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2014-03-27  Martin Maechler

	* NOTE: All newer changes are summarized in the NEWS file
	(./inst/NEWS.Rd) and detailed & timestamped in the svn logs.


2014-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.15.2
	* R/*.q updates to make messages translatable; proposed by Lukasz Daniel

2014-03-12  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.15.1

	* man/mona.Rd: anyNA2[cbind(<i>, <j>)] <- NA  fails in R < 3.0.x

2013-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.15.0;  also using  Authors@R

	* R/agnes.q (agnes): method "gaverage" contributed by Pierre Roudier.

2013-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.14.5, never released

2013-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.14.4, released to CRAN, 2013-03-26
	* po/R-de.po: trivial update from Detlef,

2012-02-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.14.2, released to CRAN today
	* R/clusGap.R (maxSE): with 5 methods to compute "maximal gap",
	used also in print() method.

2012-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/clusGap.R (print.clusGap, plot.clusGap): added

2012-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/clusGap.R: new clusGap() for computing the cluster gap statistic.

2011-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/coef.R (coefHier): newly export coefHier(), interfacing to C's bncoef().

	* tests/diana-boots.R (dianaBoot): add a "bootstrap", for considerably more tests.
	* tests/diana-ex.R: reorganized

	* src/twins.c: newly translated from Fortran, for more future flexibility
	* src/twins.f: no longer there

	* R/agnes.q (as.dendrogram.twins): define for 'twins' rather than
	just 'agnes'.

2011-12-03  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plotpart.q (clusplot.default): xlab, and ylab arguments;
	new 's.x.2d' argument which allows to specify the plot setup in details.
	(clas.snijpunt): also check for NAs in x[1:2,m].
	Suggestions originally from Peter Ruckdeschel

2011-10-16  Martin Maechler  <maechler@stat.math.ethz.ch>

	* po/: setup of for translation

2011-09-14  Martin Maechler  <maechler@stat.math.ethz.ch>

	* inst/CITATION: update according to state-of-the-art.

2011-08-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.14.1, released to CRAN, 2011-10-16

	* R/silhouette.R (plot.silhouette): col = <one per cluster> had
	ordering bug.
	* man/silhouette.Rd: added example

2011-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.14.0, released to CRAN, 2011-06-07

	* R/plotpart.q (clusplot.default): use message() and warning()
	appropriately instead of just cat().  Further, add a 'add = FALSE'
	argument which allows *adding* ellipses to an existing plot.

2011-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plotpart.q (clusplot.default): new 'cex' and 'cex.txt', the
	latter for the "point" labels.

2011-05-20  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/pam.c (cl_pam): trace_lev: also trace the computation of
	dissimilarities (a very expensive part, for large n).

	* R/pam.q (pam): cluster.only=TRUE: if the *computed*
	dissimilarities have NA's the necessary error was not signalled.

2011-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/*.Rout.save: update after R-devel's  "scientific()" patch.
	* DESCRIPTION (Version): 1.13.4, *not* released

2011-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.13.3, released to CRAN today

2010-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/ellipsoidhull.R, *: use "full argument names"

2010-11-09  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/clara.q (clara): enforce  sampsize > k {as the help file always said};
	allow to disable 'DUP=FALSE' via env variable.

2010-11-08  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/clara.c (cl_clara): inserting rand_k into nsel[]: simplified
	and avoiding (typically inconsequential) out_of_bound array access.

2010-10-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.13.2 ; Enhances: MASS; released to CRAN, 2010-11-10

	* src/cluster.h, src/daisy.f, src/mona.f:
	* src/init.c (FortEntries): s/cl_/cl/ for now,
	as some f77/g77 setups cannot deal with it correctly.

2010-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.13.1

2010-06-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/daisy.Rd: add our *generalized* Gower formula (LaTeX), and
	update the detailled description accordingly.

2010-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.13.0

	* src/daisy.f (cl_daisy): renamed from daisy
	* src/init.c, src/*.[chf]: renamed others, so we can use
	* NAMESPACE (useDynLib): .registration = TRUE

2010-05-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q (daisy): using variable weights (for gower).
	* src/daisy.f: ditto

2010-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.12.3
	* R/plothier.q (bannerplot): do not use formals(pretty)

2009-12-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/daisy.Rd: fix page number for Gower (1971) reference.

2009-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.12.1

	* man/ellipsoidhull.Rd: fix missing \link ((parts former 'graphics'
	have long been moved to 'grDevices'.

2009-05-13  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.12.0 -- released to CRAN

	* R/silhouette.R (silhouette.default, print.summary.*, plot.*):
	silhouette(x, *) and its methods now also work when x uses integer
	codes different than 1:k.  Previously, this could seg.fault.

	* tests/silhouette-default.R: test it.


2009-03-12  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/daisy.Rd: fix typo/thinko (thanks to Felix Mueller).

2009-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/agnes.q (as.dendrogram.agnes): new utility
	* NAMESPACE: exported

2009-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/plot.agnes.Rd: link to pltree.twins() directly

	* R/agnes.q (print.summary.agnes): output 'agnes' instead of `agnes'

2009-01-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version, Date): 1.11.12 and CRAN-released

2009-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/ellipsoidhull.Rd: fix for more stringent Rd parsing

2008-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/ellipsoidhull.R (print.ellipsoid): and others: replace
	backquotes ( ` ) by regular quotes.

2008-06-15  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (sortSilhouette): do *not* overwrite the
	correctly reordered rownames: Fixes very long standing bug
	which lead to wrong observation labels in silhouette plots.

2008-04-10  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/zzz.R (.onUnload): add ..dynam.unload()ing

2008-02-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date, Version): 1.11.10 and release

2007-12-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/pam.c (cstat, dark): move variable declarations to local context.
	(bswap): add a few R_CheckUserInterrupt() calls

	* R/pam.q (pam): new argument 'do.swap = TRUE'.  Setting it to
	FALSE allows to skip the more expensive "SWAP" phase.
	* man/pam.Rd: (ditto)

2007-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/ind_2.h (ind_2): for m := max(i,j) > 46342, (m-2)*(m-1) give
	integer overflow which leads to a seg.fault.  Now fixed.
	* src/pam.c (bswap): slightly improve trace output.
	* tests/pam.R, tests/pam.Rout.save: corresponding slight adaptions.

