NEWS
SOMbrero 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
SOMbrero 1.4-1 (2022-01-03)
Fixed bugs:
- fixed a bug related to issue #4 on Github
SOMbrero 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
SOMbrero 1.3-1 (2020-08-11)
Improvements:
- make trainSOM a method for different classes
- create a trainSOM method for outputs of mixKernel package
SOMbrero 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- plots are now ggplot2 based and former plot arguments are no longer valid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- print.titles is deprecated and has been replaced by show.names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
SOMbrero 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
SOMbrero 1.2-4 (2019-03-07)
Fixed bugs:
- changed unitary tests because of changes in RGN for devel
Misc:
- changed maintainer name and address
SOMbrero 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)
SOMbrero 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
SOMbrero 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
SOMbrero 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
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:
SOMbrero 0.1