Man pages for kalden/spartan
Simulation Parameter Analysis R Toolkit ApplicatioN: 'spartan'

aa_getATestResultsCalculates the A-Test scores observed for all sets, for each...
aa_getATestResults_overTimeGet A-Test results for multiple simulation timepoints
aa_graphATestsForSampleSizeProduce a plot for each sample size, showing the A-Test...
aa_graphSampleSizeSummaryPlots a comparison of the maximum A-Test score for each...
aa_sampleSizeSummaryDetermines the median and maximum A-Test score observed for...
aa_sampleSizeSummary_overTimeDetermines median and maximum A-Test score for each sample...
aa_summariseReplicateRunsSummarise results in set folder structure into one single CSV...
aa_summariseReplicateRuns_overTimeCalculate summary responses for consistency analysis...
add_parameter_value_to_fileIterates through the parameters, adding their sampled value...
analysenetwork_structuresAnalyse each network structure provided as a potential NN...
append_time_to_argumentAppends the time to an argument if processing timepoints
atestCalculates the A-test score for two distributions
a_test_resultsAnalysed results from tutorial_consistency_set: a-test scores...
build_curve_results_from_r_objectWhen developing spartanDB, it became clear curve results may...
build_performance_statisticsInternal function to build performance statistics (MSE, R2,...
calculate_atest_scoreCalculate the A-Test score for a parameter set in comparison...
calculate_fold_MSECalculate the mean squared error for this fold in k-fold...
calculate_medians_for_all_measuresCalculate medians for all measures for a simulation parameter...
calculate_prcc_for_all_measuresFor all measures, calculate the prcc for each parameter
calculate_prccs_all_parametersCalculate PRCC values for all parameter-measure pairs
calculate_weights_for_ensemble_modelInternal function to calculate the weights for all emulators...
check_acceptable_model_typeInternal function to check whether acceptable models have...
check_argument_positive_intCheck that an argument that should be a positive integer has...
check_booleanCheck that an argument that should be a boolean has been...
check_column_rangesFor aleatory analysis, checks the analysis start and end...
check_confidence_intervalCheck that a confidence interval is within a specified range
check_consistency_result_typeCheck that the user has declared either a file name or an R...
check_double_value_in_rangeCheck that a double argument is within a specified range
check_file_existChecks for the existence of a file
check_file_existsCheck whether a file exists
check_file_extensionCheck the file extension of a file and return it
check_filepath_existsCheck that the filepath of required data or output exists
check_function_dependent_paramvalsCall the correct paramvals check for the calling function, as...
check_global_param_sampling_argsChecks the input values for global parameter sampling...
check_graph_output_typeCheck the requested graph types are correct (PDF, PNG, TIFF,...
check_input_argsWrapper function called by all spartan methods to check input...
check_lengths_parameters_rangesCheck that the lengths of the parameters, minimum values, and...
check_lhs_algorithmCheck that the chosen lhc sampling algorithm is either normal...
check_list_all_integersCheck that all objects of a list are integers
check_nested_filepathsCheck that result filepaths under the root directory exist
check_netlogo_parameters_and_valuesChecks the netlogo parameters and values are formatted...
check_numeric_list_valuesCheck that two lists are numeric, and the values of one are...
check_package_installedCheck that a required package has been installed
check_parameters_and_rangesPre-Check of the parameters and ranges specified for sampling...
check_paramvals_length_equals_parameter_lengthWhere used in robustness analysis, check that the length of...
check_robustness_parameter_and_ranges_lengthsWhere used, checks that PARAMETERS, PMIN, PMAX, PINC, and...
check_robustness_paramvals_contains_baselineChecks that the parameter values specified in PARAMVALS...
check_robustness_range_contains_baselineChecks that the range specified by PMIN and PMAX contains the...
check_robustness_range_or_valuesFor robustness, check whether using PMIN/PMAX/PINC entry or...
check_robustness_sampling_argsPre-execution checks to perform before the spartan robustness...
