Changes in version 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.

                 Changes in version 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

                 Changes in version 2.2.1 (2025-07-02)                  

  - Relax some tests as to avert floating point shenanigans

                 Changes in version 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).

                 Changes in version 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.

                 Changes in version 2.0.2 (2025-02-20)                  

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

                 Changes in version 2.0.1 (2025-02-19)                  

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

                 Changes in version 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.

                 Changes in version 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

                 Changes in version 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

                 Changes in version 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

                 Changes in version 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

                 Changes in version 0.1.5 (2024-10-04)                  

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

                        Changes in version 0.1.4                        

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

                 Changes in version 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.

                        Changes in version 0.1.2                        

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

                        Changes in version 0.1.1                        

                        Changes in version 0.1.0                        

  - Initial CRAN submission.