| aa_getATestResults | Calculates the A-Test scores observed for all sets, for each... |
| aa_getATestResults_overTime | Get A-Test results for multiple simulation timepoints |
| aa_graphATestsForSampleSize | Produce a plot for each sample size, showing the A-Test... |
| aa_graphSampleSizeSummary | Plots a comparison of the maximum A-Test score for each... |
| aa_sampleSizeSummary | Determines the median and maximum A-Test score observed for... |
| aa_sampleSizeSummary_overTime | Determines median and maximum A-Test score for each sample... |
| aa_summariseReplicateRuns | Summarise results in set folder structure into one single CSV... |
| aa_summariseReplicateRuns_overTime | Calculate summary responses for consistency analysis... |
| add_parameter_value_to_file | Iterates through the parameters, adding their sampled value... |
| analysenetwork_structures | Analyse each network structure provided as a potential NN... |
| append_time_to_argument | Appends the time to an argument if processing timepoints |
| atest | Calculates the A-test score for two distributions |
| a_test_results | Analysed results from tutorial_consistency_set: a-test scores... |
| build_curve_results_from_r_object | When developing spartanDB, it became clear curve results may... |
| build_performance_statistics | Internal function to build performance statistics (MSE, R2,... |
| calculate_atest_score | Calculate the A-Test score for a parameter set in comparison... |
| calculate_fold_MSE | Calculate the mean squared error for this fold in k-fold... |
| calculate_medians_for_all_measures | Calculate medians for all measures for a simulation parameter... |
| calculate_prcc_for_all_measures | For all measures, calculate the prcc for each parameter |
| calculate_prccs_all_parameters | Calculate PRCC values for all parameter-measure pairs |
| calculate_weights_for_ensemble_model | Internal function to calculate the weights for all emulators... |
| check_acceptable_model_type | Internal function to check whether acceptable models have... |
| check_argument_positive_int | Check that an argument that should be a positive integer has... |
| check_boolean | Check that an argument that should be a boolean has been... |
| check_column_ranges | For aleatory analysis, checks the analysis start and end... |
| check_confidence_interval | Check that a confidence interval is within a specified range |
| check_consistency_result_type | Check that the user has declared either a file name or an R... |
| check_double_value_in_range | Check that a double argument is within a specified range |
| check_file_exist | Checks for the existence of a file |
| check_file_exists | Check whether a file exists |
| check_file_extension | Check the file extension of a file and return it |
| check_filepath_exists | Check that the filepath of required data or output exists |
| check_function_dependent_paramvals | Call the correct paramvals check for the calling function, as... |
| check_global_param_sampling_args | Checks the input values for global parameter sampling... |
| check_graph_output_type | Check the requested graph types are correct (PDF, PNG, TIFF,... |
| check_input_args | Wrapper function called by all spartan methods to check input... |
| check_lengths_parameters_ranges | Check that the lengths of the parameters, minimum values, and... |
| check_lhs_algorithm | Check that the chosen lhc sampling algorithm is either normal... |
| check_list_all_integers | Check that all objects of a list are integers |
| check_nested_filepaths | Check that result filepaths under the root directory exist |
| check_netlogo_parameters_and_values | Checks the netlogo parameters and values are formatted... |
| check_numeric_list_values | Check that two lists are numeric, and the values of one are... |
| check_package_installed | Check that a required package has been installed |
| check_parameters_and_ranges | Pre-Check of the parameters and ranges specified for sampling... |
| check_paramvals_length_equals_parameter_length | Where used in robustness analysis, check that the length of... |
| check_robustness_parameter_and_ranges_lengths | Where used, checks that PARAMETERS, PMIN, PMAX, PINC, and... |
| check_robustness_paramvals_contains_baseline | Checks that the parameter values specified in PARAMVALS... |
| check_robustness_range_contains_baseline | Checks that the range specified by PMIN and PMAX contains the... |
| check_robustness_range_or_values | For robustness, check whether using PMIN/PMAX/PINC entry or... |
| check_robustness_sampling_args | Pre-execution checks to perform before the spartan robustness... |
