SOMbrero 1.4-1

Fixed bugs:
  fixed a bug related to issue #4 on Github

********************************************************************************
SOMbrero 1.4 (major release)

New features:
  numeric SOM can now handle missing data: training is done without accounting
  for missing entries and resulting SOM can be used to impute missing entries

Fixed bugs:
  proto0 was incorrectly used for 'numeric' (see bug report #4 on Github)
  
  dist.type was improperly handled for types other than 'euclidean' and 
  'letremy' when radius.type was letremy
  
  minor bug in computation of tolerance for numerical approximations with 
  Gaussian radius
  
  removed 'tolerance' from the prediction (not used any more)
  
  fixed minor issues in OO for trainSOM
  
Improvements:
  Heskes' affectation now account for total neighbord weight in order to not 
  favor too much the borders of the map
  
Misc: 
  refactorization of most of the code

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SOMbrero 1.3-1

Improvements:
  make trainSOM a method for different classes
  
  create a trainSOM method for outputs of mixKernel package

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SOMbrero 1.3
Fixed bugs:
  eps0 parameter taken into account in shiny app
  correct use of "what" parameter for superclasses plot
  fixed a minor problem in Heskes' assignment when distance is Euclidean

Improvements:
  hexagonal topography is now available
  
  plots are now ggplot2 based and former plot arguments are no longer valid 
  since ggplot2 syntax is now used
  
  the shiny app has been entirely remade
  
  data from the environment can be loaded directly in the shiny application and
  3 examples datasets are loaded automatically in the shiny app
  
  titles and legends in plots have been improved

  code used in the app is printed to ease reproducibility
  
  protoDist (for neighbors) has been improved by adding, for the case 
  'neighbors' a radius argument. When this radius is passed the Euclidean 
  distance between unit coordinates
  
  print.titles is deprecated and has been replaced by show.names
  
  
Misc:
  radar plots are no longer available

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SOMbrero 1.2-5
Fixed bugs:
  adapted script to the new stringsAsFactor policy on devel
  fixed a bug for non significant variables in summary
  
Misc:
  roxygenized documentation
  changed maintainer name and address, added new contributors
  fixed URI in package vignette

********************************************************************************  
SOMbrero 1.2-4
Fixed bugs:
  changed unitary tests because of changes in RGN for devel
  
Misc:
  changed maintainer name and address

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SOMbrero 1.2-3
Fixed bugs:
  removed unecessary scaling checks for 'relational' in predict
  
Improvements:
  used testthat to implement unitary tests
  remove redundant code in trainSOM
  fixed seed in unitary tests for reproducibility reasons

Misc:
  changed message at start (that might be construed as offensive by colorblinds)

********************************************************************************
SOMbrero 1.2-2
Fixed bugs:
  fix a bug in plot.somSC for customized colors (reported by Duncan Murdoch)
  fix a bug in shiny app (downloading CSV files with rownames)
  fix a bug in 'plot.legend' for SC plot of type 'color'
  
Improvements:
  improved rendering of data in shiny app
  added 'legend' to all SC plots for shiny app
  added features to display titles (cluster number) in package and shiny app
  added CSV download for result of the clustering in shiny app
  
Misc:
  updated (and improved references)
  changed maintener's email
  
********************************************************************************
SOMbrero 1.2
Fixed bugs:
  fixed heskes predictions for relation SOM
  updated scripts for latest igraph version
  removed predict.somRes for cosine preprocessing (relational)

Code improvements:
  faster version of dissimilarity SOM as in Mariette et al., 2016
  
********************************************************************************
SOMbrero 1.1
Fixed bugs:
  Changed observation weights in KORRESP: they now correspond to the 2005 KDISJ
version and not to the 1993 version
  Fixed bug when passing proto0 (reported by Renaud Dufour)

Code improvements:
  changed the function predict.somRes to speed it up
  
********************************************************************************
SOMbrero 1.0 (CRAN first release)
New features:
  projectIGraph now handles weighted graphs
  added a type in plot.somSC that displays a projected graph based on 
super-graph (see Olteanu & Villa-Vialaneix, Journal de la SFdS, 2015)

Fixed bugs:
  Fixed a bug related to proto0 when type was not set in trainSOM
  Fixed a bug in summary.somSC when the number of clusters is not chosen yet
  Removed parameter 'view' that was not used in internal function 'plotAdd'

Misc:
  Changed default neighbourhood to Gaussian. The default parameters for this
neighbourhood are those already implemented in the R package 'yasomi'
  Changed the internal function projGraph to handle projection for the SOM grid
and for the super-clustering in a single function
  Added the neighborhood type of the SOM in method print for the class somRes

********************************************************************************
SOMbrero 0.5
New features:
  Added an option for affectation type ("standard"/hard or "heskes"/soft
affectation)
  Updated shiny interface accordingly

Fixed bugs:
  Fixed a bug related to dist.type in selectNei. This bug did not affect the
learning in previous versions but could provide false values for protoDist
after the training.

