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 ******************************************************************************** SOMbrero 1.3-1 Improvements: make trainSOM a method for different classes create a trainSOM method for outputs of mixKernel package ******************************************************************************** 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Euclidean Improvements: hexagonal topography is now available plots are now ggplot2 based and former plot arguments are no longer valid since ggplot2 syntax is now used the shiny app has been entirely remade data from the environment can be loaded directly in the shiny application and 3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 When this radius is passed the Euclidean distance between unit coordinates print.titles is deprecated and has been replaced by show.names Misc: radar plots are no longer available ******************************************************************************** SOMbrero 1.2-5 Fixed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 ******************************************************************************** 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