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>
* 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.
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