SOMbrero 1.4-2 [2024-01-24]

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

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• plots are now ggplot2 based and former plot arguments are no longer valid since ggplot2 syntax is now used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• print.titles is deprecated and has been replaced by show.names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 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

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 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

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