	* man/pam.Rd: "large" and
	* man/clara.Rd: "small" datasets; pam() works with thousands ...

	* R/clara.q (clara): error out when users try clara(<dist>, ...).

2007-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date, Version): 1.11.9

	* man/pam.Rd: in invisible example, do not use partially matched [[.

2007-09-04  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/mona.f (mona): dummy initializations for "-Wall"
	* src/fanny.c (fygur): dummy init 'lang'

2007-08-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/daisy.f et al: de-tabify the fortran sources

2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.11.7  (mainly for R-devel)

2007-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/plot.diana.Rd, etc: s/dendrogramm/dendrogram/

2007-05-31  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/plantTraits.Rd: add \encoding{latin1}

2007-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.11.6 - needed
	for R version >= 2.6.0.

	* R/daisy.q (daisy): for 2-valued variables only warn about
	non-specified type when  n >= 10.

2007-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/diana.q (diana): don't use as.double(.) and DUP=FALSE !

2007-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/diana.Rd: merge man/diana.object.Rd into *one* help file

	* DESCRIPTION (Version): 1.11.5 - for R 2.5.0

2007-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (silhouette.default): use x$clustering only when x is
	a list.

2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.11.4 -- ready

	* tests/to-25x, tests/to-24x:    different outputs for R 2.5.0 (unstable)
	* tests/clara.Rout.save-R25x,..: and R-2.4.x

	* tests/silhouette-default.R: use [as.integer(rownames(.)), ]
		since we cannot guarantee rownames there.

2006-12-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/fanny.c (fuzzy): 14 instead of 15 sign.digits for trace_lev >= 2
		printing.

	* R/clara.q (stop): message for NA-observations: only show first
	dozen of observation numbers.
	* tests/clara-NAs.R: test the above
	* tests/clara-NAs.Rout.save: ditto

2006-12-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.11.3 -- released to CRAN

	* R/daisy.q (daisy): finish metric "gower", and test an example

2006-12-01  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/daisy.Rd: more content about Gower; thanks to Gavin Simpson

2006-11-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q (daisy): metric = "gower" -- not yet finished

2006-09-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.11.2  released

	* src/init.c: register dysta3 as C, not Fortran; drop trailing "_"
		==> need to adapt these:
	* src/fanny.c:
	* src/cluster.h:
	* tests/dysta-ex.R:
	* tests/dysta-ex.Rout.save:

2006-08-24  Martin Maechler  <maechler@stat.math.ethz.ch>

        * DESCRIPTION (Version): 1.11.1 released to CRAN

	* R/silhouette.R (sortSilhouette): make sure "iOrd" is there also
	if "Ordered" is TRUE. (fixes plotting w/ col = 'clusterwise'.)

2006-08-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/mona.R: update (slightly extend) regression test
	* tests/mona.Rout.save: consequence

	* R/mona.q (mona): replace apply(<matrix>, 2, factor) with safer
	code, to work correctly in R 2.4.0 and later (thanks to Brian).

2006-06-12  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plotpart.q (clusplot.default): new argument 'sub'; default is
	unchanged, but you can suppress the subtitle.

2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/fanny.c (fygur): a little more cleanup --
		for compatibility with dark() in src/pam.c

	* DESCRIPTION (Version): 1.11.0, to be released to CRAN

2006-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Depends): require R >= 2.2.1 -- which should have
	happened earlier, since registration of Fortran symbols failed before.

2006-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/plantTraits.Rd: new dataset with many variables, including
		all kinds of factors, provided by Jeanne Vallet.
	* data/plantTraits.rda: useful for daisy() illustrations

2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/fanny.q (fanny): several new options: metric = "SqEuclidean",
		iniMem.p: initial membership matrix can be specified;
		cluster.only, keep.diss, keep.data: for saving memory/speed.
		warning when k.crisp < k.
		printing of $membership is now in rounded percent
	* man/fanny.Rd: document the above
	* tests/fanny-ex.R: much extended

2006-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/chorSub.Rd: new dataset;
	* data/chorSub.Rd: useful for fanny() illustrations

	* R/fanny.q (fanny): Dunn's partition coefficient (and its
	normalization) now always use sum.. u.. ^ 2  (and not "^ memb.exp").
	option 'trace.lev' for iteration monitoring
	* src/fanny.c (fuzzy): (dito)

2006-04-08  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/fanny.c: Translated from Fortran (fanny.f); potentially with
		more options, etc.

2006-03-20  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.10.5  for CRAN

	* .rsync-exclude: new file useful since I moved my RCS archive to SVN
		(using 'cvs2svn' and a perl script on 'svn-stat').

2006-02-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/sildist.c (sildist): 2nd round (by Romain and me)

2006-02-25  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (silhouette.default): new C version in file
	* src/sildist.c (sildist): provided by Romain Francois

2006-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/ellipsoidhull.R (print.ellipsoid): also work without 'conv' slot

	* man/ellipsoidhull.Rd: finally explain 'd2'; and \link to other
		ellipse implementations.

	* man/volume.ellipsoid.Rd: + example of 'ellipsoid' construction

2006-01-31  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/bannerplot.Rd: (et al.): use \dQuote{} and \sQuote{}

2006-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/pltree.twins.Rd: explain the as.hclust() dispatch; add
		example, particularly for plot(as.dendrogram(.)).

2006-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.10.4 -- released to CRAN

2006-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (silhouette.clara): added (for "full = TRUE" option)

2006-01-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.10.3

	* src/init.c: registering all (R-callable) C and Fortran routines

	* src/cluster.h: declare the remaining callable routines

2005-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* inst/CITATION: first version

	* R/silhouette.R (plot.silhouette): 'nmax.lab' was not obeyed
		properly (labels were drawn for large n when the
		silhouette had rownames).

