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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 sources2007-06-05 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 - neededfor R version >= 2.6.0.* R/daisy.q (daisy): for 2-valued variables only warn aboutnon-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 2.5.02007-03-29 Martin Maechler <maechler@stat.math.ethz.ch>* R/silhouette.R (silhouette.default): use x$clustering only when x isa 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 >= 2printing.* R/clara.q (stop): message for NA-observations: only show firstdozen of observation numbers.* tests/clara-NAs.R: test the above* tests/clara-NAs.Rout.save: ditto2006-12-02 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 example2006-12-01 Martin Maechler <maechler@stat.math.ethz.ch>* man/daisy.Rd: more content about Gower; thanks to Gavin Simpson2006-11-23 Martin Maechler <maechler@stat.math.ethz.ch>* R/daisy.q (daisy): metric = "gower" -- not yet finished2006-09-07 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 alsoif "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 safercode, 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 isunchanged, 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 CRAN2006-05-03 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Depends): require R >= 2.2.1 -- which should havehappened 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, includingall kinds of factors, provided by Jeanne Vallet.* data/plantTraits.rda: useful for daisy() illustrations2006-04-12 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 extended2006-04-11 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 itsnormalization) 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 withmore 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 Francois2006-02-04 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 otherellipse implementations.* man/volume.ellipsoid.Rd: + example of 'ellipsoid' construction2006-01-31 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; addexample, particularly for plot(as.dendrogram(.)).2006-01-26 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Version): 1.10.4 -- released to CRAN2006-01-25 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 routines2005-12-30 Martin Maechler <maechler@stat.math.ethz.ch>* inst/CITATION: first version* R/silhouette.R (plot.silhouette): 'nmax.lab' was not obeyedproperly (labels were drawn for large n when thesilhouette 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 cosmetic2005-08-30 Martin Maechler <maechler@stat.math.ethz.ch>* R/daisy.q (daisy): the case of a *binary*-only matrix (notdata 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 tosave even more memory; do not assign 'data' whenkeep.data=FALSE.* man/clara.Rd: + 'i.med' + 'medoids.x' - 'keepdata'* man/clara.object.Rd: dito2005-07-19 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.x2005-06-29 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() whichreturns 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 ofsilhouette.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} = 1the 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): 1.10.02005-06-08 Martin Maechler <maechler@stat.math.ethz.ch>* R/pam.q (pam): new argument 'trace.lev = 0'* man/pam.object.Rd: pam() also return $medID* src/pam.c (dark): take special care of empty clusters (ntt == 0)* src/pam.c (pam): also work when medoids are not increasing.* R/pam.q (pam): user-supplied 'medoids': even more checks2005-06-02 Martin Maechler <maechler@stat.math.ethz.ch>* tests/fanny-ex.R: use new RNG (hence change example); add samplesof memb.exp -> 1* DESCRIPTION (Author): new formulation for better auto-citation()* src/fanny.f (fanny): 'r' ("membership exponent") becomesuser-specifiable argument; dito for 'maxit'* R/fanny.q (fanny): new arguments 'memb.exp' ("membership exponent");'tol' and 'maxit'* R/fanny.q (.print.fanny): utility to be used in both print.*()methods; nicer, using formatC() and 'digits' explicitly.* man/fanny.Rd: new arguments, see above* man/fanny.object.Rd: mention new '$ 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 onprint.hclust().* R/zzz.R (gettextf): ..etc: define substitutes such as to allowrunning in R < 2.1.0* man/ellipsoidhull.Rd: fixed outdated "link[pkg]"* man/clusplot.default.Rd: dito* man/*.Rd : etc2005-03-22 Martin Maechler <maechler@stat.math.ethz.ch>* R/clara.q (clara): start to 'rationalize' messages for futuretranslation.* 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 character2004-12-14 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 forcomputing the agglomerative/divisive coefficient.* man/coef.hclust.Rd: new; including example* man/predict.ellipsoid.Rd: wrong link2004-11-26 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 typo2004-10-28 Martin Maechler <maechler@stat.math.ethz.ch>* man/predict.ellipsoid.Rd: add nice example2004-08-19 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (LazyData): yes2004-08-12 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 above2004-08-03 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Version): 1.9.5 --> to CRAN2004-07-21 Martin Maechler <maechler@stat.math.ethz.ch>* man/mona.Rd: drop an extraneous "}\n" that Kurt's new tools found* man/twins.object.Rd: dito2004-07-06 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 loopas 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 usejtmd[] 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 Long2004-03-11 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Version): 1.8.1 for R versions <= 1.8.11.9.1 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 couldcause wrong results and segmentation faults, instead of endingwith 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 here2004-03-09 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 functions2004-01-23 Martin Maechler <maechler@stat.math.ethz.ch>* R/silhouette.R (silhouette.default): do not require clustercodes in 1:k (Murad Nayal <mn216@columbia.edu>).