Changes in version 1.5.0 (2025-10-06) New feature - addition of a 'clustering' option in superClasses Bug fix - fixed a bug in cutree for somSC results Changes in version 1.4.4 (2025-08-18) Bug fixes - fixed a bug in MDS prototype plot for relational case - fixed a bug related to issue #8 on Github (PCA initialization for relational case) - added a method to cut dendrogram in somSC results Changes in version 1.4-3 (2025-06-19) Bug fix - corrected a bug for datasets with NA columns - corrected a bug in ggplot tests Misc - added reference to sk8 instance of the shiny app Changes in version 1.4-2 (2024-01-25) Bug fix - corrected two notes (on documentation and vignettes) from CRAN checks - replaced aes_string by aes Misc - changed CITATION format according to new standards - removed cache from vignettes Changes in version 1.4-1 (2022-01-03) Fixed bugs: - fixed a bug related to issue #4 on Github Changes in version 1.4 (2022-01-03) 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 Changes in version 1.3-1 (2020-08-11) Improvements: - make trainSOM a method for different classes - create a trainSOM method for outputs of mixKernel package Changes in version 1.3 (2020-06-08) 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Improvements: - hexagonal topography is now available - plots are now ggplot2 based and former plot arguments are no longer valid since ggplot2 syntax is now used - the shiny app has been entirely remade - data from the environment can be loaded directly in the shiny application and 3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 Changes in version 1.2-5 (2020-03-05) 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 Changes in version 1.2-4 (2019-03-07) Fixed bugs: - changed unitary tests because of changes in RGN for devel Misc: - changed maintainer name and address Changes in version 1.2-3 (2018-02-05) 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) Changes in version 1.2-2 (2017-09-20) 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 Changes in version 1.2 (2016-09-02) 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 Changes in version 1.1 (2015-11-04) 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 Changes in version 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. Changes in version 0.4-2 - New features: - Added PCA initialization - Added Gaussian neighborhood (default parameters are still tentative) - Added cosine 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 Changes in version 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 Changes in version 0.4 - New features: - Implementation of the "dissimilarity" algorithm to handle dissimilarity data - Plots, quality functions and super-clustering have been updated to handle tjos 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 Changes in version 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) Changes in version 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 Changes in version 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 Changes in version 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