seriation - seriation 1.5.7

New Features

• Added seriation method BK_unconstrained by kbvernon.
• All methods now gracefully handle data with two few objects.
• serpermutationvector() now updates method name.

Bug Fixes

• Fixed label order for seriate.matrix.
• Fixed typo in parameter name for seriation method ARSA (reported by Brian Ripley)

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Published by mhahsler over 1 year ago

seriation -

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.

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Published by mhahsler almost 2 years ago

seriation - 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.

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Published by mhahsler about 2 years ago

seriation -

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.

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Published by mhahsler almost 3 years ago

seriation -

seriation 1.5.0 (07/19/2023)

New Features

• The seriation registry now contains help information for the seriation method parameters.
• New function seriatebest, seriaterep, 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 seriationmethod "HCMean".
• New seriation criterion "Rho" calculates the absolute Spearman's rank correlation coefficient.
• listseriationmethods() and listcriterionmethods() 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
• 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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Published by mhahsler almost 3 years ago

seriation -

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

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Published by mhahsler almost 4 years ago

seriation -

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.

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Published by mhahsler about 4 years ago

seriation -

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

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Published by mhahsler over 4 years ago

seriation -

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.

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Published by mhahsler over 4 years ago

seriation -

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
  • listseriationmethods and listcriterionmethods without kind return now a list.
  • showseriationmethods and showcriterionmethods 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.

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Published by mhahsler almost 5 years ago

seriation -

• removed dependency on methods.
• added DOIs.

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Published by mhahsler over 5 years ago

seriation -

New features

• getseriationmethod now has better information and also show available control parameters.

Bugfixes

• GA: Updated parameter names after change in package ga.

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Published by mhahsler almost 7 years ago

seriation -

New features

• bertinplot: panel colors can now be specified in highlight and as shading.function.

Bugfixes

• bertinplot: fix white squares when frame = TRUE (by Dirk Seidensticker).
• seriation method "BEA" has now a slight code improvement (suggested by RichardKav)
• Fixed compilation warnings in Fortran code.

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Published by mhahsler about 7 years ago

seriation -

Bugfixes

• seriation method "BEA" is now not longer masked by "BEA_TSP". Also the FORTRAN calls now work.
• SPIN: making the matrix doubly stochastic now checks all rows/columns (reported and fixed by cerebis)

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Published by mhahsler over 8 years ago

seriation -

New features

• Added new seriation method SA which provides simulated annealing for all criterion measures.
• Added criterion Cor_R (ME for the moment ordering algorithm by Deutsch and Martin).
• Added uniscale to produce a unidimensional scaling configuration given a distance matrix and a permutation.
• Criterion gained parameter force_loss (default is FALSE). Merit measures are converted into loss values by multiplying with -1.
• Added Supreme Court dataset.

Changes and bugfixes

• Default for seriate (dist) and dissplot is now "Spectal" since it gives a better tradeoff between quality and speed.
• Seriaiton method ARSA's control argument nreps is now for consistency called reps.
• Criterion: dist objects are now automatically converted into a similarity matrix for ME, Moore_stress and Neumann_stress.
• pimage now suppresses the color key for logical matrices and checks for all NAs and infinite entries.
• Correction: ARSA minimizes the linear seriation criterion (man page and vignette).

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Published by mhahsler about 9 years ago

seriation -

Changes in version 1.2-1 (08/06/2016)

• The default setting for serdist and sercor is now reverse is TRUE.
• Bugfix: pimage did now work with matrices containing only a single value.
• Bugfix: control parameters for method TSP are now correctly passed on (reported by David Aliyev)
• Added new distance measure called absolute pairwise rank differences.

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Published by mhahsler almost 10 years ago

seriation - CRAN Release 1.2-0

Changes in version 1.2-0 (2/22/2016) - Fixed RGAR (w needs to be in [2,n-1]). - RGAR gained parameter pct to specify the window as a percentage. - added the lazy path length criterion. - added the banded anti-Robinson form (BAR) criterion. - added QAPInertia and QAPBAR solver. - added DendSer using registerDendSer(). - added GA using registerGA(). - registry now warns and modifies entries with the same name. - registry now lists methods in alphabetical order. - seriation method alias Chen was removed. Use R2E.

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Published by mhahsler over 10 years ago

seriation -

• added is.robinson to recognize (pre) Robinson matrices.
• added random.robinson to create random Robinson matrices.
• added seriation methods "QAPLS" and "QAP2SUM" (QAP-based seriation).
• added criteria "LS" and "2SUM" from QAP-based seriation.
• Fixed Spectral_norm seriation.
• hmap now honors zlim also in dendrogram-based maps.
• hmap gained option sym for seriation based maps. showdist can now be one of "none" (default), "row", "column", or "both".
• sercor and serdist gained parameter y. ser_cor gained parameter test to perform tests for association.
• added permute method for hclust and dendrogram objects.

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Published by mhahsler over 10 years ago