full-factorial simdesign to a nl objectsimdesign_ff
Add a Genetic Algorithm simdesign to a nl objectsimdesign_GenAlg
Add a Simulated Annealing simdesign to a nl objectsimdesign_GenSA
Add a latin-hypercube simdesign to a nl objectsimdesign_lhs
Add a morris elementary effects simdesign to a nl objectsimdesign_morris
Add a simple simdesign to a nl objectsimdesign_simple
Add a sobol simdesign to a nl objectsimdesign_sobol
Add a sobol2007 simdesign to a nl objectsimdesign_sobol2007
Add a soboljansen simdesign to a nl objectsimdesign_soboljansen
Report supported NetLogo versionssupported_netlogo_versions
Test if nlrx runs on the local systemtest_nlrx
Get spatial data from metrics.turtles and metrics.patches outputunnest_simoutput
Write attached NetLogo simulation output to filewrite_simoutput