Files in kalden/spartan
Simulation Parameter Analysis R Toolkit ApplicatioN: 'spartan'
.Rbuildignore
.Rhistory
.gitignore
.travis.yml
CRAN-RELEASE
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/abc_utilities.R
R/aleatory_analysis.R
R/aleatory_analysis_plotting.R
R/atest_utilities.R
R/datadoc.R
R/efast_analysis.R
R/efast_analysis_netlogo.R
R/efast_plotting.R
R/efast_sampling.R
R/efast_sampling_netlogo.R
R/efast_utilities.R
R/emulation_evolution.R
R/emulation_generation.R
R/emulation_plotting.R
R/emulation_sensitivity_analysis.R
R/emulation_utilities.R
R/ensemble_generation.R
R/ensemble_utilities.R
R/lhc_analysis.R
R/lhc_analysis_netlogo.R
R/lhc_plotting.R
R/lhc_prcc_utilities.R
R/lhc_preprocess.R
R/lhc_sampling.R
R/lhc_sampling_netlogo.R
R/method_argument_check.R
R/netlogo_sampling_utilities.R
R/neural_network_utilities.R
R/robustness_analysis.R
R/robustness_analysis_netlogo.R
R/robustness_plotting.R
R/robustness_sampling.R
R/spartan_utilities.R
README.md
cran-comments.md
data/a_test_results.rda
data/emulated_lhc_values.rda
data/exemplar_sim_output.rda
data/sim_data_for_emulation.rda
data/tutorial_consistency_set.rda
man/a_test_results.Rd
man/aa_getATestResults.Rd
man/aa_getATestResults_overTime.Rd
man/aa_graphATestsForSampleSize.Rd
man/aa_graphSampleSizeSummary.Rd
man/aa_sampleSizeSummary.Rd
man/aa_sampleSizeSummary_overTime.Rd
man/aa_summariseReplicateRuns.Rd
man/aa_summariseReplicateRuns_overTime.Rd
man/add_parameter_value_to_file.Rd
man/analysenetwork_structures.Rd
man/append_time_to_argument.Rd
man/atest.Rd
man/build_curve_results_from_r_object.Rd
man/build_performance_statistics.Rd
man/calculate_atest_score.Rd
man/calculate_fold_MSE.Rd
man/calculate_medians_for_all_measures.Rd
man/calculate_prcc_for_all_measures.Rd
man/calculate_prccs_all_parameters.Rd
man/calculate_weights_for_ensemble_model.Rd
man/check_acceptable_model_type.Rd
man/check_argument_positive_int.Rd
man/check_boolean.Rd
man/check_column_ranges.Rd
man/check_confidence_interval.Rd
man/check_consistency_result_type.Rd
man/check_double_value_in_range.Rd
man/check_file_exist.Rd
man/check_file_exists.Rd
man/check_file_extension.Rd
man/check_filepath_exists.Rd
man/check_function_dependent_paramvals.Rd
man/check_global_param_sampling_args.Rd
man/check_graph_output_type.Rd
man/check_input_args.Rd
man/check_lengths_parameters_ranges.Rd
man/check_lhs_algorithm.Rd
man/check_list_all_integers.Rd
man/check_nested_filepaths.Rd
man/check_netlogo_parameters_and_values.Rd
man/check_numeric_list_values.Rd
man/check_package_installed.Rd
man/check_parameters_and_ranges.Rd
man/check_paramvals_length_equals_parameter_length.Rd
man/check_robustness_parameter_and_ranges_lengths.Rd
man/check_robustness_paramvals_contains_baseline.Rd
man/check_robustness_range_contains_baseline.Rd
man/check_robustness_range_or_values.Rd
man/check_robustness_sampling_args.Rd
man/check_text.Rd
man/check_text_list.Rd
man/close_and_write_netlogo_file.Rd
man/compare_all_values_of_parameter_to_baseline.Rd
man/construct_result_filename.Rd
man/createAndEvaluateFolds.Rd
man/createTrainingFold.Rd
man/create_abc_settings_object.Rd
man/create_ensemble.Rd
man/create_neural_network.Rd
man/createtest_fold.Rd
man/dataset_precheck.Rd
man/denormalise_dataset.Rd
man/determine_optimal_neural_network_structure.Rd
