NEWS

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mappeR 2.4.0 (2026-01-27)

• Remove error on filtered data point names not matching; if names are not given, then mappeR will assume the output of the filter is in the same order as the original data points.
• The generic create_mapper_object function should correctly handle non 1D lens functions.
• Fixed a bug where sometimes empty bins could get through to the clusterers and mess them up.

mappeR 2.3.0 (2025-07-27)

• Add more input sanitization for distance matrices
• Add more cluster metrics to output, namely medoid name, maximum distance to medoid, and sum of squared distances to medoid
• Examples now use actual noisy circle data; better examples coming soon

mappeR 2.2.1 (2025-07-02)

• Relax some tests as to avert floating point shenanigans

mappeR 2.2.0 (2025-06-28)

• Force user to have the names of the filtered data match the names of the original data set. You may need to call names(filtered_data) = row.names(data) or similar before making a call to generate a mapper object. The Ball Mapper flavored versions should still work fine.
• Add the option to specify a global cut height when using the global hierarchical clusterer.
• Update existing documentation and remove .Rd pages written about unexported functions (documentation still exists in source).

mappeR 2.1.0 (2025-06-09)

• Add better hierarchical clusterers; there is one which cuts each dendrogram uniformly, and one which cuts per patch. The cut height is at the beginning of the longest unbroken branch in the dendrogram (note this is not always the "correct" number of clusters!).
• Remove igraph dependency; see shinymappeR for an example of how to use igraph with mappeR.
• Change output vertex dataframe column names from tightness to mean_dist_to_medoid and bin to patch.
• Change edge weight to use Jaccard index.

mappeR 2.0.2 (2025-02-20)

• Really, for real this time, make the default clusterer cut correctly.

mappeR 2.0.1 (2025-02-19)

• Default hierarchical clusterer now correctly cuts dendrograms at the midpoint of their tallest branches.

mappeR 2.0.0 (2025-02-16)

• Clustering is now handled by a clusterer, which is a function that can handle a list of distance matrices (one for each bin/level set) and output clustering results for each one. The hierarchical clustering included previously is now available as a clusterer called hierarchical_clusterer because I am very creative.
• User-defined clusterers are possible as long as they can handle inputs/outputs correctly. The basic idea is that the output of a clusterer should look like a list of calls to cutree from the hclust package. Look to the clusterer farm for more examples in the future.

mappeR 1.3.0 (2024-10-30)

• Adjust compute_tightness to no longer normalize by the maximum distance from the medoid (easier to see behavior in a single mapper graph, may add options in future)
• Add option to consider each level set locally when clustering; default is still to do it globally

mappeR 1.2.0 (2024-10-23)

• Add other hierarchical clustering methods (those available from fastcluster)
• Fix issues with 100 percent overlap situations caused by mapply simplifications

mappeR 1.1.0 (2024-10-16)

• Added safety checks for mapper input functions (no NA inputs, etc)
• Removed Cytoscape interfacing for the release version; will remain in a separate branch

mappeR 1.0.0 (2024-10-07)

• Balls/bins with equal amounts of data no longer cause wonkiness
• Zero overlap situations should work correctly with igraph
• Added eccentricity lens/filter fuction

mappeR 0.1.5 (2024-10-04)

• 1D tests will not fail due to a one interval cover

mappeR 0.1.4

• Reduced edge widths for Cytoscape visualization.
• Rescaled tightness calculation down a bit.

mappeR 0.1.3 (2024-10-04)

• Edge overlap data is now present in output mapper objects.
• Cytoscape edges are styled by width instead of transparency.

mappeR 0.1.2

• The algorithm now still runs even if there is only one level set to be considered.

mappeR 0.1.1

mappeR 0.1.0

• Initial CRAN submission.