	* man/silhouette.Rd: explain clara's silhouette and "full" one.

2005-09-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/pluton.Rd: \source: new URL @ www.agoras.ua.ac.be
	* man/clusplot.default.Rd: dito
	* man/ellipsoidhull.Rd: ""
	* README: ""

2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.10.2 released to CRAN

	* src/clara.c (bswap2): minor cosmetic

2005-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q (daisy): the case of a *binary*-only matrix (not
		data frame), used to fail, now works fine, tested in
	* tests/daisy-ex.R:

	* src/twins.f: get rid of gfortran warnings
	* src/mona.f:  dito
	* src/fanny.f:	"
	* src/meet.f:	"

2005-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/clara*: adapt to slightly changed output

	* src/clara.c (clara), (bswap2): better trace_lev printing;
		code more in line with 'pam'.

2005-08-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.10.2 {not released}

	* R/clara.q (clara): no longer support deprecated 'keepdata';
		also return 'i.med'; new argument 'medoids.x' allowing to
		save even more memory; do not assign 'data' when
		keep.data=FALSE.

	* man/clara.Rd: + 'i.med' + 'medoids.x' - 'keepdata'
	* man/clara.object.Rd: dito

2005-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/silhouette-default.R: if(FALSE) library(*, lib="..MM..")

2005-06-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/silhouette-default.R (isTRUE): need for R < 2.1.x

2005-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date):
	* DESCRIPTION (Version): 1.10.1

	* R/silhouette.R (plot.silhouette): format() clus.avg.widths more nicely
	* R/silhouette.R (silhouette.default): don't use max.col() which
	returns random.
	* tests/silhouette-default.R: test only 3rd column difference
	* tests/silhouette-default.Rout: update {for non-random sil*.default()}

2005-06-20  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/silhouette-default.R: added test for equivalence of
	  silhouette.default() and silhouette.partition()
	* tests/silhouette-default.Rout.save: new output
	  --> The silhouette() results are *still* not always the same (-> fixed)

	* R/silhouette.R (silhouette.default): if Nj := #{obs. in C_j} = 1
	  the silhouette width is 0, not 1, as in pam's original code.

	* man/silhouette.Rd: document the case of 1-obs-clusters.

2005-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.10.0

2005-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/pam.q (pam): new argument 'trace.lev = 0'

	* man/pam.object.Rd: pam() also return $medID

	* src/pam.c (dark): take special care of empty clusters (ntt == 0)
	* src/pam.c (pam): also work when medoids are not increasing.

	* R/pam.q (pam): user-supplied 'medoids': even more checks

2005-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/fanny-ex.R: use new RNG (hence change example); add samples
	of memb.exp -> 1

	* DESCRIPTION (Author): new formulation for better auto-citation()

	* src/fanny.f (fanny): 'r' ("membership exponent") becomes
		user-specifiable argument; dito for 'maxit'

	* R/fanny.q (fanny): new arguments 'memb.exp' ("membership exponent");
			     'tol' and 'maxit'
	* R/fanny.q (.print.fanny): utility to be used in both print.*()
			methods; nicer, using formatC() and 'digits' explicitly.

	* man/fanny.Rd: new arguments, see above

	* man/fanny.object.Rd: mention new '$ objective' result component

	* man/print.fanny.Rd: now also for [print.]summary.fanny();
		mention new explicit 'digits' argument to print methods.

2005-04-04  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.9.8

	* R/daisy.q (print.dissimilarity): rewritten, now based on
	print.hclust().

	* R/zzz.R (gettextf): ..etc: define substitutes such as to allow
	running in R < 2.1.0

	* man/ellipsoidhull.Rd: fixed outdated "link[pkg]"
	* man/clusplot.default.Rd: dito
	* man/*.Rd : etc

2005-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/clara.q (clara): start to 'rationalize' messages for future
	translation.

	* src/cluster.h: define the  _(String) macro (for i18n), not yet used.

2005-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/clara.Rd: get rid of iso-latin1 character

2004-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/agnes.Rd: concept{UPGMA ..}

2004-11-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.9.7	  (not yet CRAN)

	* R/plothier.q (bannerplot): ouse default 'main' and 'sub'
	* man/bannerplot.Rd: + example

	* R/coef.R (coef.hclust): Implement R function for
		   computing the agglomerative/divisive coefficient.
	* man/coef.hclust.Rd: new; including example

	* man/predict.ellipsoid.Rd: wrong link

2004-11-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/twins.f (bncoef): drop unused argument 'ner'

2004-11-20  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/clusplot.default.Rd: fix typo

2004-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/predict.ellipsoid.Rd: add nice example

2004-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (LazyData): yes

2004-08-12  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.9.6
		      (Depends): added standard packages

	* R/daisy.q (daisy): scale=TRUE didn't collaborate with NAs
				(since 2003-11-29).
	* tests/daisy-ex.R: add an example, testing the above


2004-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.9.5 --> to CRAN

2004-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/mona.Rd: drop an extraneous "}\n" that Kurt's new tools found
	* man/twins.object.Rd: dito

2004-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.9.5 (not yet released)

	* man/pam.Rd: note on 'medoids'

2004-07-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/pam.q: new argument 'medoids'
	* man/pam.Rd: ex.with 'medoids'
	* src/pam.c (bswap): new argument 'med_given'

2004-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/pam.c (bswap): moved ammax/nmax computation into same loop
	as beter[]. added many comments.
	GOAL: Allow initial medoids user-specification.
	>>> TODO: do the analogous thing in src/clara.c 's bswap2()

2004-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.9.4 -- fix dysta() using jtmd[] problems
		(thanks to valgrind and BDR).

