topolow-package {topolow}R Documentation

Latin Hypercube and Adaptive Monte Carlo Sampling Functions

Description

This file contains functions for performing Latin Hypercube and adaptive Monte Carlo sampling in parameter space. The AMC sampling adapts based on previous evaluations to focus sampling in high-likelihood regions. The functions run locally using parallel processing.

Functions handle:

Helper functions for running RACMACS and Topolow during algorithm comparisons.

Core implementations of the TopoLow algorithm for mapping distances in high dimensions. This file contains the main optimization functions and their variants.

Functions for standardizing and preprocessing antigenic assay data from various sources into consistent formats. Handles titer and IC50 measurements, threshold values, and produces both long and matrix formats suitable for mapping.

This file contains functions for assessing model convergence, analyzing chains, and performing diagnostic tests. Functions are designed to be general-purpose and usable with any iterative optimization or sampling procedure.

Functions handle:

This file contains functions for calculating error metrics and validation statistics between predicted and true distance matrices. Functions handle missing values and special cases like threshold measurements.

Functions for running parameter optimization, comparison experiments, and other computational experiments.

Functions for comparing different map configurations using Procrustes analysis. These functions help assess:

An implementation of the TopoLow algorithm for antigenic cartography mapping and analysis. The package provides tools for optimizing point configurations in high-dimensional spaces, handling missing and thresholded measurements, processing antigenic assay data, and visualizing antigenic maps.

This file contains functions for transforming data between different formats used in antigenic cartography. Functions handle conversion between:

This file contains utility functions used throughout the topolow package. Functions include data manipulation, and format conversion.

This file contains functions for visualizing topolow results including dimension reduction plots and cluster visualizations. Supports multiple plotting methods and customization options.

Functions handle:

Details

The package implements a physics-inspired approach combining spring forces and repulsive interactions to find optimal point configurations. Key features include:

Main Functions

Output Files

Functions that generate output files (like parameter optimization results) will create subdirectories in either:

The following subdirectories may be created:

Citation

If you use this package, please cite: Omid Arhami, Pejman Rohani, Topolow: A mapping algorithm for antigenic cross-reactivity and binding affinity assays, Bioinformatics, 2025;, btaf372, https://doi.org/10.1093/bioinformatics/btaf372 doi:10.1093/bioinformatics/btaf372.

Author(s)

Maintainer: Omid Arhami omid.arhami@uga.edu (ORCID) [copyright holder]

See Also

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[Package topolow version 1.0.0 Index]