Antigenic Mapping and Antigenic Velocity Algorithm

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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