	* R/agnes.q (agnes): initialize 'jtmd' to length p in any case
	* R/diana.q (diana): ditto
	* R/fanny.q (fanny):  "
	* R/pam.q (pam):      "

	* R/daisy.q (daisy): pass 'mdata' to Fortran
	* src/daisy.f (daisy): new "boolean" argument 'mdata'

	* src/clara.c (clara): pass has_NA to dysta2() and don't use
		jtmd[] and valmd[] if(!has_NA)
	* src/cluster.h (dysta2): new arg 'has_NA'


2004-06-18  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.9.3 {only change = below}
	* src/ind_2.h (ind_2): use __inline__ only for gcc (__GNUC__)

2004-06-11  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/clara.Rd: finish \note{} about 'rngR' (thanks to Christian H).

2004-06-01  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/ind_2.h: new file for __inline__ definition of  ind_2(),
		#included from these two files:
	* src/clara.c:
	* src/pam.c:

	* tests/agnes-ex.R: test for "weighted" == "flexible"(0.5)

2004-05-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.9.2	(not yet released)

	* R/agnes.q (agnes): New method = "flexible" (and 'par.method = ..')
	* src/twins.f (averl): implementing "flexible" Lance-Williams formula.
	* man/agnes.Rd:

2004-05-25  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (silhouette.default): give silhouette 0 (not NaN)
	when a_i = b_i {thanks to example and suggestions by Witek Wolsky}.

2004-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/pam.c: cosmetic efficiency improvement from Li Long

2004-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.8.1 for R versions <= 1.8.1
				 1.9.1 for R versions >= 1.9.0
	  -- released to CRAN

	* src/clara.c (clara): fixed second NA-handling bug:
		the test should be "nunfs+1 != jran"
	  Fixed "rngR = TRUE" bug: accidentally still used internal RNG.
	  Fixed 3rd bug if (lrg_sam) : need jk < n_sam for nsel[jk].
	  More & nicer printing for 'trace > 0'.

	* R/clara.q (clara): more useful error msg for too many NAs (jstop=1)


2004-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/clara.c (clara): finally fixed longstanding bug which could
		cause wrong results and segmentation faults, instead of ending
		with the following error:

	* tests/clara-NAs.R: new file w/ former seg.fault

	* src/cluster.h (ind_2): new function instead of F77_CALL(meet)
	* src/clara.c (clara): defined here (and used).
	* src/pam.c (pam): used here

2004-03-09  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/clara.q (clara): sampsize = min(n, <old_default>)

2004-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/agnes-ex.R: do not use object.size(), since
	* tests/diana-ex.R: it's different on 64 bit, e.g.

	* R/agnes.q (agnes): \	when diss = TRUE,
	* R/diana.q (diana):  \ but 'x' is not a "dissimilarity",
	* R/fanny.q (fanny):  / try  as.dist(x)
	* R/pam.q (pam):     /	and be consistent in all 4 functions

2004-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (silhouette.default): do not require cluster
	codes in 1:k (Murad Nayal <mn216@columbia.edu>).
	* man/silhouette.Rd: accordingly; mention 2 <= k <= n-1

2003-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.8.0 for R versions <= 1.8.1
				 1.9.0 for R versions >= 1.9.0

2003-12-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* NAMESPACE: Finally make a namespaced package

2003-12-01  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/pam.q (print.summary.pam): readable indication *no* L/L*
	clusters.
	(print.pam): improve as well.

	* man/pam.Rd: documenting `cluster.only'

2003-11-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q (daisy): better checking & handling	 if(stand)

	* R/pam.q (pam): new argument `cluster.only = FALSE'.  If true,
	  only return the clustering vector, no other info.

	* src/pam.c: translated from src/pam.f and "cleaned";
	 `all_stats' := NOT(cluster_only).

	* src/cluster.h: new pam.c related headers
	* src/dysta.f (dysta): new file: part of former src/pam.f
	* R/pam.q (pam): use .C

2003-11-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q (daisy): fix the new scale 0 code (from 11-17)

2003-11-17  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.7.7 -- (not released)

	* tests/daisy-ex.R: new test for this:

	* R/daisy.q (daisy): scale 0 does not give NaN dissimilarities
	anymore.  Use pColl() in messages

	* R/zzz.R (sQuote): & dQuote() for R version < 1.8

2003-10-25  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/fanny.Rd: typo in the text-part of \deqn{}

2003-09-24  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date): Sept.24: 20th anniversary w/ Lilo! -- release

	* man/plot.mona.Rd: yet another codoc

2003-09-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.7.6 (for R 1.8.0)

	* man/daisy.Rd:		codoc difference for argument *defaults*
	* man/ellipsoidhull.Rd:	  "	  "	  "	"
	* man/plot.mona.Rd:	  "	  "	  "	"
	* man/plot.diana.Rd:	  "	  "	  "	"
				 use \method{..}{..} (more!) also for these:
	* man/predict.ellipsoid.Rd
	* man/silhouette.Rd:
	* man/plot.agnes.Rd:
	* man/plot.partition.Rd:
	* man/ellipsoidhull.Rd:



2003-09-03  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date): -> release

2003-08-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/flower.Rd: use V1-V8 in doc (since can't change the data).

2003-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.7.5 -- not yet released

2003-08-13  Martin Maechler  <maechler@stat.math.ethz.ch>

  __ All these are thanks to Luke Tierney's checkUsagePackage() !! __

	* R/silhouette.R (plot.silhouette): `clw'
			 (sortSilhouette): `clid' & `k'
			 (summary.silhouette): `n'
	* R/ellipsoidhull.R (ellipsoidhull): `ina' unneeded
	* R/plotpart.q (clusplot.default): extraneous if() in "funny case"

2003-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date): updated --> release to CRAN

	* R/daisy.q (daisy): checking "> 2 levels" for binary vars
		(gave wrong error when only 1 level; thanks to
		 Duncan.Mackay@flinders.edu.au).
		Now allow "only 1 level" for binary vars

2003-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date): update; not released, but put up on FTP
	* R/silhouette.R (sortSilhouette): keep ordering; use it to
	* R/silhouette.R (plot.silhouette): order colors, allow cluster colors

2003-07-09  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.7.4 -- not yet released