check_textCheck that an argument that should be a text label has been...
check_text_listCheck that an arguments of a list that should be a text label...
close_and_write_netlogo_fileClose the current netlogo sample file and write out
compare_all_values_of_parameter_to_baselineFor one parameter, compare responses for all values with...
construct_result_filenameAppends the time to an eFAST argument, if processing multiple...
create_abc_settings_objectCreates ensemble-specific parameters for ABC analysis
createAndEvaluateFoldsCreate and evaluate folds within k-fold cross validation
create_ensembleInternal function to create the ensemble
create_neural_networkCreate neural network emulator, using neuralnet package
createtest_foldCreate test data fold for k-fold cross validation
createTrainingFoldCreate training data fold for k-fold cross validation
dataset_precheckBefore partitioning data, removes any columns where the value...
denormalise_datasetRescale normalised data back to it's original scale
determine_optimal_neural_network_structureDetermine the optimal hidden layer structure from those...
efast_cvmethodInternal function used in calculating the partitions of...
efast_generate_medians_for_all_parameter_subsetsGenerates summary file for stochastic simulations stored in...
efast_generate_medians_for_all_parameter_subsets_overTimePre-process analysis settings if multiple timepoints are...
efast_generate_sampleGenerates parameter sets for variance-based eFAST Sensitivity...
efast_generate_sample_netlogoPrepares Netlogo experiment files for a variance-based...
efast_get_overall_mediansCalculates the summary stats for each parameter set (median...
efast_get_overall_medians_overTimePre-process analysis settings if multiple timepoints are...
efast_graph_ResultsPlot the parition of variance in a simulation response for...
efast_netlogo_get_overall_mediansDeprecated: Use 'efast_netlogo_get_overall_medians'
efast_netlogo_run_AnalysisDeprecated: Use 'efast_run_Analysis'
efast_parameterdistInternal function used in calculating the partitions of...
efast_process_netlogo_resultAnalyses Netlogo simulation data for parameter sets generated...
efast_run_AnalysisRuns the eFAST Analysis for the pre-generated summary file
efast_run_Analysis_from_DBRuns the eFAST Analysis for a set of results stored in a...
efast_run_Analysis_overTimePre-process analysis settings if multiple timepoints are...
efast_sdInternal function used in calculating the partitions of...
efast_setfreqInternal function used in calculating the partitions of...
efast_ttestInternal function used in calculating the partitions of...
emulated_lhc_valuesLatin-hypercube value set use to demonstrate emulated...
emulate_efast_sampled_parametersEmulate simulations for a set of eFAST generated parameter...
emulate_lhc_sampled_parametersEmulate simulations for a set of latin-hypercube generated...
emulation_algorithm_settingsInitialise machine-learning algorithms settings for emulation...
emulator_parameter_evolutionEvolve parameter sets that meet a desired ensemble outcome
emulator_predictionsUsed to generate predictions from an emulator, normalising...
ensemble_abc_wrapperWrapper to allow EasyABC functions to run using Ensemble
execute_checksExecutes the list of check functions compiled for the calling...
exemplar_sim_outputExample of a dataset output from an agent-based simulation,...
extract_predictions_from_result_listInternal function used to extract the predictions made in...
format_efast_result_for_outputJoins the various results objects into an output ready format
generate_a_test_results_headerGenerates the CSV file header for the A-Test results file
generate_a_test_scoreTake the first set and compare it to a distribution from...
generate_efast_parameter_setsUse the eFAST approach to generate parameter sets
generate_emulator_modelInternal function used to generate the requested emulator,...
generate_emulators_and_ensembleGenerate a set of emulators and combine into an ensemble
generate_ensemble_from_existing_emulationsGenerate an ensemble from previously created spartan...
generate_ensemble_training_setInternal function used to combine test set predictions from...
generate_headers_for_atest_fileGenerates headers for the A-Test summary CSV and R Object
generate_list_of_checksDefines which functions to call to check an input argument.
