spartan: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan

Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.

Author
Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Date of publication
2015-10-19 23:57:19
Maintainer
Kieran Alden <kieran.alden@gmail.com>
License
GPL-2
Version
2.3

View on CRAN

Man pages

spartan-internal
Internal Functions
Technique1-aleatory_analysis
Technique 1: Aleatory Analysis
Technique2-oat_create_parameter_sample
Technique 2: One-At-A-Time - Generate Parameter Value Sets
Technique2-oat_generate_analysis
One-At-A-Time - Perform Analysis of Results
Technique3-lhc_create_parameter_sample
LHC
Technique3-lhc_perform_analysis
LHC: Perform Analysis of Results
Technique4-efast_create_parameter_sample
eFAST
Technique4-efast_generate_analysis_results
eFAST: Perform Analysis of Results
Technique5-spartan_and_netlogo
Technique 5: SPARTAN and Netlogo
Utility-getMediansSubset
Generate Medians Subset (getMediansSubset)
Utility-sampleData
Utility: Sample Data

Files in this package

spartan
spartan/inst
spartan/inst/extdata
spartan/inst/extdata/AA_5Samples.pdf
spartan/inst/extdata/Install_spartan.pdf
spartan/inst/extdata/chemoLowerLinearAdjust_DisplacementBP.pdf
spartan/inst/extdata/LHC_Folder_Struc.png
spartan/inst/extdata/eFAST_Displacement.pdf
spartan/inst/extdata/AA_Tutorial.pdf
spartan/inst/extdata/eFAST_Folder_Struc.png
spartan/inst/extdata/LHC_maxVCAMeffectProbabilityCutoff_Velocity.pdf
spartan/inst/extdata/AA_Folder_Struc.png
spartan/inst/extdata/OAT_Tutorial.pdf
spartan/inst/extdata/OAT_Folder_Struc.png
spartan/inst/extdata/LHC_chemoThreshold_Velocity.pdf
spartan/inst/extdata/Netlogo.pdf
spartan/inst/extdata/OAT_chemoUpperLinearAdjust.pdf
spartan/inst/extdata/OAT_chemoLowerLinearAdjust.pdf
spartan/inst/extdata/eFAST_Velocity.pdf
spartan/inst/extdata/AA_Results.pdf
spartan/inst/extdata/LHC_Tutorial.pdf
spartan/inst/extdata/Example_Simulation_Replicates_and_Medians.zip
spartan/inst/extdata/eFAST_Tutorial.pdf
spartan/NAMESPACE
spartan/data
spartan/data/OAT_Sampling_chemoThreshold_Values.csv.gz
spartan/data/AA_Example_ATestMaxAndMedians.csv.gz
spartan/data/EgSet_LHC_corCoeffs.csv.gz
spartan/data/eFAST_Analysis.csv.gz
spartan/data/OAT_Example_ATests_chemoLowerLinearAdjust.csv.gz
spartan/data/Curve1_thresholdBindProbability.csv.gz
spartan/data/Curve1_vcamSlope.csv.gz
spartan/data/LHC_Summary.csv.gz
spartan/data/OAT_Medians.csv.gz
spartan/data/Curve1_chemoLowerLinearAdjust.csv.gz
spartan/data/Curve1_chemoThreshold.csv.gz
spartan/data/Curve1_Dummy.csv.gz
spartan/data/Curve1_chemoUpperLinearAdjust.csv.gz
spartan/data/LHC_Parameters_for_Runs.csv.gz
spartan/data/Curve1_Results_Summary.csv.gz
spartan/data/OAT_Sampling_maxVCAMeffectProbabilityCutoff_Values.csv.gz
spartan/data/Curve1_maxVCAMeffectProbabilityCutoff.csv.gz
spartan/R
spartan/R/lhc_generate_netlogo_PRCoEffs.R
spartan/R/aa_summariseReplicateRuns.R
spartan/R/lhc_generate_lhc_sample_netlogo.R
spartan/R/oat_generate_netlogo_behaviour_space_XML.R
spartan/R/getMediansSubset.R
spartan/R/efast_parameterdist.R
spartan/R/efast_generate_sample.R
spartan/R/lhc_graphPRCCForMultipleTimepoints.R
spartan/R/plotATestsFromTimepointFiles.R
spartan/R/efast_netlogo_run_Analysis.R
spartan/R/oat_parameter_sampling.R
spartan/R/oat_graph_Leish_ATestsMultipleTimepoints.R
spartan/R/lhc_process_sample_run_subsets.R
spartan/R/efast_generate_sample_netlogo.R
spartan/R/efast_graph_Results.R
spartan/R/lhc_generate_lhc_sample.R
spartan/R/efast_get_overall_medians.R
spartan/R/efast_generate_medians_for_all_parameter_subsets.R
spartan/R/aa_graphSampleSizeSummary.R
spartan/R/oat_plotResultDistribution.R
spartan/R/efast_sd.R
spartan/R/prepare_parameter_value_list.R
spartan/R/table_header_check.R
spartan/R/normaliseATest.R
spartan/R/lhc_constructCoEffDataSet.R
spartan/R/oat_countResponsesOfDesiredValue.R
spartan/R/pcor.mat.R
spartan/R/efast_run_Analysis.R
spartan/R/lhc_generateTimepointFiles.R
spartan/R/oat_csv_result_file_analysis.R
spartan/R/atest.R
spartan/R/aa_sampleSizeSummary.R
spartan/R/oat_process_netlogo_result.R
spartan/R/Make_AA_Table_Result.R
spartan/R/num_decimals.R
spartan/R/efast_netlogo_get_overall_medians.R
spartan/R/efast_setfreq.R
spartan/R/ploteFASTSiFromTimepointFiles.R
spartan/R/aa_graphATestsForSampleSize.R
spartan/R/lhc_process_netlogo_result.R
spartan/R/plotPRCCSFromTimepointFiles.R
spartan/R/pcor.test.R
spartan/R/pcor.rec.R
spartan/R/subset_results_by_param_value_set.R
spartan/R/aa_getATestResults.R
spartan/R/lhc_countSignificantParametersOverTime.R
spartan/R/efast_ttest.R
spartan/R/lhc_calculatePRCCForMultipleTimepoints.R
spartan/R/efast_cvmethod.R
spartan/R/lhc_generateLHCSummary.R
spartan/R/perform_aTest_for_all_sim_measures.R
spartan/R/lhc_graphMeasuresForParameterChange.R
spartan/R/lhc_generatePRCoEffs.R
spartan/R/lhc_netlogo_graphMeasuresForParameterChange.R
spartan/R/efast_process_netlogo_result.R
spartan/R/lhc_plotCoEfficients.R
spartan/R/oat_graphATestsForSampleSize.R
spartan/R/oat_processParamSubsets.R
spartan/MD5
spartan/DESCRIPTION
spartan/man
spartan/man/Technique3-lhc_create_parameter_sample.Rd
spartan/man/Technique2-oat_create_parameter_sample.Rd
spartan/man/Utility-getMediansSubset.Rd
spartan/man/Technique1-aleatory_analysis.Rd
spartan/man/Technique4-efast_generate_analysis_results.Rd
spartan/man/Technique5-spartan_and_netlogo.Rd
spartan/man/Technique3-lhc_perform_analysis.Rd
spartan/man/Utility-sampleData.Rd
spartan/man/Technique4-efast_create_parameter_sample.Rd
spartan/man/Technique2-oat_generate_analysis.Rd
spartan/man/spartan-internal.Rd