	* R/daisy.q (daisy): better error message for invalid type
	components; now also works for
	* man/daisy.Rd: new example `dfl3'

2003-06-10  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.7.3

	* R/silhouette.R (silhouette.default): fix bugs for case "Nj == 1"
	* tests/silhouette-default.Rout.save:
	* tests/silhouette-default.R: new test for the above

2003-06-04  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/clara-ex.R and man/clara.Rd: add "drop = FALSE"

2003-06-03  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/clara.Rd: the "simulation" example is now correct for any seed.
	* tests/clara-ex.R: using "correct" ex. above

2003-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q (daisy): s/codes/unclass/

	* tests/ellipsoid-ex.R: no need for try() anymore; use new RNG

	* tests/clara.R:
	* tests/clara-ex.R:	better if(...) RNGdefault("1.6")
	* tests/fanny-ex.R:
	* tests/mona.R:

2003-05-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.7.2

	* R/plotpart.q: clusplot.partition(): try to find `x$diss' by
	looking up x$call.

2003-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.7.1

	* man/pam.object.Rd: add example about assessing #{clusters} via
		silhouette widths from Ch.Hennig.

	* R/plotpart.q (plot.partition): new argument `dist'
	  It doesn't try a clusplot if `keep.diss' was FALSE and no `dist'
	  is specified.
	* R/plotpart.q (clusplot.partition): new `dist' argument

	* R/pam.q (pam): keep.diss passed wrong `jdyss' to Fortran!

2003-04-08  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plothier.q (pltree.twins): simplified label construction;
	call plot( <hclust object> ) instead of plot.hclust().

2003-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/clara-ex.R: new, because of unclear non-reproducibility
	* tests/clara.R: not example(clara) and smaller, moved some to above

	* DESCRIPTION (Version): 1.7.0 (for R 1.7.0)
	* DESCRIPTION (Depends): at least R 1.4
	* R/zzz.R: requiring 1.4 needs much less

	* R/zzz.R: define colSums() substitute for old R versions
	* tests/ : updated *.Rout.save files
	* .Rbuildignore: R/README-Splus is way outdated and irrelevant

2003-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/0aaa.R: Make sure assigning class c("dissimilarity", "dist")
	  (had many cases where only "dissim.." was used!).
	* R/*.q: assign (dissim.., dist) class

2003-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/clara.q (clara): new argument `rngR' allowing to use R's RNG
		instead of the primitive builtin randm().
	* man/clara.Rd: example showing its use.
	* src/clara.c (clara):

	* R/pam.q (pam): new `keep.data' and DUP=FALSE in .Fortran


2003-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/agnes.q (agnes): use  DUP = FALSE
	* R/diana.q (diana): for both "twins()" routines --> 3x less memory!

2003-02-22  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/clara.q (clara): do *not* transpose the x[,] matrix anymore
	* src/clara.c (clara): C code accesses un-transposed x[,] \
	--> + 10% speed

2003-02-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (silhouette.default): fixed k=2 case;
	* man/silhouette.Rd:		       new argument `dmatrix'.

2003-02-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/plot.partition.Rd: new `main' argument (instead of "...")
	* R/plotpart.q:		 passed to plot.silhouette().

2003-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/agnes.q (agnes): store `method' with object for as.hclust.twins()!
			      \	 new logical args `keep.diss' and `keep.data'
	* R/diana.q (diana):   > if (!keep.diss), do not need "dis2"
	* src/twins.f (twins):/	 and don't copy the dist()s here.

	* man/pltree.twins.Rd: mention new `ylab' argument.
	* R/plothier.q:	     __unfinished__ : xlab/ylab depend on "which.plot"!

2002-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/bannerplot.Rd: and
	* R/plothier.q (bannerplot): new `labels' e.g. passed from plot.agnes().

	* man/plot.agnes.Rd: finally added `labels = ' example

	* tests/clara.R: for() loops were silly; + other ex + comments
	* src/clara.c: cosmetic
	* src/fanny.f: and
	* src/pam.f: cosmetic "syncing" of almost identical parts

2002-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/clara.Rout.save:
	* tests/clara.R: add ruspini examples

	* src/clara.c: finally found & fixed "clara(ruspini, 4)" problem

2002-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.6-4	{for R 1.6.2}

	* R/diana.q (diana): since 1.6-1, integer x was not coerced

	* tests/agnes-ex.R,
	* tests/diana-ex.R, and *.Rout.save: new test files

	* src/twins.f: some comments added; gotos removed
	banag() and bandy() were identical --> renamed to bncoef()

2002-12-17  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/agnes.q: agnes(*, method = "no") no longer segfaults

	* R/silhouette.R (plot.silhouette): adj=1.04 (not "1.05")

	* R/plothier.q (pltree.twins): new `labels' arg. such that it can
	be given to plot.agnes() e.g.

2002-12-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date, Version): 1.6-3

	* src/cluster.h: F77_NAME(meet)
	* src/clara.c:	 F77_CALL(meet)

2002-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/pam.f (pam): comments, (bswap): variable renaming

2002-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.6-003 := pre-1.6-3

2002-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/agnes.q (print.summary.agnes): oops: had `clara' there!

2002-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* Version 1.6-2 ==> released to CRAN

2002-10-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q (daisy): allow "+- Inf" in `x' (gave error from Fortran)

2002-10-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (plot.silhouette): also use border = 0 and new
	  default col = "gray".

	* R/plothier.q (bannerplot): arguments inside = . , border = 0
	  work with R 1.6.1's barplot() {give "not yet .."  otherwise}.

	* tests/mona.R and mona.Rout.save: new tests

	* R/mona.q (mona): get rid of 1:nchar() warnings; other cosmetic
	* src/mona.f (mona): variable renaming; logical cleanup in NA dealing

	* R/zzz.R (stop): multi-argument version for R versions < 1.6

2002-10-18  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R CMD check now okay.

	* man/plot.mona.Rd: update (for bannerplot() usage), same for
	* man/plot.agnes.Rd and
	* man/plot.diana.Rd.