generate_medians_for_param_setGenerate the median responses for a set of parameter values
generate_model_formulaInternal function to generate the formula for training the...
generate_parameter_tableTakes the value list and generates the sample that is output...
generate_prcc_results_headerGenerates the CSV file header for the prcc results file
generate_predictions_from_emulatorInternal function to generate predictions from an emulator
generate_requested_emulationsGenerate emulators for specified machine learning techniques...
generate_sensitivity_indicesGenerate eFAST Sensitivity Indices
generate_summary_stats_for_all_param_setsGenerate summary statistics for each value of all parameters...
get_argument_correct_caseTries upper and lower case names for input arguments
get_correct_file_path_for_functionGets the correct filepath for the column range input checker
get_file_and_object_argument_namesGets the correct file and R object argument names for the...
get_max_and_median_atest_scoresReturn the max and median A-Test score for all measures for a...
get_median_results_for_all_measuresFor a model result, calculate the medians of the desired...
get_medians_for_size_subsetsFor a given sample size, get the median results to summarise...
getMediansSubsetFunction used to calculate the median results for those run...
graph_Posteriors_All_ParametersGraph posterior distributions generated for all parameters,...
graph_sample_size_resultsGraph the A-Test results for a sample size
import_model_resultImport a model result from either a CSV or XML file
initialise_netlogo_xml_fileInitialises the Netlogo setup file for this experiment
join_stringsJoin strings and separate by specified character
join_strings_nospaceJoin strings and separate with no space
join_strings_spaceJoin strings and separate by a space
kfoldCrossValidationPerform k-fold cross validation for assessing neural network...
lhc_calculatePRCCForMultipleTimepointsCalculates the PRCC for each parameter at each timepoint,...
lhc_constructcoeff_datasetUtility function used to create data structure for...
lhc_generate_lhc_sampleGenerates sets of simulation parameters using latin-hypercube...
lhc_generate_lhc_sample_netlogoPrepares Netlogo experiment files for a sampling-based...
lhc_generateLHCSummarySummarises simulation behaviour for each parameter set, by...
lhc_generateLHCSummary_overTimePre-process analysis settings if multiple timepoints are...
lhc_generate_netlogo_PRCoEffsDeprecated. Use 'lhc_generatePRCoEffs' instead
lhc_generatePRCoEffsGenerate Partial Rank Correlation Coefficients for...
lhc_generatePRCoEffs_db_linkGenerate Partial Rank Correlation Coefficients for...
lhc_generatePRCoEffs_overTimePre-process analysis settings if multiple timepoints are...
lhc_generateTimepointFilesGenerates spartan-compatible timepoint files if simulation...
lhc_graphMeasuresForParameterChangeGenerates parameter/measure plot for each pairing in the...
lhc_graphMeasuresForParameterChange_from_dbGenerates parameter/measure plot for each pairing in the...
lhc_graphMeasuresForParameterChange_overTimeWrapper for graphing LHC results for multiple timepoints
lhc_netlogo_graphMeasuresForParameterChangeDeprecated. Use 'lhc_graphMeasuresForParameterChange' instead
lhc_plotCoEfficientsPlots the PRCC coefficients against each other for ease of...
lhc_polarplotCreates a polar plot for each response, showing PRCC for each...
lhc_process_netlogo_resultAnalyses Netlogo simulations generated for a latin-hypercube...
lhc_process_sample_run_subsetsSummarises results of runs for parameter sets generated by a...
lhc_process_sample_run_subsets_overTimePre-process analysis settings if multiple timepoints are...
make_extensionAdds an extension to a filename
make_filenameMakes a filename from a list of strings, separated by "_"
make_graph_titleMake graph title, sub title, and file name
make_lhc_plotMake the LHC output plot
make_pathCombines a list of elements into a filepath separated by "/"
meanSquaredErrorCalculate the mean squared error between predictions and...
