adaptive_MC_sampling    Perform Adaptive Monte Carlo Sampling
add_noise_bias          Add Noise and Bias to Matrix Data
analyze_network_structure
                        Calculate Network Analysis Metrics
calculate_annual_distances
                        Calculate Annual Distance Metrics
calculate_cumulative_distances
                        Calculate Cumulative Distance Metrics
calculate_diagnostics   Calculate Adaptive Monte Carlo Sampling
                        Diagnostics
calculate_prediction_interval
                        Calculate prediction interval for distance
                        estimates
calculate_procrustes_difference
                        Calculate Procrustes Difference Between Maps
calculate_procrustes_significance
                        Calculate Statistical Significance Between Maps
                        Using Procrustes Analysis
calculate_weighted_marginals
                        Calculate Weighted Marginal Distributions
check_gaussian_convergence
                        Check Multivariate Gaussian Convergence
clean_data              Clean Data by Removing MAD-based Outliers
color_palettes          Color Palettes
coordinates_to_matrix   Convert coordinates to distance matrix
create_and_optimize_RACMACS_map
                        Create and Optimize a RACMACS Map
create_cv_folds         Create Cross-validation Folds for Distance
                        Matrix
create_diagnostic_plots
                        Create Diagnostic Plots for Multiple Chains
create_topolow_map      Main TopoLow algorithm implementation
denv_data               Dengue Virus (DENV) Titer Data
dist_to_titer_table     Convert Distance Matrix to Titer Panel Format
error_calculator_comparison
                        Calculate comprehensive error metrics between
                        predicted and true distances
example_positions       Example Antigenic Mapping Data
find_mode               Find Mode of Density Distribution
generate_complex_data   Generate Complex High-Dimensional Data for
                        Testing
generate_synthetic_datasets
                        Generate Synthetic Distance Matrices with
                        Missing Data
generate_unique_string
                        Generate unique string identifiers with year
                        suffix
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
increase_na_percentage
                        Increase Missing Values in a Matrix
initial_parameter_optimization
                        Run Parameter Optimization Via Latin Hypercube
                        Sampling
log_transform_parameters
                        Log Transform Parameter Samples
long_to_matrix          Convert Long Format Data to Distance Matrix
make_interactive        Create Interactive Plot
new_aesthetic_config    Plot Aesthetic Configuration Class
new_annotation_config   Plot Annotation Configuration Class
new_dim_reduction_config
                        Dimension Reduction Configuration Class
new_layout_config       Plot Layout Configuration Class
only_virus_vs_as        Filter matrix to only virus vs antiserum
                        distances
parameter_sensitivity_analysis
                        Parameter Sensitivity Analysis
plot.parameter_sensitivity
                        Plot Method for Parameter Sensitivity Analysis
plot.profile_likelihood
                        Plot Method for Profile Likelihood Objects
plot.topolow_amcs_diagnostics
                        Plot Method for Adaptive Monte Carlo Sampling
                        Diagnostics
plot.topolow_convergence
                        Plot Method for Convergence Diagnostics
plot_3d_mapping         Create 3D Visualization
plot_cluster_mapping    Create Clustered Mapping Plots
plot_distance_heatmap   Plot Distance Matrix Heatmap
plot_network_structure
                        Plot Network Structure Analysis
plot_temporal_mapping   Create Temporal Mapping Plot
prepare_heatmap_data    Generate Distance Matrix Heatmap Data
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_amcs_diagnostics
                        Print Method for Adaptive Monte Carlo Sampling
                        Diagnostics
print.topolow_convergence
                        Print Method for Convergence Diagnostics
process_antigenic_data
                        Process Raw Antigenic Assay Data
profile_likelihood      Profile Likelihood Analysis
prune_distance_network
                        Prune Distance Data for Network Quality
run_adaptive_sampling   Run Adaptive Monte Carlo Sampling
save_plot               Save Plot to File
scatterplot_fitted_vs_true
                        Plot Fitted vs True Distances
summary.topolow         Summary method for topolow objects
symmetric_to_nonsymmetric_matrix
                        Convert distance matrix to assay panel format
unweighted_kde          Unweighted Kernel Density Estimation
weighted_kde            Weighted Kernel Density Estimation