	* R/plothier.q (bannerplot): finally working for all three;
	  argument `xax.pretty = TRUE' (set to FALSE for old behavior).
	(plot.mona): using bannerplot(); {and is.na(.) <- .}

2002-10-16  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plothier.q (bannerplot): newly standalone function,
		called from plot.diana(), plot.agnes() -- not yet plot.mona()

2002-10-15  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.6-2 (not yet released)

	* R/plothier.q (plot.diana, bannerplot): rev(.) x-axis labels
	  --> fixing bug introduced at/before version 1.2-5

	* R/plothier.q (plot.agnes, bannerplot) and plot.diana:
		add "las = 2" to vertical axis(), and add space to right
		for plot.diana.

2002-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date): -- released locally only

2002-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/clara.q (clara): for the case of k = 1 (and diss=FALSE),
	* R/pam.q (pam):     medoids should stay matrix

	* src/pam.f (pam): put under RCS; replaced goto by if..else..

	* man/pam.Rd: mention silhouette() directly
	* man/silhouette.Rd: document summary(); + 1ex

2002-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.6-1 ==> for CRAN and R 1.6.0

2002-09-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/silhouette.R (silhouette): New class, generic generator, methods;
		particularly, plot.silhouette() was plot.partition internal.
		improve documentation about silhouette info; update
	* R/clara.q:
	* R/plotpart.q (plot.partition):

2002-09-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/partition.object.Rd,
	* man/pam.object.Rd, man/clara.object.Rd, man/fanny.object.Rd,
	* man/plot.partition.Rd:
	reorganize documentation on silhouette information, thanks to
	thoughts from Christian Hennig.

2002-09-04  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/agnes.object.Rd: mention as.hclust() properly

	* src/spannel.c (spannel): bail out also when *last* deter became <= 0
	* tests/ellipsoid-ex.R (and *.Rout.save): updated

	* DESCRIPTION (Version): 1.6-0

	* R/zzz.R: dev.interactive(), warnings(),... for old R versions
	* man/summary.clara.Rd: make example run for R versions < 1.5.0

2002-09-03  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plotpart.q (plot.partition): new `data' argument and
	smart `which.plots' default for clara(*, keep = FALSE)

	* R/daisy.q (summary.dissimilarity): fix ``number of dissim''

	* R/*.q: 1) use apply(inax,2, any)--- really want colNAs()
		 2) use better "valmisdat" (missing value).

	* tests/dysta-ex.R (dysta): new file, explore "dysta" & "dysta3"
	in Fortran

	* src/fanny.f: get rid of many gotos

2002-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/fanny-ex.R: and ...Rout.save : new files

	* src/twins.f (twins): drop dysta4(), use dysta() from pam.f

2002-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.5-4	-- have achieved something {want more}

	* src/clara.c (clara): finally found and fixed the rare segfault bug:
	   jran == 1 was wrong test (when 1st sample was unusable)

	   (randm): faster implementation of primitive RNG

	* src/spannel.c: new translated from src/spannel.f
	  in order to debug the compiler-dependent outputs in
	* tests/ellipsoid-ex.Rout.save	etc
	* tests/sweep-ex.R (.C)

2002-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/clara.c (clara):
	* man/clara.object.Rd:
	* R/clara.q: new argument `keepdata' and `trace'

	* R/plotpart.q (clusplot.default): xlim, ylim: believe user

2002-08-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/clara.c (clara): new file, translated from Fortran; easier
	to debug the (rare!) seg.fault. "make check fine"

	* DESCRIPTION (Depends): R >= 1.2
	* R/plothier.q (pltree.twins): (drop code for R version < 1.2.0)

2002-08-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.5-3 {released only locally}

	* R/plotpart.q (clusplot.default): xlim, ylim had "<" and ">" reversed
	* man/clusplot.default.Rd: fix interactive(), add x- and ylim example

2002-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/twins.f (twins) et al:
	* src/fanny.f (fanny) et al:
	* src/mona.f (mona):
	* src/daisy.f (daisy): explicit instead of "implicit" var.declaration
	* src/spannel.f (spannel) et al: no "implicit none"

2002-07-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.5-2


	* R/daisy.q (print.summary.dissimilarity): new function and
	  summary.dissimilarity() now returns a classed object.

	* R/agnes.q (print.summary.agnes),
	* R/clara.q (print.summary.clara),
	* R/diana.q (print.summary.diana),
	* R/fanny.q (print.summary.fanny),
	* R/pam.q (print.summary.pam):
	print.summary.*() now only *summarizes* dissimilarities (if at all)

2002-07-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/pam.R and tests/pam.Rout.save : new files

	* man/summary.agnes.Rd: + example
	* man/summary.clara.Rd: + example

	* R/clara.q (print.clara): improvements: call, no long clus. vector
	* R/agnes.q (print.agnes): similar

	* man/daisy.Rd : added "[mva]" to \link{}s.  The same in:
	* man/clusplot.default.Rd: new `col.clus' argument,
		new option `labels = 5'.
	* R/plotpart.q (clusplot.default): cosmetical cleaning;
		`col.p' is now vectorized for point coloring.
		The cluster ellipse is now labeled with font=4 and proper color

2002-06-17  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/sizeDiss.Rd: fix \value{}

	* tests/daisy-ex.R: new file (and *.Rout.save)

2002-06-17  Martin Maechler  <maechler@stat.math.ethz.ch>

	* submit to CRAN -- won't be in R's 1.5.1-recommended

	* R/daisy.q (daisy): make sure "0","1" factors are valid binary vars
			     several extra checks {incl apply(<empty>) `bug'

	* man/diana.object.Rd: show how to use cutree().

2002-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q (daisy): warn if binary variables have non-{0,1} values.

