https://github.com/cran/kohonen
Tip revision: 1ea0af30383e5a82f19b0ddf6d22c26667b2e8c2 authored by Ron Wehrens on 28 August 2017, 17:51:19 UTC
version 3.0.4
version 3.0.4
Tip revision: 1ea0af3
NEWS
The kohonen package version 3.0.3 is described in
R. Wehrens and J. Kruisselbrink, J. Stat. Softw. 2017 (to appear)
Changes in version 3.0.4:
- if whatmap is used during training, some of the codebook layers
will be NULL. In version 3.0.2 this led to errors in
predict.kohonen, which now explicitly only checks codebook layers
in whatmap.
- Added text in the supersom man page about the incorrect naming of
the Tanimoto distance (noted by Pau CarriĆ³ Gaspar).
- Added a check in supersom to make sure the Tanimoto distance is
not used for data outside the range [0-1].
- Added extra check in the remove.data.na function for empty
data layers after the maxNA.fraction check (pointed out by Xu Kai)
- Added pepper image (incl man file) used in JSS software
description: peppaPic
- added BC.cpp and wcc.cpp to inst/Distances directory
- added JSSdemo1.R, JSSdemo2.R, JSSdemo3.R to demo directory
- added kohonen-package.Rd to man pages
- reordered NEWS contents to list most recent entry first
Changes in version 3.0.3:
- improved manual pages
- fixed a bug in checking whether meanDistances contain zeros
Changes in version 3.0.2:
- added checks for the presence of openMP headers
Changes in version 3.0.1:
- added correct OpenMP headers
- removed wine.classes from the wines data set; this is simply
as.integer(vintages)
Changes in version 3.0.0:
- som and xyf training methods are now considered to be special
cases of supersom
- function bdk is deprecated
- C engine replaced by C++
- several new distance functions have been added, including the
possibility to provide user-defined distances (function pointers,
made possible by the Rcpp package)
- distances may now be defined per layer
- many performance improvements, in particular reducing memory
consumption
- much more consistent syntax for the predict function
The kohonen package version 2.0.0 is described in
R. Wehrens and L.M.C. Buydens, J. Stat. Softw. 21(5), 2007
Changes in version 2.0.20:
- added support for hexagonal and square units in plotting maps
(contribution by Romain Bossart)
Changes in version 2.0.19:
- replaced MASS:::eqscplot simply by eqscplot
- added imports from default packages to NAMESPACE file
Changes in verson 2.0.18:
- added a package-specific NAMESPACE file
Changes in version 2.0.16:
- added check to xyf and bdk functions to avoid matrices with
differing numbers of rows. This was happily accepted but led to
incorrect results. (Thanks to Johanna Laibe for noticing this
behaviour)
Changes in version 2.0.15:
- renamed this file to "NEWS"
- updated maintainer email address
Changes in version 2.0.14:
- fixed a bug, disguised as a memory leak, where map.kohonen
attempted to calculate a distance between elements of a factor,
rather than using the membership matrix. (Spotted by CRAN checks
focusing on memory leaks, BDRipley)
Changes in version 2.0.13:
- predict.kohonen choked on a matrix containing only one sample (Max
Kuhn, who also provided the solution)
- plotting for toroidal maps has been improved once again: not only
are the bonudaries finally shown correctly, also the cluster
boundaries at the edges of the map are shown twice when necessary
for better interpretability.
Changes in version 2.0.12:
- removed the restriction that a legend in a codes plot was only
shown when the number of variables was smaller than 15 (segments)
- fixed a bug in add.cluster.boundaries: now the correct boundaries
are shown also for toroidal maps (Thomas Campagne)
- added identify.kohonen
- predict.kohonen now returns a factor if the training was also done
with a factor; man page is updated so that the examples reflect
this correctly. (Triggered by Ben Harrison)
Changes in version 2.0.11:
- parameter contin was effectively not used in functions xyf,
supersom and bdk (spotted by Andrey Ziyatdinov); now corrected
- in supersom the original code to estimate contin was giving
errors; now corrected
- removed a bug in assigning column names to the codebook vectors in
supersom
- added topographic error measures (proposed independently by John
Pearce and Marco Pomati)
Changes in version 2.0.10:
- added xpd = NA to add.cluster.boundaries so that also segments
outside the official plotting area are shown
- added an example for component planes (suggestion by Andreas Henelius)
- fixed a bug concerning maxlegendcols (spotted by Andreas Henelius)
Changes in version 2.0.9:
- Added useDynLib directive to NAMESPACE for compatibility with
older R versions
Changes in version 2.0.8:
- changed contact email address once again to fmach.it
- added name space
- compressed documentation file kohonen-manual.pdf
Changes in version 2.0.6:
- Added palette.name as argument to plot.kohcode
- Function-specific default palettes
- Changed contact address to ron.wehrens at iasma.it
- Added visualisation of clustering of units (Leo Lopes)
Changes in version 2.0.5:
- Changed title of the "quality" type plotting function to
"Distance" rather than "Similarity"
- Extra parameter "heatkeywidth" (thanks to Henning Rust) for
control over the size of the heatkey. Useful for cases with
multiple plots, and probably elsewhere too.
- Added plotting type "dist.neighbours" which shows Ultsch' U-matrix:
units are coloured according to the sum of the distances to their
immediate neighbours. A high distance can be interpreted as being
on a class boundary.
- Plotting types "quality", "dist.neighbours" and "counts" now
invisibly return what they show.
- Added information on the wine varieties, as well as a reference to
the original publication.
- Cleaned up C-code and man pages to eliminate warnings in the
development version of R 2.9.0
Changes in version 2.0.4:
- introduction of tricolor function
- prediction of multiple layers
- Y in function xyf now can also be a factor
- any element of the data argument in function supersom can now also
be a factor
- added new prediction examples for som, xyf and supersom
- uniform output of som, xyf and supersom functions
Changes in version 2.0.3:
- removed a bug in supersom, introduced in 2.0.1 when checking if
the data are numeric.
- added an example for supersom.
- removed a bug in plot.kohcounts, arising when empty units are
present
- updated man files for methods 'plot', 'predict', and 'map'
Changes in version 2.0.2:
- changed the 'predict.kohonen' function to take account of a change
in the behaviour of 'aggregate' in R version 2.6.0 and later
Changes in version 2.0.1:
- fixed a bug in unit.distances: for rectangular maps the toroidal
argument was ignored. Updated the corresponding example as well.
- added an argument 'n.hood' to functions som, xyf, bdk and
supersom, so that the user can decide what distance measure to use
when calculating distances between units. Useful to compare the
results with other som implementations.
- specification of radius as (start, stop), similar to alpha. This
gives better control (suggestion of Hadley Wickham).
- more sanity checking in functions som, xyf, bdk and supersom
(suggestion of Hadley Wickham).
- added the J. Stat. Softw. paper and a CITATION file to the distribution.