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
SOMbrero 1.4-3 [2025-06-25]
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
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plots are now ggplot2 based and former plot arguments are no longer
valid since ggplot2 syntax is now used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print.titles is deprecated and has been replaced by show.names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