********************************************************************************
SOMbrero 0.4-2
New features:
  Added PCA initialization
  Added Gaussian neighborhood (default parameters are still tentative)
  Added cosinus normalization for dissimilarity
  Added ANOVA like analyses for relational SOM interpretation
  Included a function to project an 'igraph' object on the grid

Fixed bugs:
  Fixed a bug in the computation of projected graph. Only edges with non zero
counts for the number of links are now listed in the edge list.

Misc:
  Added tests: to check the equivalence between automatic and manual scaling and
the equivalence between predicted clustering and the output of predict
  Updated vignettes

********************************************************************************
SOMbrero 0.4-1
New features:
  Added a parameter that tunes the gradient descent step
  Added a web user interface, implemented with shiny
  Added the topographic error to somRes.summary
  Improved the summary of somSC (table of neuron numbers and superclass numbers)

Code improvements:
  Changed default value of init.proto to "obs" for "relational" algorithm

Fixed bugs:
  Changed scree plot title and ylabel to "proportion of unexplained variables"

Misc:
  Added test: equivalence of numeric SOM and relational SOM on squared 
euclidian distance

********************************************************************************
SOMbrero 0.4
New features:
  Implementation of the "dissimilarity" algorithm to handle dissimilarity data
  Plots, quality functions and super-clustering have been updated to handle this
case

Code improvements:
  New way to handle distance calculations
  New way to handle the 'korresp' preprocessing (full matrix is now included)
  Slightly changed default values for Letremy's radius and neighborhood: they
are now exactly the same than in the original programs

Fixed bugs:
  Fixed bug with default options in korresp case
  Fixed bug with affectation step in korresp case
  Fixed bug for what="add" and type="graph" (node sizes were wrong)

Misc:
  Added markdown vignettes: one general and one for each case; hence, the
package now depends on R version 3.0 or higher
  Added citation file
  Added demos
  Removed unecessary tests and examples


********************************************************************************
SOMbrero 0.3
New features:
  Implementation of the "korresp" algorithm to handle contingency table
  Plots, quality functions and super-clustering have been updated to handle this
case

Fixed bugs:
  Bug fixed in the dendrogram of super-clustering (percentage of explained
variance was incorrectly displayed)
  Bug fixed in smooth.dist and umatrix (distances were reversed)


********************************************************************************
SOMbrero 0.2-2
New options:
  The argument 'the.titles' has been introduced in plot.somRes

New features:
  Implementation of a quality function for somRes object
  Implementation of a super-clustering for the resulting prototypes
  Implementation of a plot method for the results of the super-clustering


********************************************************************************
SOMbrero 0.2
Name changes :
  The argument 'scale' of 'somRes' object is now called 'scaling' (conflict with
  a R base function)

Argument changes :
  The argument 'dist.type' has been transfered from 'somRes' to 'myGrid' objects.

New options:
  Distance type on the grid   :   maximum, euclidean, manhattan, canberra, 
                                  binary or minkowski
New plots:
  Observations                :   color, lines, barplot, radar, boxplot and 
                                  names
  Prototypes                  :   lines, barplot, radar, 3d, poly.dist, umatrix 
                                  and smooth.disy
  Additional variable         :   pie, color, lines, barplot, radar, boxplot, 
                                  words, names and graph


********************************************************************************
SOMbrero 0.1
  The initial version of onlineSOM package considers only numerical data.

Available parameters of the SOM algorithm:
  Grid                        :   square topology
  SOM type                    :   numeric
  SOM mode                    :   online
  Radius type                 :   letremy
  Prototypes initialization   :   random or obs
  Scale                       :   unitvar, center or none

Available plots:
  Observations                :   hitmap
  Prototypes                  :   color
  Energy
