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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.