Force-Directed Euclidean Embedding of Dissimilarity Data

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Documentation for package ‘topolow’ version 2.0.1

• 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