* man/silhouette.Rd: accordingly; mention 2 <= k <= n-12003-12-22 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Version): 1.8.0 for R versions <= 1.8.11.9.0 for R versions >= 1.9.02003-12-19 Martin Maechler <maechler@stat.math.ethz.ch>* NAMESPACE: Finally make a namespaced package2003-12-01 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 .C2003-11-28 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 dissimilaritiesanymore. Use pColl() in messages* R/zzz.R (sQuote): & dQuote() for R version < 1.82003-10-25 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 codoc2003-09-23 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): -> release2003-08-27 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 released2003-08-13 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 toDuncan.Mackay@flinders.edu.au).Now allow "only 1 level" for binary vars2003-07-10 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 colors2003-07-09 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Version): 1.7.4 -- not yet released* R/daisy.q (daisy): better error message for invalid typecomponents; 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 above2003-06-04 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. above2003-06-02 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$diss' bylooking up x$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} viasilhouette 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 irrelevant2003-03-17 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) class2003-03-11 Martin Maechler <maechler@stat.math.ethz.ch>* R/clara.q (clara): new argument `rngR' allowing to use R's RNGinstead 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 .Fortran2003-03-05 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% speed2003-02-07 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 parts2002-12-28 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)" problem2002-12-21 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 removedbanag() 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 canbe 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 renaming2002-10-26 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Version): 1.6-003 := pre-1.6-32002-10-23 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 CRAN2002-10-21 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 newdefault col = "gray".* R/plothier.q (bannerplot): arguments inside = . , border = 0work 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 < 1.62002-10-18 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 rightfor plot.diana.2002-09-12 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Date): -- released locally only2002-09-11 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(); + 1ex2002-09-09 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Version): 1.6-1 ==> for CRAN and R 1.6.02002-09-07 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 tothoughts 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 < 1.5.02002-09-03 Martin Maechler <maechler@stat.math.ethz.ch>* R/plotpart.q (plot.partition): new `data' argument andsmart `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 gotos2002-09-02 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.f2002-08-31 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.fin 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 user2002-08-27 Martin Maechler <maechler@stat.math.ethz.ch>* src/clara.c (clara): new file, translated from Fortran; easierto 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 example2002-08-02 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 andsummary.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 color2002-06-17 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 varsseveral 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): + comment2002-05-21 Martin Maechler <maechler@stat.math.ethz.ch>* DESCRIPTION (Version): 1.5-1new 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 + comments2002-01-24 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 1.4-02002-01-23 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: clean2002-01-21 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 ourellipses 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 internalkleur() & plotje(); and "spannel" arguments; new maxit; lower epsuse which.min() and which.max(); ...* R/pam.q (pam): diss has new default = inherits(x, "dist") whichis 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 twinscalling 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 sometimesfix 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 .Alias2001-11-06 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: ditto2001-11-05 Martin Maechler <maechler@stat.math.ethz.ch>* R/pam.q: `call' via match.call() instead of sys.call, and aslist 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: ditto2001-10-09 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 cleanup2001-08-27 Martin Maechler <maechler@stat.math.ethz.ch>* README.orig: renamed from R/README-splus2001-08-22 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 callpar(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 fixes2001-05-26 Martin Maechler <maechler@stat.math.ethz.ch>* man/*.Rd: indenting in all dataset examples* man/votes.repub.Rd: usage fix2001-05-23 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 cleanup2001-05-22 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 cleanup2001-05-21 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 places2001-03-21 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 1.2-5.2000-12-14 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 plots2000-11-30 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{.}2000-12-24 Kurt Hornik <Kurt.Hornik@ci.tuwien.ac.at>* DESCRIPTION (Version): New version is 1.2-4.(Maintainer): New entry.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() whichseems 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.