seriation_1.5.6

seriation 1.5.6 (08/19/2024)

New Features

• Added registered_by field to registries.

Changes

• We replaced the FORTRAN implementation for BEA with code from package TSP.
• ME is now calculated using C code.
• optimal.c: updated memory allocation to R allocation.
• stress.c: updated memory allocation to R allocation.

Bug Fixes

• Added two missing package anchors to palette man page.

seriation 1.5.5

seriation 1.5.5 (04/17/2024)

• Updated man pages.

seriation 1.5.4 (12/11/2023)

Bug Fixes

• Fixed MDS_angle order for different BLAS implementation giving different
  results for eigen().

seriation 1.5.3 (11/28/2023)

New Features

• permute for dendrograms gained parameter dist and accepts now seriation
  methods.
• Added method "AOE" for correlation matrices.
• registry for seriation methods now contains the name of the seriation criterion
  and a description. seriate_rep now automatically uses the criterion from
  the registry.
• all seriation methods gained parameter rep.

Bug Fixes

• optimal.c: use now the correct data type for Rprintf
• Skip deterministic tests on Mac M1 because of numerical differences.

seriation_1.5.1

seriation 1.5.1 (07/20/2023)

New Fearures

• pimage and permute now accept order = TRUE to perform the default seriation.
• hmap gained parameter col_dist to define the color palette used for distance
  matrices.
• hmap dropped parameter showDend and gained parameter plot_margins instead.

Bug Fixes

• pimage/ggpimage now use zlim correctly to choose the color palette.
• BEA for matrix is now correctly registered as randomized.
• fixed col/row_labels parameter.
• rev() for seriations based on hclust now reverses the dendrogram.
• tests now also accept reverse orders for testing deterministic methods.

seriation_1.5.0

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)

seriation_1.3.6

New Features

• ggpimage has now a zlim parameter.

Bug Fixes

• added register functions back to export (reported by thomasp85).
• fixed viewports for pimage with colorkey.
• fixed ggplot diverging color palette direction.

Bug Fixes in seriation 1.3.4

• fixed length calculation in optimal.c

seriation_1.3.3

New Features

• pimage and dissplot gained parameter diag. pimage for dist by default does not show the diagonal now.
• C code now supports long vectors for dist objects.

Changes

• we now use roxygen for documentation.
• added check for long vectors that FORTRAN cannot handle.
• removed deprecated show functions for the registries.

seriation_1.3.2

• Improved argument checking for ser_permutation_vector().
• ggplot uses now standard ggplot2 color palettes.

seriation_1.3-1

seriation 1.3-1 (10/15/2021)

New Features

• added seriation based on 1D t-SNE embedding.
• added seriation based on 1D UMAP embedding.
• added seriation based on OPTICS.

Changes

• VAT plots now default to upper_tri = TRUE to show the whole matrix.

seriation_1.3-0

Changes

• Plotting
  • Most plotting functions have now a common interface. This changed many parameters.
  • hmap now uses heatmap from package stats.
  • dissplot shows now averages in the top triangles.
  • improved layout (less white space) for grid-based plots.
• Registry
  • list_seriation_methods and list_criterion_methods without kind return now a list.
  • show_seriation_methods and show_criterion_methods are deprecated
• Other Changes
  • criterion returns now NA with a warning for ME for non-positive matrices (used to stop with an error).
  • dependency dendextend is now only suggested (used for testing).
  • get_order now returns also labels.
  • hclust-based seriations now defaults for linkage to complete instead of average.

New Features

• Plotting
  • Major refactoring of plotting functions to provide a more consistent interface.
  • added ggplot2-based plots, ggimage, gghmap, ggVAT, ggiVAT, ggbertinplot, ggdissplot.
  • colors are now more consistent and all have bias and power.
• Seriation methods
  • seriate for matrix has now method "Heatmap".
  • seriate now accepts data.frames and used method "heatmap" as the default.
  • added seriation method "Reverse" for reverse identity order.
• Permutation
  • permute for matrix-like objects gained parameter margin.
  • permute for data.frame works now identical to permute for matrix.

seriation_1.2-9

• removed dependency on methods.
• added DOIs.