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.