Files in topolow

Force-Directed Euclidean Embedding of Dissimilarity Data

NEWS.md README.md R/error_metrics.R R/core.R R/visualization.R R/topolow-package.R R/adaptive_sampling.R R/algorithm_comparison_helpers.R R/data.R R/diagnostics.R R/globals.R R/data_preprocessing.R R/utils.R inst/doc/Comprehensive_Evaluation.Rmd inst/doc/Comprehensive_Evaluation.R inst/scripts/check_dependencies.R build/topolow-manual.pdf tests/testthat.R tests/testthat/test-edge-cases.R tests/testthat/test-utils.R tests/testthat/test-deprecated.R tests/testthat/test-data-preprocessing.R tests/testthat/test-transformations.R tests/testthat/test-data.R tests/testthat/test-antigenic-cartography.R tests/testthat/test-adaptive-sampling.R tests/testthat/test-S3-methods.R tests/testthat/test-diagnostics.R tests/testthat/test-integration.R tests/testthat/test-core.R tests/testthat/test-visualization.R vignettes/Comprehensive_Evaluation.Rmd man/plot.topolow_convergence.Rd man/print.topolow_diagnostics.Rd man/new_layout_config.Rd man/reduce_dimensions.Rd man/extract_numeric_values.Rd man/calculate_diagnostics.Rd man/likelihood_function.Rd man/plot.topolow_diagnostics.Rd man/scale_to_original_distances.Rd man/table_to_matrix.Rd man/print.parameter_sensitivity.Rd man/process_antigenic_data.Rd man/hiv_viruses.Rd man/adaptive_MC_sampling.Rd man/detect_outliers_mad.Rd man/run_adaptive_sampling.Rd man/coordinates_to_matrix.Rd man/new_aesthetic_config.Rd man/topolow-package.Rd man/Euclidify.Rd man/color_palettes.Rd man/create_base_theme.Rd man/generate_kde_samples.Rd man/plot.profile_likelihood.Rd man/calculate_weighted_marginals.Rd man/plot_cluster_mapping.Rd man/log_transform_parameters.Rd man/list_to_matrix.Rd man/calculate_prediction_interval.Rd man/hiv_titers.Rd man/create_topolow_map.Rd man/example_positions.Rd man/ggsave_white_bg.Rd man/plot_network_structure.Rd man/plot_temporal_mapping.Rd man/make_interactive.Rd man/scatterplot_fitted_vs_true.Rd man/plot.parameter_sensitivity.Rd man/symmetric_to_nonsymmetric_matrix.Rd man/vectorized_process_distance_matrix.Rd man/parameter_sensitivity_analysis.Rd man/denv_data.Rd man/print.topolow_convergence.Rd man/initial_parameter_optimization.Rd man/create_diagnostic_plots.Rd man/get_grid.Rd man/plot_3d_mapping.Rd man/print.profile_likelihood.Rd man/profile_likelihood_result.Rd man/summary.topolow.Rd man/h3n2_data.Rd man/analyze_network_structure.Rd man/check_gaussian_convergence.Rd man/new_annotation_config.Rd man/euclidean_embedding.Rd man/print.topolow.Rd man/titers_list_to_matrix.Rd man/new_dim_reduction_config.Rd man/profile_likelihood.Rd man/save_plot.Rd man/validate_topolow_df.Rd man/weighted_kde.Rd man/create_cv_folds.Rd man/clean_data.Rd man/error_calculator_comparison.Rd