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@mhahsler mhahsler released this 20 Jul 01:16
· 67 commits to master since this release
seriation_1.5.0
f28de7c

seriation 1.5.0 (07/19/2023)

New Features

  • The seriation registry now contains help information for the seriation method
    parameters.
  • New function seriate_best, seriate_rep, and seriate_improve() to easily find a good order for
    randomized algorithms. Parallel execution is supported.
  • Seriation method registry has new fields 'randomized' to indicate if an algorithm
    is randomized and can be run several times and 'optimizes' to indicate
    what criterion is optimized. This information is used by seriate_rep.
  • Seriation for arrays (including matrix) gained margin parameter.
  • tsne and umap can now be used on data matrices.
  • get_rank() returns now labels.
  • Embedding-based methods now return the order with an attribute called configuration.
  • New MDS_stress() function.
  • Added register_smacof().
  • Added seriation method "Reverse" for dist.
  • New seriation methods from vegan: isomap, monoMDS, metaMDS.
  • New seriation method "Enumerate" for complete enumeration.
  • New seriation method "Mean" for matrix.
  • New seriation method "SGD" for distances to improve solutions using stochastic gradient descent.
  • New seriation method "LLE" (locally linear embedding) for matrix.
  • Heatmap seriation has now special seriation_method "HC_Mean".
  • New seriation criterion "Rho" calculates the absolute Spearman's rank correlation coefficient.
  • list_seriation_methods() and list_criterion_methods() gained parameter names_only.

Changes

  • Seriation methods for MDS are now MDS, isoMDS and Sammon_mapping and have now
    individual control parameters.
  • orderplot() is now called plot_config() and can also visualize 2D configurations.
  • HC-based seriation: The control parameter method is now linkage so it can be used
    in seriate() in the ...
  • Seriation method spectral now also returns the embedding.
  • Seriation method simulated annealing is now called "GSA".
  • Simplified generics for pimage and ggpimage. Defaults for pimage.dist have changed.
  • DendSer methods now return hclust objects.

Bug Fixes

  • fixed labels returned by uniscale()
  • FORTRAN: replaced old DFLOAT with DBLE (reported by Brian D. Ripley).

seriation 1.4.2 (03/07/2023)

Bug Fixes

  • pimage: ... is now passed on to the seriation method.
  • added missing S3 method registrations.

New Features

  • methods umap and tsne can now return the embedding.

seriation 1.4.1 (12/27/2022)

New Features

  • get_order not consistently returns permutation vectors with names (by david-barnett).

Bug Fixes

  • criterion.c: replaced enum for bool with <stdbool.h>
  • Additional contributors are not in alphabetical order.

seriation 1.4.0 (10/21/2022)

New Features

  • seriate for arrays (including matrices) now returns a complete ser_permutation for all
    dimensions even if margins are specified. For not specified margins, identity permutations
    are returned.
  • added support for tables.
  • added new seriation method CA (correspondence analysis) contributed by Michael Friendly.
  • permute now accepts more than one margin.
  • permute now accepts a seriation method instead of order.

Bug Fixes

  • seriate.dist now throws correct error upon encountering NAs (by david-barnett)
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