topolow 0.3.2

• Initial release to CRAN (revised per CRAN reviewr’s instructions).
• Introduces the Topolow algorithm, a physics-inspired method for antigenic cartography.
• Provides robust mapping and complete positioning of all antigens, even with highly sparse datasets (>95% missing values).
• Implements automatic, likelihood-based estimation to determine the optimal dimensionality of the antigenic map.
• Includes functionality to calculate “antigenic velocity” vectors to quantify the rate and direction of antigenic drift.
• Features tools for handling and processing cross-reactivity and binding affinity assay data, including those with thresholded values.
• Demonstrates improved prediction accuracy and run-to-run stability compared to traditional MDS methods.

topolow 1.0.0 (2025-07-01)

• All exported methods now include \value documentation describing the output’s class, structure, and meaning.
• Examples for unexported functions have been omitted, and \dontrun{} wrappers have been removed5. Slower examples are now wrapped in \donttest{} as appropriate.
• Functions no longer write to user directories by default. Functions where writing a file is the main purpose now require the user to specify an output directory.
• The complex distributed processing functionality has been removed, as it was not essential for typical use cases.
• The link to our paper and citation information have been updated.