Man pages for topolow
Force-Directed Euclidean Embedding of Dissimilarity Data
| adaptive_MC_sampling | Perform Adaptive Monte Carlo Sampling (Internal) |
| analyze_network_structure | Analyze Network Structure |
| calculate_diagnostics | Calculate MCMC-style Diagnostics for Sampling Chains |
| calculate_prediction_interval | Calculate Prediction Interval for Dissimilarity Estimates |
| calculate_weighted_marginals | Calculate Weighted Marginal Distributions |
| check_gaussian_convergence | Model Diagnostics and Convergence Testing Check Multivariate... |
| clean_data | Clean Data by Removing MAD-based Outliers |
| color_palettes | Color Palettes |
| coordinates_to_matrix | Convert Coordinates to a Distance Matrix |
| create_base_theme | Create Base Theme |
| create_cv_folds | Create Cross-Validation Folds for a Dissimilarity Matrix |
| create_diagnostic_plots | Create Diagnostic Plots for Multiple Sampling Chains |
| create_topolow_map | Main TopoLow algorithm implementation (DEPRECATED) |
| denv_data | Dengue Virus (DENV) Titer Data |
| detect_outliers_mad | Detect Outliers Using Median Absolute Deviation |
| error_calculator_comparison | Error calculation and validation metrics for topolow... |
| euclidean_embedding | Main topolow algorithm implementation |
| Euclidify | Automatic Euclidean Embedding with Parameter Optimization |
| example_positions | Example Antigenic Mapping Data |
| extract_numeric_values | Utility functions for the topolow package Extract Numeric... |
| generate_kde_samples | Generate New Parameter Samples Using KDE |
| get_grid | Create Grid Around Maximum Likelihood Estimate (Internal) |
| ggsave_white_bg | Save ggplot with white background |
| h3n2_data | H3N2 Influenza HI Assay Data from Smith et al. 2004 |
| hiv_titers | HIV Neutralization Assay Data |
| hiv_viruses | HIV Virus Metadata |
| initial_parameter_optimization | Parameter Space Sampling and Optimization Functions for... |
| likelihood_function | Evaluate a Parameter Set with Cross-Validation |
| list_to_matrix | topolow Data Preprocessing Functions |
| log_transform_parameters | Log Transform Parameter Samples |
| make_interactive | Create Interactive Plot |
| new_aesthetic_config | Plot Aesthetic Configuration Class |
| new_annotation_config | Visualization functions for the topolow package Plot... |
| new_dim_reduction_config | Dimension Reduction Configuration Class |
| new_layout_config | Plot Layout Configuration Class |
| parameter_sensitivity_analysis | Parameter Sensitivity Analysis |
| plot_3d_mapping | Create 3D Visualization |
| plot_cluster_mapping | Create Clustered Mapping Plots |
| plot_network_structure | Plot Network Structure |
| plot.parameter_sensitivity | Plot Parameter Sensitivity Analysis |
| plot.profile_likelihood | Plot Method for profile_likelihood Objects |
| plot_temporal_mapping | Create Temporal Mapping Plot |
| plot.topolow_convergence | Plot Method for topolow Convergence Diagnostics |
| plot.topolow_diagnostics | Plot Method for topolow parameter estimation Diagnostics |
| print.parameter_sensitivity | Print Method for Parameter Sensitivity Objects |
| print.profile_likelihood | Print Method for profile_likelihood Objects |
| print.topolow | Print method for topolow objects |
| print.topolow_convergence | Print Method for topolow Convergence Diagnostics |
| print.topolow_diagnostics | Print Method for topolow parameter estimation Diagnostics |
| process_antigenic_data | Process Raw Antigenic Assay Data |
| profile_likelihood | Profile Likelihood Analysis |
| profile_likelihood_result | S3 Constructor for Profile Likelihood Results |
| reduce_dimensions | Perform Dimension Reduction |
| run_adaptive_sampling | Performs adaptive Monte Carlo sampling |
| save_plot | Save Plot to File |
| scale_to_original_distances | Scale Reduced Dimensions to Match Original Distances |
| scatterplot_fitted_vs_true | Plot Fitted vs. True Dissimilarities |
| summary.topolow | Summary method for topolow objects |
| symmetric_to_nonsymmetric_matrix | Convert distance matrix to assay panel format |
| table_to_matrix | Convert Table Format Data to Dissimilarity Matrix |
| titers_list_to_matrix | Convert Long Format Data to Distance Matrix |
| topolow-package | Algorithm Comparison Helper Functions |
| validate_topolow_df | Validate Input Data Frame |
| vectorized_process_distance_matrix | TopoLow Core Functions Vectorized Processing of Dissimilarity... |
| weighted_kde | Weighted Kernel Density Estimation |