| check_text | Check that an argument that should be a text label has been... |
| check_text_list | Check that an arguments of a list that should be a text label... |
| close_and_write_netlogo_file | Close the current netlogo sample file and write out |
| compare_all_values_of_parameter_to_baseline | For one parameter, compare responses for all values with... |
| construct_result_filename | Appends the time to an eFAST argument, if processing multiple... |
| create_abc_settings_object | Creates ensemble-specific parameters for ABC analysis |
| createAndEvaluateFolds | Create and evaluate folds within k-fold cross validation |
| create_ensemble | Internal function to create the ensemble |
| create_neural_network | Create neural network emulator, using neuralnet package |
| createtest_fold | Create test data fold for k-fold cross validation |
| createTrainingFold | Create training data fold for k-fold cross validation |
| dataset_precheck | Before partitioning data, removes any columns where the value... |
| denormalise_dataset | Rescale normalised data back to it's original scale |
| determine_optimal_neural_network_structure | Determine the optimal hidden layer structure from those... |
| efast_cvmethod | Internal function used in calculating the partitions of... |
| efast_generate_medians_for_all_parameter_subsets | Generates summary file for stochastic simulations stored in... |
| efast_generate_medians_for_all_parameter_subsets_overTime | Pre-process analysis settings if multiple timepoints are... |
| efast_generate_sample | Generates parameter sets for variance-based eFAST Sensitivity... |
| efast_generate_sample_netlogo | Prepares Netlogo experiment files for a variance-based... |
| efast_get_overall_medians | Calculates the summary stats for each parameter set (median... |
| efast_get_overall_medians_overTime | Pre-process analysis settings if multiple timepoints are... |
| efast_graph_Results | Plot the parition of variance in a simulation response for... |
| efast_netlogo_get_overall_medians | Deprecated: Use 'efast_netlogo_get_overall_medians' |
| efast_netlogo_run_Analysis | Deprecated: Use 'efast_run_Analysis' |
| efast_parameterdist | Internal function used in calculating the partitions of... |
| efast_process_netlogo_result | Analyses Netlogo simulation data for parameter sets generated... |
| efast_run_Analysis | Runs the eFAST Analysis for the pre-generated summary file |
| efast_run_Analysis_from_DB | Runs the eFAST Analysis for a set of results stored in a... |
| efast_run_Analysis_overTime | Pre-process analysis settings if multiple timepoints are... |
| efast_sd | Internal function used in calculating the partitions of... |
| efast_setfreq | Internal function used in calculating the partitions of... |
| efast_ttest | Internal function used in calculating the partitions of... |
| emulated_lhc_values | Latin-hypercube value set use to demonstrate emulated... |
| emulate_efast_sampled_parameters | Emulate simulations for a set of eFAST generated parameter... |
| emulate_lhc_sampled_parameters | Emulate simulations for a set of latin-hypercube generated... |
| emulation_algorithm_settings | Initialise machine-learning algorithms settings for emulation... |
| emulator_parameter_evolution | Evolve parameter sets that meet a desired ensemble outcome |
| emulator_predictions | Used to generate predictions from an emulator, normalising... |
| ensemble_abc_wrapper | Wrapper to allow EasyABC functions to run using Ensemble |
| execute_checks | Executes the list of check functions compiled for the calling... |
| exemplar_sim_output | Example of a dataset output from an agent-based simulation,... |
| extract_predictions_from_result_list | Internal function used to extract the predictions made in... |
| format_efast_result_for_output | Joins the various results objects into an output ready format |
| generate_a_test_results_header | Generates the CSV file header for the A-Test results file |
| generate_a_test_score | Take the first set and compare it to a distribution from... |
| generate_efast_parameter_sets | Use the eFAST approach to generate parameter sets |
| generate_emulator_model | Internal function used to generate the requested emulator,... |
| generate_emulators_and_ensemble | Generate a set of emulators and combine into an ensemble |
| generate_ensemble_from_existing_emulations | Generate an ensemble from previously created spartan... |
| generate_ensemble_training_set | Internal function used to combine test set predictions from... |
| generate_headers_for_atest_file | Generates headers for the A-Test summary CSV and R Object |
