Files in kalden/spartan
Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan

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.gitignore
.travis.yml
DESCRIPTION
DESCRIPTION~
LICENSE
NAMESPACE
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_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/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_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_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_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_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_Result_Hour12.Rda
tests/testthat/LHC_Result_Hour36.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/built_ensemble_72.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/netlogo_efast.zip
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
kalden/spartan documentation built on Dec. 19, 2017, 10:43 a.m.