# 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)

* Fixed dependence on MASS

# 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)

* service release.

# 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)

* service release

# 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)

* Initial beta release.
