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 |