| generate_list_of_checks | Defines which functions to call to check an input argument. |
| generate_medians_for_param_set | Generate the median responses for a set of parameter values |
| generate_model_formula | Internal function to generate the formula for training the... |
| generate_parameter_table | Takes the value list and generates the sample that is output... |
| generate_prcc_results_header | Generates the CSV file header for the prcc results file |
| generate_predictions_from_emulator | Internal function to generate predictions from an emulator |
| generate_requested_emulations | Generate emulators for specified machine learning techniques... |
| generate_sensitivity_indices | Generate eFAST Sensitivity Indices |
| generate_summary_stats_for_all_param_sets | Generate summary statistics for each value of all parameters... |
| get_argument_correct_case | Tries upper and lower case names for input arguments |
| get_correct_file_path_for_function | Gets the correct filepath for the column range input checker |
| get_file_and_object_argument_names | Gets the correct file and R object argument names for the... |
| get_max_and_median_atest_scores | Return the max and median A-Test score for all measures for a... |
| get_median_results_for_all_measures | For a model result, calculate the medians of the desired... |
| get_medians_for_size_subsets | For a given sample size, get the median results to summarise... |
| getMediansSubset | Function used to calculate the median results for those run... |
| graph_Posteriors_All_Parameters | Graph posterior distributions generated for all parameters,... |
| graph_sample_size_results | Graph the A-Test results for a sample size |
| import_model_result | Import a model result from either a CSV or XML file |
| initialise_netlogo_xml_file | Initialises the Netlogo setup file for this experiment |
| join_strings | Join strings and separate by specified character |
| join_strings_nospace | Join strings and separate with no space |
| join_strings_space | Join strings and separate by a space |
| kfoldCrossValidation | Perform k-fold cross validation for assessing neural network... |
| lhc_calculatePRCCForMultipleTimepoints | Calculates the PRCC for each parameter at each timepoint,... |
| lhc_constructcoeff_dataset | Utility function used to create data structure for... |
| lhc_generate_lhc_sample | Generates sets of simulation parameters using latin-hypercube... |
| lhc_generate_lhc_sample_netlogo | Prepares Netlogo experiment files for a sampling-based... |
| lhc_generateLHCSummary | Summarises simulation behaviour for each parameter set, by... |
| lhc_generateLHCSummary_overTime | Pre-process analysis settings if multiple timepoints are... |
| lhc_generate_netlogo_PRCoEffs | Deprecated. Use 'lhc_generatePRCoEffs' instead |
| lhc_generatePRCoEffs | Generate Partial Rank Correlation Coefficients for... |
| lhc_generatePRCoEffs_db_link | Generate Partial Rank Correlation Coefficients for... |
| lhc_generatePRCoEffs_overTime | Pre-process analysis settings if multiple timepoints are... |
| lhc_generateTimepointFiles | Generates spartan-compatible timepoint files if simulation... |
| lhc_graphMeasuresForParameterChange | Generates parameter/measure plot for each pairing in the... |
| lhc_graphMeasuresForParameterChange_from_db | Generates parameter/measure plot for each pairing in the... |
| lhc_graphMeasuresForParameterChange_overTime | Wrapper for graphing LHC results for multiple timepoints |
| lhc_netlogo_graphMeasuresForParameterChange | Deprecated. Use 'lhc_graphMeasuresForParameterChange' instead |
| lhc_plotCoEfficients | Plots the PRCC coefficients against each other for ease of... |
| lhc_polarplot | Creates a polar plot for each response, showing PRCC for each... |
| lhc_process_netlogo_result | Analyses Netlogo simulations generated for a latin-hypercube... |
| lhc_process_sample_run_subsets | Summarises results of runs for parameter sets generated by a... |
| lhc_process_sample_run_subsets_overTime | Pre-process analysis settings if multiple timepoints are... |
| make_extension | Adds an extension to a filename |
| make_filename | Makes a filename from a list of strings, separated by "_" |
| make_graph_title | Make graph title, sub title, and file name |
| make_lhc_plot | Make the LHC output plot |
| make_path | Combines a list of elements into a filepath separated by "/" |
| meanSquaredError | Calculate the mean squared error between predictions and... |
| normaliseATest | Normalises the A-Test such that it is above 0.5 |