	* src/pam.f (cstat) et al: eliminated many gotos; +comments
	* src/meet.f (meet): + comment

2002-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>


	* DESCRIPTION (Version): 1.5-1
	  new daisy() behavior for binary variables

	* src/daisy.f (daisy): add comments; use if..else.. instead of goto

	* man/dissimilarity.object.Rd: new "Types" attribute in mixed case.
	* man/daisy.Rd:
	* R/daisy.q (daisy): fix data.class "integer",
	  allow type = "symm"; return types used in mixed case;
	  correctly modify jtmd[] for binary variables (!)


2002-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plotpart.q: replace `` == "NA" '' by  is.na(.)
	* R/mona.q (mona): <ditto>

2002-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.4-1

	* R/zzz.R (.First.lib),
	* R/plothier.q: replace plclust() by plot[.hclust]() everywhere.

2002-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/pam.q (pam): comment on "valmisdat"; same in
	* R/fanny.q, R/agnes.q, R/clara.q, R/diana.q

	* src/pam.f (dysta): comment + white space
	* src/fanny.f (fanny): lowercase and indent + comments

2002-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/agnes.Rd, diana.Rd, pam.Rd, clara.Rd, mona.Rd, fanny.Rd :
	  Reference and BACKGROUND section only in agnes.Rd;
	  the others refer to agnes.

	* man/fanny.Rd: clean

	* R/agnes.q (agnes): \	``diss = inherits(x, "dist")''
	* R/diana.q (diana):  > instead of "diss = FALSE"
	* R/fanny.q (fanny): /	 as we have changed pam() already in 1.4-0

2002-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.4-0

	* man/ellipsoidhull.Rd: example

	* tests/ellipsoid-ex.R and *.Rout: finalized

	* man/pluton.Rd: work around Rdconv \eqn{.}{.} bug.

2002-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/ellipsehull.R (ellipsehull) et al:
	  generalized from 2 to p dimensions. -- points generation: not yet!

	* tests/ellipsehull.R: new test file

	* man/clusplot.partition.Rd: clean up
	* man/clusplot.default.Rd: proper reference to Pison et al
	* man/clusplot.Rd: clean

2002-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/ellipsehull.R (ellipsehull) and others: new functions
	* R/plotpart.q (clusplot.default) use new ellipsePoints();
	  simplification by using "d2" (= dist^2) instead of "dist".

2002-01-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plotpart.q (clusplot.default) re-scale cov.wt() result:
	  Finally return the smallest possible ellipses.

	  NOTA BENE ===>  (numerical) results are *different* !

2002-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plotpart.q (clusplot.default) {spannel}: Finally found why our
	ellipses are not quite ok : R's cov.wt() differs from S-plus' !

	* src/spannel.f (spannel): new argument `maxit' (was 5000).

	* R/plotpart.q (cusplot.default): cleanup, eliminating internal
	  kleur() & plotje(); and "spannel" arguments; new maxit; lower eps
	  use which.min() and which.max(); ...

	* R/pam.q (pam): diss has new default  = inherits(x, "dist") which
	  is TRUE therefore for dissimilarity or dist objects.

2002-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
	 |
2002-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/agnes.q, R/diana.q : a bit of cleanup in the two twins
	calling functions.

	* man/lower.to.upper.tri.inds.Rd,
	* man/cluster-internal.Rd: new for formerly local functions, now in
	* R/internal.R (sizeDiss),
	* R/internal.R (lower.to.upper.tri.inds), and upper.to...:
	new functions instead of local functions in several places, e.g.,
	* R/diana.q, R/fanny.q, ...

	* R/plotpart.q (clusplot.default):
	fix bug PR#1249: cmd() != cmdscale(); use new cmdscale(*, add=TRUE)
	 ---> (slightly) different result sometimes
	fix long-standing typo in NA case + more cleanup

	* R/plotpart.q (clusplot.partition):
		explicit `main' argument with better default.


2001-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.3-6

	* R/plotpart.q: enable `density =' for polygon shading.


2001-11-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/zzz.R: get rid of .Alias

2001-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.3-5

	* R/plothier.q: Fix menu() bug thanks to Richard Rowe.
	* R/plotpart.q: ditto

	* R/agnes.q: properly allow integer matrix input:
	   don't use  all(sapply(x, data.class) == "numeric") anymore.
	* R/clara.q, R/diana.q, R/fanny.q, R/pam.q: ditto

2001-11-05  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/pam.q: `call' via match.call() instead of sys.call, and as
	list component instead of attribute. [R philosophy compatibility]
	* R/mona.q:  ditto
	* R/fanny.q, R/diana.q, R/clara.q, R/agnes.q,
	* R/plothier.q, R/plotpart.q: ditto


2001-10-09  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 1.3-5b (beta) for sending to Robert G

	* R/plothier.q: plot.diana() must have main=NULL

	* R/diana.q: minor code cleanup

2001-08-27  Martin Maechler  <maechler@stat.math.ethz.ch>

	* README.orig: renamed from R/README-splus

2001-08-22  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): New version is 1.3-4

	* man/flower.Rd: nicer using \describe{}

	* man/plot.partition.Rd (and R/plotpart.q): new argument `which.plots'
	  (as in the other plot.* functions).
	* R/plothier.q:
	  All plot.* methods which produce more than one plot now call
	  par(ask = TRUE) automagically when `needed' (as e.g., in plot.lm()).

	* man/*.Rd: document all arguments; a bit more cleanup.
	  R (1.4.0) CMD check is now okay.

2001-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/*.q and man/*.Rd:  generic/method argument fixes

2001-05-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/*.Rd: indenting in all dataset examples
	* man/votes.repub.Rd: usage fix

2001-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* INDEX: structured logically, rather than alphabetically
	* tests/clara.R: new test
	* src/clara.f (clara): added comments
	* R/clara.q (clara)  : comments and cleanup

2001-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): New version is 1.3-3.

