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.

Install the latest version of this package by entering the following in R:
install.packages("spartan")
AuthorKieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Date of publication2015-10-19 23:57:19
MaintainerKieran Alden <kieran.alden@gmail.com>
LicenseGPL-2
Version2.3

View on CRAN

Functions

AA_Example_ATestMaxAndMedians Man page
aa_getATestResults Man page
aa_graphATestsForSampleSize Man page
aa_graphSampleSizeSummary Man page
aa_sampleSizeSummary Man page
aa_summariseReplicateRuns Man page
atest Man page
Curve1_chemoLowerLinearAdjust Man page
Curve1_chemoThreshold Man page
Curve1_chemoUpperLinearAdjust Man page
Curve1_Dummy Man page
Curve1_maxVCAMeffectProbabilityCutoff Man page
Curve1_Results_Summary Man page
Curve1_thresholdBindProbability Man page
Curve1_vcamSlope Man page
eFAST_Analysis Man page
efast_cvmethod Man page
efast_generate_medians_for_all_parameter_subsets Man page
efast_generate_sample Man page
efast_generate_sample_netlogo Man page
efast_get_overall_medians Man page
efast_graph_Results Man page
efast_netlogo_get_overall_medians Man page
efast_netlogo_run_Analysis Man page
efast_parameterdist Man page
efast_process_netlogo_result Man page
efast_run_Analysis Man page
efast_sd Man page
efast_setfreq Man page
efast_ttest Man page
EgSet_LHC_corCoeffs Man page
getMediansSubset Man page
lhc_calculatePRCCForMultipleTimepoints Man page
lhc_constructCoEffDataSet Man page
lhc_countSignificantParametersOverTime Man page
lhc_generate_lhc_sample Man page
lhc_generate_lhc_sample_netlogo Man page
lhc_generateLHCSummary Man page
lhc_generate_netlogo_PRCoEffs Man page
lhc_generatePRCoEffs Man page
lhc_generateTimepointFiles Man page
lhc_graphMeasuresForParameterChange Man page
lhc_graphPRCCForMultipleTimepoints Man page
lhc_netlogo_graphMeasuresForParameterChange Man page
LHC_Parameters_for_Runs Man page
lhc_plotCoEfficients Man page
lhc_process_netlogo_result Man page
lhc_process_sample_run_subsets Man page
LHC_Summary Man page
normaliseATest Man page
num.decimals Man page
oat_countResponsesOfDesiredValue Man page
oat_csv_result_file_analysis Man page
OAT_Example_ATests_chemoLowerLinearAdjust Man page
oat_generate_netlogo_behaviour_space_XML Man page
oat_graphATestsForSampleSize Man page
oat_graph_Leish_ATestsMultipleTimepoints Man page
OAT_Medians Man page
oat_parameter_sampling Man page
oat_plotResultDistribution Man page
oat_process_netlogo_result Man page
oat_processParamSubsets Man page
OAT_Sampling_chemoThreshold_Values Man page
OAT_Sampling_maxVCAMeffectProbabilityCutoff_Values Man page
pcor.mat Man page
pcor.rec Man page
pcor.test Man page
perform_aTest_for_all_sim_measures Man page
plotATestsFromTimepointFiles Man page
ploteFASTSiFromTimepointFiles Man page
plotPRCCSFromTimepointFiles Man page
prepare_parameter_value_list Man page
subset_results_by_param_value_set Man page
table_header_check Man page
testP-internal Man page

Files

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

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