| normalise_dataset | Normalise a dataset such that all values are between 0 and 1 |
| nsga2_set_user_params | Initialise analysis specific parameters for NSGA-2 |
| num.decimals | Diagnostic function used to determine number of decimal... |
| oat_csv_result_file_analysis | Performs a robustness analysis for supplied simulation data,... |
| oat_csv_result_file_analysis_from_DB | Performs a robustness analysis for simulation results stored... |
| oat_csv_result_file_analysis_overTime | Pre-process analysis settings if multiple timepoints are... |
| oat_generate_netlogo_behaviour_space_XML | Creates a Netlogo compatible behaviour space experiment for... |
| oat_graphATestsForSampleSize | Takes each parameter in turn and creates a plot showing... |
| oat_parameter_sampling | Create parameter samples for robustness (local) analysis |
| oat_plotResultDistribution | For stochastic simulations plots the distribution of results... |
| oat_process_netlogo_result | Takes a Netlogo behaviour space file and performs a... |
| oat_processParamSubsets | Summarises stochastic, repeated, simulations for all... |
| oat_processParamSubsets_overTime | Summarises stochastic, repeated, simulations for all... |
| output_ggplot_graph | Output a ggplot graph in the requested formats |
| output_param_sets_per_curve | Output the generated parameter sets for each curve |
| partition_dataset | Partition latin-hypercube summary file to training, testing,... |
| pcor.mat | Internal function used to calculate the Partial Rank... |
| pcor.rec | Internal function used to calculate the Partial Rank... |
| pcor.test | Internal function used to calculate the Partial Rank... |
| perform_aTest_for_all_sim_measures | Performs A-Test to compare all simulation measures |
| plotATestsFromTimepointFiles | Plots the A-Tests for all timepoints being examined |
| plot_compare_sim_observed_to_model_prediction | Internal function used to create accuracy plots of the... |
| ploteFASTSiFromTimepointFiles | Plot the Si value for all parameters for multiple simulation... |
| plotPRCCSFromTimepointFiles | Plots Graphs for Partial Rank Correlation Coefficients Over... |
| prepare_parameter_value_list | Prepares the parameter value list, as either an interval... |
| process_netlogo_parameter_range_info | Processes netlogo parameter information to generate names of... |
| process_parameter_value_if_exists | Process parameter value set if results exist |
| produce_accuracy_plots_all_measures | Internal function used to create accuracy plots of the... |
| produce_accuracy_plots_single_measure | Internal function used to create accuracy plots of the... |
| produce_atest_score_summary | Generates A-Test score summary for all sample sizes |
| produce_summary_for_all_values_of_parameter | For one parameter, evaluate the results of all values that... |
| read_all_curve_results | Reads results from each curve into a multi-dimensional array |
| read_from_csv | To save retyping all options, function to read CSV data |
| read_model_result_file | Reads a model result file, either CSV or XML |
| read_simulation_results | Read in the simulation results either from a file, or R... |
| retrieve_results_for_comparison_result_set | Get the first result set, to which all others are compared |
| rSquared | Calculate the R squared statistic for predictions and... |
| sample_parameter_space | Generate the LHC design for the chosen algorithm |
| scale_lhc_sample | Scale the LHC design to be the range explored for each... |
| screen_nsga2_parameters | Screens NSGA-2 related parameters, guiding which to select... |
| selectSuitableStructure | Selects the most suitable neural network structure from the... |
| set.nsga_sensitivity_params | Set parameters for NSGA-2 sensitivity analysis |
| sim_data_for_emulation | Set of parameter and response pairs for training an emulator... |
| summarise_lhc_sweep_responses | Processes an LHC sample, returning summary stats for all... |
| summarise_replicate_runs | Summarises replicate runs of a parameter set. Used by LHC and... |
| tutorial_consistency_set | Example dataset showing the structure for consistency... |
| updateErrorForStructure | Add the MSE for a newly examined structure to the list of... |
| use_ensemble_to_generate_predictions | Predict simulation responses for a parameter set using an... |
| visualise_data_distribution | Used to diagnose skew in a training dataset before use in... |
| weight_emulator_predictions_by_ensemble | Internal function to weight emulator predictions by that... |
| write_data_to_csv | Shortcut function for writing data to CSV file |
