seriation 1.3.5 (03/28/2022)
Bigfixes
- added register functions back to export (reported by thomasp85).
seriation 1.3.4 (3/16/2022)
Bigfixes
- fixed length calculation in optimal.c
seriation 1.3.3 (3/3/2022)
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 (2/10/2022)
Changes
- improved argument checking for ser_permutation_vector().
- ggplot uses now standard ggplot2 color palettes.
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 (06/29/2021)
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 (09/29/2020)
- removed dependency on methods.
- added DOIs.
seriation 1.2-8 (08/27/2019)
New features
- get_seriation_method now has better information and also show available control parameters.
Bugfixes
- GA: Updated parameter names after change in package ga.
seriation 1.2-7 (06/07/2019)
Bugfixes
- Added missing void * to init.c
seriation 1.2-6 (06/03/2019)
Bugfixes
- Converted print routines in Fortran code to dblepr, intpr, etc.
- seriate.matrix also prints now method name for control verbose = TRUE.
seriation 1.2-5 (05/30/2019)
Bugfixes
- Fixed compilation warnings in Fortran code.
seriation 1.2-4 (05/29/2019)
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)
seriation 1.2-3 (02/05/2018)
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)
seriation 1.2-2 (05/08/2017)
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.
- Seriation 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).
seriation 1.2-1 (08/06/2016)
New features
- Added new distance measure called absolute pairwise rank differences.
Changes and bugfixes
- The default setting for ser_dist and ser_cor is now reverse is TRUE.
- pimage does now work with matrices containing only a single value.
- control parameters for method TSP are now correctly passed on (reported by David Aliyev).
seriation 1.2-0 (2/22/2016)
New features
- 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 QAP_Inertia and QAP_BAR solver.
- Added DendSer using register_DendSer().
- Added GA using register_GA().
Changes and bugfixes
- Fixed RGAR (w needs to be in [2,n-1]).
- 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.
seriation 1.1-3 (12/18/2015)
- Added is.robinson to recognize (pre) Robinson matrices.
- Added random.robinson to create random Robinson matrices.
- Added seriation methods “QAP_LS” and “QAP_2SUM” (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”.
- ser_cor and ser_dist gained parameter y. ser_cor gained parameter test to perform tests for association.
- Added permute method for hclust and dendrogram objects.
seriation 1.1-2 (8/23/2015)
- Argument (control and …) check warns now instead of throwing an error.
- seriation_dist, seriation_cor and seriation_align are now shortened to ser_dist, ser_cor and ser_align.
- Method “ppc” is now faster and also available in ser_cor.
- Fixed ser_cor for “spearman” and “Kendall” (uses now rank correctly).
- ser_cor and ser_dist gained parameter reverse to indicate that permuations are also tried in reverse and the best value is reported.
seriation 1.1-1 (7/1/2015)
- get_permutation_matrix added.
- seriation_dist measure “ppc” (positional proximity coefficient) added.
- Fixed bug with permute and ser_permutation_vectors.
- Identity permutations (NA) give now an error for get_order and get_permutation_matrix.
- Fixed imports for non-base R packages.
seriation 1.1-0 (06/09/2015)
- Seriation method ‘Identity’ added.
- Seriation method ‘Random’ added.
- Seriation method ‘VAT’ added.
- Seriation methods ‘Spectral’ and ‘Spectral_norm’ added.
- Seriation methods ‘PCA_angle’ and ‘MDS_angle’ added.
- Seriation methods ‘SPIN_NH’ and ‘SPIN_STS’ added.
- Several aliases for seriation methods added.
- Criterion ‘RWGAR’ added.
- permutation_matrix2vector and permutation_vector2matrix added.
- Identity permutation (value NA) added.
- ser_permutation and ser_permutation_vector can now be used interchangably,
- get_rank for permutation vectors added.
- seriation_dist and seriation_alignment to calculate dissimilarities between seriation orders added.
- Wood data set added.
Chameleon data sets added.
- create_lines_data, create_ordered_data added.
- pimage, hmap and dissplot: Simplified and made interfaces more consistent (all use now zlim, consistent default color palettes).
- pimage gained axes and prop; NA in matrix now works.
- seriation checks now control arguments consistently.
- We use now package registry to manage methods.
- reorder for hclust added.
- iVAT with path distance added.
- color palettes (bluered, greenred, grays) added.
- Improved speed of C code.
- Fixed problem with testthat filenames fixed.
- bburg.f/bbwrg.f: memory access problem fixed.
seriation 1.0-14 (12/02/2014)
- arsa.f: removed 0 flag in rand() so it compiles under AIX (reported by Lei Zhang)
- arsa.f/bburg.f/bbwrg.f: calls now R RNG to be compatible with certain compilers (e.g., Intel FORTRAN) (reported by Rohan Shah)
seriation 1.0-13 (3/11/2014)
seriation 1.0-12 (2/18/2014)
- ser_permutation_vectors can now be reversed with rev
- get_order: removed the weird labels.
- we use now testthat
- fixed bug with intra-cluster ordering using silhouette width (reported by Bettina Gruen)
- Cleaned up dependencies: TSP, grid, cluster, gclus and colorspace are now imports instead of dependencies.
seriation 1.0-11 (9/6/2013)
seriation 1.0-10 (2/15/2013)
- pimage has now a colorkey and a range argument
- fixed bug in ARSA when the distance matrix contains all 0s
- added PACKAGE argument to .Fortran calls
seriation 1.0-8 and 1.0-9 (11/6/2012)
- get_order: labels are now in the correct order (Bug report by Crt Ahlin)
- Replaced Fortran I/O with R I/O for verb=TRUE
- Fixed pop/newpage bug in pimage.dist (reported by Bettina Gruen)
seriation 1.0-7 (9/25/2012)
- Fixed out-of-bounds bug in arsa.f (reported by Rohan Shah)
- Fixed out-of-bounds bug in bburcg.f
seriation 1.0-6 (10/19/2011)
- removed deprecated parameter gamma for dissplot()
seriation 1.0-5 (9/2/2011)
- bertinplot(): fixed representation for 0, neg. values and highlight. (Bug report by G. Sawitzki).
- bertinplot(): added panel.blocks and option for shading
- bertinplot(): added bertin_cut_line()
seriation 1.0-4 (6/28/2011)
- pimage() now uses grid.raster.
- dissplot() now uses grid.raster.
seriation 1.0-3 (1/14/2011)
- improved validity check for permutations and added check for dist with neg. entries to seriate.dist.
seriation 1.0-2 (3/13/2010)
seriation 1.0-1 (8/25/2009)
- added drop=FALSE in permute for matrix.
- fixed reordering for labels.
- added permute for character.
- added different methods to calculate between cluster dissimilarities (min, max, avg, Hausdorff).
- dissplot has now additional options hue, power, gamma, flip and changed behavior for averages. dissplot depends now on colorspace.
Version 1.0-0 (3/24/2009)
- many changes and first stable release.
Version 0.1-1 (9/1/2007)