# Force-Directed Euclidean Embedding of Dissimilarity Data

## Documentation for package ‘topolow’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

analyze_network_structure | Analyze Network Structure
c25 | Color Palettes
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
Euclidify | Automatic Euclidean Embedding with Parameter Optimization
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