Euclidify               Automatic Euclidean Embedding with Parameter
                        Optimization
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 Gaussian Convergence
clean_data              Clean Data by Removing MAD-based Outliers
color_palettes          Color Palettes
coordinates_to_matrix   Convert Coordinates to a Distance Matrix
create_cv_folds         Create Cross-Validation Folds for a
                        Dissimilarity Matrix
create_diagnostic_plots
                        Create Diagnostic Plots for Multiple Sampling
                        Chains
denv_data               Dengue Virus (DENV) Titer Data
error_calculator_comparison
                        Error calculation and validation metrics for
                        topolow Calculate Comprehensive Error Metrics
euclidean_embedding     Main topolow algorithm implementation
example_positions       Example Antigenic Mapping Data
extract_numeric_values
                        Utility functions for the topolow package
                        Extract Numeric Values from Mixed Data
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 topolow
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 Annotation Configuration Class
new_dim_reduction_config
                        Dimension Reduction Configuration Class
new_layout_config       Plot Layout Configuration Class
parameter_sensitivity_analysis
                        Parameter Sensitivity Analysis
plot.parameter_sensitivity
                        Plot Parameter Sensitivity Analysis
plot.profile_likelihood
                        Plot Method for profile_likelihood Objects
plot.topolow_convergence
                        Plot Method for topolow Convergence Diagnostics
plot.topolow_diagnostics
                        Plot Method for topolow parameter estimation
                        Diagnostics
plot_3d_mapping         Create 3D Visualization
plot_cluster_mapping    Create Clustered Mapping Plots
plot_network_structure
                        Plot Network Structure
plot_temporal_mapping   Create Temporal Mapping Plot
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
run_adaptive_sampling   Performs adaptive Monte Carlo sampling
save_plot               Save Plot to File
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
weighted_kde            Weighted Kernel Density Estimation