man/efast_cvmethod.Rd
man/efast_generate_medians_for_all_parameter_subsets.Rd
man/efast_generate_medians_for_all_parameter_subsets_overTime.Rd
man/efast_generate_sample.Rd
man/efast_generate_sample_netlogo.Rd
man/efast_get_overall_medians.Rd
man/efast_get_overall_medians_overTime.Rd
man/efast_graph_Results.Rd
man/efast_netlogo_get_overall_medians.Rd
man/efast_netlogo_run_Analysis.Rd
man/efast_parameterdist.Rd
man/efast_process_netlogo_result.Rd
man/efast_run_Analysis.Rd
man/efast_run_Analysis_from_DB.Rd
man/efast_run_Analysis_overTime.Rd
man/efast_sd.Rd
man/efast_setfreq.Rd
man/efast_ttest.Rd
man/emulate_efast_sampled_parameters.Rd
man/emulate_lhc_sampled_parameters.Rd
man/emulated_lhc_values.Rd
man/emulation_algorithm_settings.Rd
man/emulator_parameter_evolution.Rd
man/emulator_predictions.Rd
man/ensemble_abc_wrapper.Rd
man/execute_checks.Rd
man/exemplar_sim_output.Rd
man/extract_predictions_from_result_list.Rd
man/format_efast_result_for_output.Rd
man/generate_a_test_results_header.Rd
man/generate_a_test_score.Rd
man/generate_efast_parameter_sets.Rd
man/generate_emulator_model.Rd
man/generate_emulators_and_ensemble.Rd
man/generate_ensemble_from_existing_emulations.Rd
man/generate_ensemble_training_set.Rd
man/generate_headers_for_atest_file.Rd
man/generate_list_of_checks.Rd
man/generate_medians_for_param_set.Rd
man/generate_model_formula.Rd
man/generate_parameter_table.Rd
man/generate_prcc_results_header.Rd
man/generate_predictions_from_emulator.Rd
man/generate_requested_emulations.Rd
man/generate_sensitivity_indices.Rd
man/generate_summary_stats_for_all_param_sets.Rd
man/getMediansSubset.Rd
man/get_argument_correct_case.Rd
man/get_correct_file_path_for_function.Rd
man/get_file_and_object_argument_names.Rd
man/get_max_and_median_atest_scores.Rd
man/get_median_results_for_all_measures.Rd
man/get_medians_for_size_subsets.Rd
man/graph_Posteriors_All_Parameters.Rd
man/graph_sample_size_results.Rd
man/import_model_result.Rd
man/initialise_netlogo_xml_file.Rd
man/join_strings.Rd
man/join_strings_nospace.Rd
man/join_strings_space.Rd
man/kfoldCrossValidation.Rd
man/lhc_calculatePRCCForMultipleTimepoints.Rd
man/lhc_constructcoeff_dataset.Rd
man/lhc_generateLHCSummary.Rd
man/lhc_generateLHCSummary_overTime.Rd
man/lhc_generatePRCoEffs.Rd
man/lhc_generatePRCoEffs_db_link.Rd
man/lhc_generatePRCoEffs_overTime.Rd
man/lhc_generateTimepointFiles.Rd
man/lhc_generate_lhc_sample.Rd
man/lhc_generate_lhc_sample_netlogo.Rd
man/lhc_generate_netlogo_PRCoEffs.Rd
man/lhc_graphMeasuresForParameterChange.Rd
man/lhc_graphMeasuresForParameterChange_from_db.Rd
man/lhc_graphMeasuresForParameterChange_overTime.Rd
man/lhc_netlogo_graphMeasuresForParameterChange.Rd
man/lhc_plotCoEfficients.Rd
man/lhc_polarplot.Rd
man/lhc_process_netlogo_result.Rd
man/lhc_process_sample_run_subsets.Rd
man/lhc_process_sample_run_subsets_overTime.Rd
man/make_extension.Rd
man/make_filename.Rd
man/make_graph_title.Rd
man/make_lhc_plot.Rd
man/make_path.Rd
man/meanSquaredError.Rd
man/normaliseATest.Rd
man/normalise_dataset.Rd
man/nsga2_set_user_params.Rd
man/num.decimals.Rd
man/oat_csv_result_file_analysis.Rd
man/oat_csv_result_file_analysis_from_DB.Rd
man/oat_csv_result_file_analysis_overTime.Rd
man/oat_generate_netlogo_behaviour_space_XML.Rd