normaliseATestNormalises the A-Test such that it is above 0.5
normalise_datasetNormalise a dataset such that all values are between 0 and 1
nsga2_set_user_paramsInitialise analysis specific parameters for NSGA-2
num.decimalsDiagnostic function used to determine number of decimal...
oat_csv_result_file_analysisPerforms a robustness analysis for supplied simulation data,...
oat_csv_result_file_analysis_from_DBPerforms a robustness analysis for simulation results stored...
oat_csv_result_file_analysis_overTimePre-process analysis settings if multiple timepoints are...
oat_generate_netlogo_behaviour_space_XMLCreates a Netlogo compatible behaviour space experiment for...
oat_graphATestsForSampleSizeTakes each parameter in turn and creates a plot showing...
oat_parameter_samplingCreate parameter samples for robustness (local) analysis
oat_plotResultDistributionFor stochastic simulations plots the distribution of results...
oat_process_netlogo_resultTakes a Netlogo behaviour space file and performs a...
oat_processParamSubsetsSummarises stochastic, repeated, simulations for all...
oat_processParamSubsets_overTimeSummarises stochastic, repeated, simulations for all...
output_ggplot_graphOutput a ggplot graph in the requested formats
output_param_sets_per_curveOutput the generated parameter sets for each curve
partition_datasetPartition latin-hypercube summary file to training, testing,...
pcor.matInternal function used to calculate the Partial Rank...
pcor.recInternal function used to calculate the Partial Rank...
pcor.testInternal function used to calculate the Partial Rank...
perform_aTest_for_all_sim_measuresPerforms A-Test to compare all simulation measures
plotATestsFromTimepointFilesPlots the A-Tests for all timepoints being examined
plot_compare_sim_observed_to_model_predictionInternal function used to create accuracy plots of the...
ploteFASTSiFromTimepointFilesPlot the Si value for all parameters for multiple simulation...
plotPRCCSFromTimepointFilesPlots Graphs for Partial Rank Correlation Coefficients Over...
prepare_parameter_value_listPrepares the parameter value list, as either an interval...
process_netlogo_parameter_range_infoProcesses netlogo parameter information to generate names of...
process_parameter_value_if_existsProcess parameter value set if results exist
produce_accuracy_plots_all_measuresInternal function used to create accuracy plots of the...
produce_accuracy_plots_single_measureInternal function used to create accuracy plots of the...
produce_atest_score_summaryGenerates A-Test score summary for all sample sizes
produce_summary_for_all_values_of_parameterFor one parameter, evaluate the results of all values that...
read_all_curve_resultsReads results from each curve into a multi-dimensional array
read_from_csvTo save retyping all options, function to read CSV data
read_model_result_fileReads a model result file, either CSV or XML
read_simulation_resultsRead in the simulation results either from a file, or R...
retrieve_results_for_comparison_result_setGet the first result set, to which all others are compared
rSquaredCalculate the R squared statistic for predictions and...
sample_parameter_spaceGenerate the LHC design for the chosen algorithm
scale_lhc_sampleScale the LHC design to be the range explored for each...
screen_nsga2_parametersScreens NSGA-2 related parameters, guiding which to select...
selectSuitableStructureSelects the most suitable neural network structure from the...
set.nsga_sensitivity_paramsSet parameters for NSGA-2 sensitivity analysis
sim_data_for_emulationSet of parameter and response pairs for training an emulator...
summarise_lhc_sweep_responsesProcesses an LHC sample, returning summary stats for all...
summarise_replicate_runsSummarises replicate runs of a parameter set. Used by LHC and...
tutorial_consistency_setExample dataset showing the structure for consistency...
updateErrorForStructureAdd the MSE for a newly examined structure to the list of...
use_ensemble_to_generate_predictionsPredict simulation responses for a parameter set using an...
visualise_data_distributionUsed to diagnose skew in a training dataset before use in...
weight_emulator_predictions_by_ensembleInternal function to weight emulator predictions by that...
write_data_to_csvShortcut function for writing data to CSV file
kalden/spartan documentation built on Dec. 7, 2018, 5:42 a.m.