# Antigenic Mapping and Antigenic Velocity Algorithm

## Documentation for package ‘topolow’ version 1.0.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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
c25 | Color Palettes
c25_claud | Color Palettes
c25_old | Color Palettes
c25_older | Color Palettes
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