man/oat_graphATestsForSampleSize.Rd
man/oat_parameter_sampling.Rd
man/oat_plotResultDistribution.Rd
man/oat_processParamSubsets.Rd
man/oat_processParamSubsets_overTime.Rd
man/oat_process_netlogo_result.Rd
man/output_ggplot_graph.Rd
man/output_param_sets_per_curve.Rd
man/partition_dataset.Rd
man/pcor.mat.Rd
man/pcor.rec.Rd
man/pcor.test.Rd
man/perform_aTest_for_all_sim_measures.Rd
man/plotATestsFromTimepointFiles.Rd
man/plotPRCCSFromTimepointFiles.Rd
man/plot_compare_sim_observed_to_model_prediction.Rd
man/ploteFASTSiFromTimepointFiles.Rd
man/prepare_parameter_value_list.Rd
man/process_netlogo_parameter_range_info.Rd
man/process_parameter_value_if_exists.Rd
man/produce_accuracy_plots_all_measures.Rd
man/produce_accuracy_plots_single_measure.Rd
man/produce_atest_score_summary.Rd
man/produce_summary_for_all_values_of_parameter.Rd
man/rSquared.Rd
man/read_all_curve_results.Rd
man/read_from_csv.Rd
man/read_model_result_file.Rd
man/read_simulation_results.Rd
man/retrieve_results_for_comparison_result_set.Rd
man/sample_parameter_space.Rd
man/scale_lhc_sample.Rd
man/screen_nsga2_parameters.Rd
man/selectSuitableStructure.Rd
man/set.nsga_sensitivity_params.Rd
man/sim_data_for_emulation.Rd
man/summarise_lhc_sweep_responses.Rd
man/summarise_replicate_runs.Rd
man/tutorial_consistency_set.Rd
man/updateErrorForStructure.Rd
man/use_ensemble_to_generate_predictions.Rd
man/visualise_data_distribution.Rd
man/weight_emulator_predictions_by_ensemble.Rd
man/write_data_to_csv.Rd
spartan.Rproj
tests/testthat.R
tests/testthat/Coeff_data_for_test.Rda
tests/testthat/LHC_Param_Result_For_Testing.Rda
tests/testthat/LHC_Sim_Data_For_Test.Rda
tests/testthat/LHC_Sim_Data_For_Test_36.Rda
tests/testthat/LHC_Summary.Rda
tests/testthat/LHC_Summary_36.Rda
tests/testthat/Robustness_hour12_data.Rda
tests/testthat/Robustness_hour36_data.Rda
tests/testthat/Robustness_result_for_test.Rda
tests/testthat/efast_curve1_summary.Rda
tests/testthat/efast_curve1_summary60.Rda
tests/testthat/efast_curve2_summary.Rda
tests/testthat/efast_curve2_summary60.Rda
tests/testthat/helper_aleatory.R
tests/testthat/helper_evolution.R
tests/testthat/helper_input_argument.R
tests/testthat/helper_load_data.R
tests/testthat/helper_netlogo.R
tests/testthat/helper_robustness_analysis.R
tests/testthat/robust_param_test_data.Rda
tests/testthat/test_aleatory_analysis.R
tests/testthat/test_atest_utilities.R
tests/testthat/test_baseline.Rda
tests/testthat/test_cor_coeffs.Rda
tests/testthat/test_cor_coeffs_36.Rda
tests/testthat/test_efast_analysis.R
tests/testthat/test_efast_sampling.R
tests/testthat/test_efast_sampling_netlogo.R
tests/testthat/test_emulation_sensitivity_analysis.R
tests/testthat/test_emulation_utilities.R
tests/testthat/test_evolution.R
tests/testthat/test_input_argument.R
tests/testthat/test_lhc_analysis.R
tests/testthat/test_lhc_plotting.R
tests/testthat/test_lhc_sampling.R
tests/testthat/test_lhc_sampling_netlogo.R
tests/testthat/test_neural_network_utilities.R
tests/testthat/test_robustness_analysis.R
tests/testthat/test_robustness_sampling.R
tests/testthat/test_spartan_utilities.R
vignettes/Figure1.png
vignettes/Figure2.png
vignettes/Figure3.png
vignettes/Figure4.png
vignettes/emulation_ensembles.Rmd
vignettes/netlogo.Rmd
vignettes/sensitivity_analysis.Rmd