	* R/agnes.q and all others: `components' not `arguments' in print.*()
	* src/meet.f (meet): use [if then else] instead of goto
	* src/clara.f (clara): all declarations explicit; some cleanup

2001-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Package): licence changed to GPL (Rousseeuw's e-mail)

	* R/pam.q: minor code cleanup for Fortran interface
	* src/pam.f (pam): all declarations explicit

	* README: integrated former ./README_MM
	* src/twins.f, many R/*.q and
	* man/pltree.Rd: replace  s/S-plus/S/ in many places


2001-03-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/print.summary.FOO.Rd: drop these files, move some to FOO.Rd
	* man/print*.Rd: cleanup, use \method{}

2001-01-04  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): New version is 1.3-2.

	* man/print*.Rd:  Better \title{.},   hence
	* INDEX
	* man/*.Rd:  Remove \keyword{libcluster}; we have {cluster}.

2001-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): New version is 1.3-1.

2001-01-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/*.Rd:  fixes for codoc()

	* src/spannel.f (spannel): improve readability, indent properly,
			add a few comments
	* src/clara.f:	<ditto>
	* src/pam.f:	<ditto>
	* src/twins.f:	<ditto>

	* R/*.q : Added	 PACKAGE = .. to all .Fortran() calls
	  =====	  Many	codoc() fixes; particularly  summary.*(*, ...)

	* R/plotpart.q: (clusplot.partition): simplified
	* R/agnes.q:  T/F -> TRUE/FALSE and more
	* R/clara.q:	<ditto>
	* R/diana.q:	<ditto>
	* R/fanny.q:	<ditto>
	* R/mona.q:	<ditto>
	* R/pam.q:	<ditto>

2000-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): New version is 1.2-5.

2000-12-24  Kurt Hornik	 <Kurt.Hornik@ci.tuwien.ac.at>

	* DESCRIPTION (Version): New version is 1.2-4.
	(Maintainer): New entry.

2000-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>

	* src/daisy.f: indented do loops; one if / else.

	* R/daisy.q: __ daisy() __
	   - "ordratio" |-> "T", was "O" erronously!
	   - `metric' and `list' argument checking

	* man/clusplot.default.Rd: updated and cleaned.

2000-12-02  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/plothier.q:	 plot.agnes() & plot.diana() :
	main=NULL defaults to two different titles for both plots

2000-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/...Rd:
	   - \section{NOTE} becomes \note
	   - fix most T/F to TRUE/FALSE, ..

	* R/plothier.q:
	   - cleanup (T/F); indenting
	   - plot.mona(): las = 1 for axis; allow main=
	   - plot.diana(): `which.plot' and main= and sub=
	   - plot.agnes(): `which.plot' and main= and sub=
	   - pltree.twins(): allow main= ; rm"plot = TRUE" (warn)
			    --> now depends on R 1.2's plot.hclust()

	* R/plotpart.q: clusplot.default() -- now works!
	   - *much* clean up
	   - color choice such as to see points
	   - got rid of NaN warning
	   - eliminated "polygon(*,density.) warnings by '##no yet'"

2000-11-29  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/daisy.q: add "dist" class (and fix T/F to TRUE/FALSE etc)
	* R/daisy.q  and
	* man/print.dissimilarity.Rd: add summary.dissimilarity()
	* man/dissimilarity.object.Rd:	cleanup, use \value{.}, doc. "dist"
	* man/daisy.Rd: cleanup, use \value{.}
	* man/agnes.Rd: cleanup.
	* man/*.object.Rd: cleanup, use \value{.}

Thu Feb 17 22:56:58 2000  Kurt Hornik  <Kurt.Hornik@ci.tuwien.ac.at>

	* DESCRIPTION (Version): New version is 1.2-3.

	* src/Makefile: Removed.

Tue Dec 28 18:41:09 1999  Kurt Hornik  <Kurt.Hornik@ci.tuwien.ac.at>

	* DESCRIPTION (Version): New version is 1.2-2.

	* data/00Index: Added entry for `xclara'.
	* man/xclara.Rd: New file.

	* data/figure2.R:
	* data/table4.R:
	Removed as unused and undocumented.

Sun Dec	 5 20:14:45 1999  Kurt Hornik  <Kurt.Hornik@ci.tuwien.ac.at>

	* DESCRIPTION (Version): New version is 1.2-1.

	* R/daisy.q:
	* src/daisy.f:
	* PORTING:
	Rewrite to pass integers rather than character strings to Fortran
	(changes provided by BDR).

Sun Apr 11 04:21:03 1999  Kurt Hornik  <Kurt.Hornik@ci.tuwien.ac.at>

	* DESCRIPTION (Version): New version is 1.2-0.

	* R/plotpart.q: Replace rep.int() by rep().

	* R/zzz.R: Make .First.lib() use plot.hclust() for plclust() which
	seems to do the job, sort of.

	* data/animals.R: Replaced by `animals.tab'.
	* data/ruspini.R: Replaced by `ruspini.tab'.
	* data/votes.repub.tab: New file.

	* man/agriculture.Rd: New file.
	* man/animals.Rd: New file.
	* man/flower.Rd: New file.
	* man/ruspini.Rd: New file.
	* man/votes.repub.Rd: New file.
	* man/*: Hand-edit all examples to make executable.

Fri Nov 27 23:53:11 1998  Kurt Hornik  <Kurt.Hornik@ci.tuwien.ac.at>

	* DESCRIPTION (Version): New version is 1.1-3.

	* R/mona.q: Barf only if neither a matrix nor a data frame
	(remember that in S, is.matrix() is TRUE for data frames).

	* man/*: Converted anew via `Sd2Rd -x' using Sd2Rd 0.3-2.

	* TODO: Removed.

Tue Jun 16 09:23:15 1998  Kurt Hornik  <Kurt.Hornik@ci.tuwien.ac.at>

	* DESCRIPTION (Version): New version is 1.1-2.

	* DESCRIPTION:
	* PORTING:
	* TITLE:
	* R/zzz.R:
	* src/Makefile:
	Change old `clus' to new name `cluster'.

Mon Jun 15 11:01:52 1998  Kurt Hornik  <Kurt.Hornik@ci.tuwien.ac.at>

	* ChangeLog: Finally started, current version is 1.1-1.