Kohonen package version 3.0.7 is described in 
R. Wehrens and J. Kruisselbrink, J. Stat. Softw. v87, i7, October 2018.

Changes in version 3.0.10 (currently develop branch):
  - replaced calls to the class function in 'check.data'

Changes in version 3.0.9:
  - removed dependency of MASS's eqcsplot (suggestion by Ulrike Groemping)
  - added na.color argument to some of the plotting functions (request
    by Ulrike Groemping)
  - added a check to see if the somgrid argument is correct: some
    users load the class library after kohonen which leads to two fields
    that are missing in a somgrid object. The check adds the defaults
    and gives a warning (reported by Neal Burger)
  - replaced 'class(x) == "kohonen"' by 'inherits(x, "kohonen")' which
    will not break in R 4.0.0 and further... 

Changes in version 3.0.8:
  - fixed bug in calculating distances where NAs are involved (found
    by Rafael M. Mas)

Changes in version 3.0.7:
  - reinstated Makevars, that is necessary for OpenMP flags (without
    it the package still compiles but no parallel computation is
    possible)
  - fixed a bug in FindBestMatchingUnit that in case of ties did not
    allow unit 1 to be the winning unit. Longstanding bug, also
    present in the class library (function VR_onlineSOM), but not very
    prominent since it only surfaces in cases of ties in distances.
  - added a working example to the degelder data, using the custom
    WCCd distance function also used in the J. Stat. Softw. paper.
  - added the published version of the 2018 J. Stat. Softw. paper to
    the doc directory
  - added the 2018 JSS paper to the CITATION file

Changes in version 3.0.6:
  - fixed a bug in object.distances
  - require Rcpp version 0.12.12, and removed Makevars and kohonen_init.c
    because of this (suggestions by Gilberto Camara)

Changes in version 3.0.5:
  - columns with too many NA values are no longer removed; it is
    virtually impossible to guarantee that the right columns are
    matched when new data are submitted to the map (based on an error
    reported by Ignacio Chacón).
  - check.data is now always called for all data layers of new data
    objects, not just for whatmap data layers. Affects functions map,
    predict, supersom. Fixes a problem where presenting a data.frame
    as test data led to a segfault (noticed by @miranska)
  - removed superfluous argument maxNA.fraction from check.data
  - added 2018 JSS paper (pre-pub) to /inst/doc

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 Carrió 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 RGBdemo.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.

