News for R Package cluster

Changes in version 2.1.8.1 (2025-03-11, svn r8502)

Misc

• use complete argument names in most cases to satisfy lovers of options(warnPartialMatch* = TRUE).

• using \(.) would need R >= 4.1.0.

Changes in version 2.1.8 (2024-12-10, svn r8468)

Bug Fixes

• C codes underlying agnes() and daisy() under UBSAN and LTO no longer show pointer expression overflow (of a length 0 vector a with a-- call).

Changes in version 2.1.7 (2024-12-06, svn r8466)

Misc

• ‘man/pam.Rd’ set.seed() for data, hence reproducible example.

• ‘src/daisy.c’ and ‘src/dysta.c’ produced from their Fortran *.f versions by f2c, my perl script f2c-clean and manual pretty editing.

  C function dysta() now returns the jhalt "flag"; it is no longer callable from R, nor is dysta3() which is 'static' now, in ‘src/fanny.c’.

  Goal: Use .Call() instead of .C() and hence allow long vectors for the length n(n-1)/2 distance vectors.

• ‘fanny-ex.R’ tests: use IGNORE_RDIFF_BEGIN .. and some explicit cheks to become less platform dependent.

Changes in version 2.1.6 (2023-11-30, svn r8311)

Bug Fixes

• clara(*, metric="gower") is too buggy, and hence removed for now, see below (2.1.5).

Misc

• tweak ‘tests/fanny-ex.{R,Rout.save}’ for less "diffs".

Changes in version 2.1.5 (2023-11-27, svn r8301)

New Features

• pam() and clara() also accept a logical matrix as input.

• clara() gets new metric = "gower" donated by Kasper Fischer-Rasmussen. — was removed in 2.1.6 because of valgrind-detected memory leaks (and problems/bugs found earlier in R experiments).

Misc

• renamed internal function silhouette.default.R to silhouetteR.

• ‘CITATION’ switched from old citEntry() to bibentry().

• clara(*, trace = <pos>) prints slightly better info.

• ‘DESCRIPTION’ gets Enhances: for packages cross-referenced in ‘man/*.Rd’.

Changes in version 2.1.4 (2022-08-19, svn r8119)

New Features

• New medoids() to compute pam-consistent medoids, given a clustering (and data).

Bug Fixes

• help(dissimilarity.object) now correctly describes the meaning of a method = "gower" result type "T". Also, help(daisy) now extensively documents the different options for type = *, notably "ordratio" and "logratio".

• pam(x, diss=TRUE) uses inherits(x, "dissimilarity") instead of semi-deprecated data.class(x) == "dissimilarity") to check.

• Using deparse1() from R version 4.0.0 and newer (even when cluster is installed into an older versions of R), e.g., in plot default titles.

Changes in version 2.1.3 (2022-03-28, svn r8062)

New Features

• as.data.frame(<silhouette>) now works; suggested by Jonathan Marshall (@Massey, NZ).

Translations

• Updated German translations (Detlef Steuer)

Tweaks

• use explicit cast, quieting -Wconversion.

Changes in version 2.1.2 (2021-04-16, svn r7959)

New Features

• Updated the Italian translations (by Daniele Medri), the French (by Philippe Grosjean) and the German (by Detlef Steuer). New Lithuanian translations by Gabriele Stupuriene & Rimantas Zakauskas.

Changes in version 2.1.1 (2021-02-11, svn r7925)

New Features

• Added Italian translations from Daniele Medri, and updated the French ones from Philippe Grosjean.

• clara() gains a cluster.only argument, entirely “in parallel” to pam().

• the silhouette() method for clara now allows full to be a number in [0,1] instead of just a logical and it gains gains new optional argument subset to specify the indices of observations for which silhouette values shold be computed.

• Faster pam() - ‘fasterPAM’ from Erich Schubert. New optional arguments medoids = "random", nstart, and variant, notably variant = "faster".

Changes in version 2.1.0 (2019-06-14, svn r7675)

Bug Fixes

• volume(obj) is now correct also for ellipsoids of dimension d > 2.

• --enable-lto compilation revealed missing weights argument in ‘src/cluster.h’'s declaration of cldaisy().

Tweaks

• Replaced many “old style” ⁠`<word>'⁠ quotations.

Changes in version 2.0.9 (2019-05-01, svn r7663)

Tweaks

• ‘src/mona.c’ now uses correct void F77_NAME and source cleaned.

Changes in version 2.0.8 (2019-04-02, svn r7643)

New Features

• pam() gets new pamonce options, for values 3, 4, or 5, choosing versions of fastpam, contributed by Erich Schubert, Univ. Dortmund.

• update ‘tests/*’ to work with R >= 3.6.0 (sample.kind)

Bug Fixes

• correct thinko in ?clusGap, the help page.

Changes in version 2.0.7 (2018-03-29, svn r7509)

New Features

• clara() gets new option metric = "jaccard", contributed by Kamil Kozlowski and Kamil Jadszko.

• pam() and clara() use match.arg(metric) and hence metric can be abbreviated (and invalid strings give an error instead of being interpreted as "euclidean").

Bug Fixes

• The bug fix of clara(*, correct.d = TRUE) (from version 2.0.4) for the NA-data case now also applies to the internal C function selec().

Changes in version 2.0.6 (2017-03-10, svn r7332)

New Features

• mona() now C- instead of Fortran-based (having used f2c etc) and now has a trace.lev option which allows progress reporting “remembers” if the original data had missing values.

Bug Fixes

• mona(<1-column>) no longer loops infinitely but signals an error.

Changes in version 2.0.5 (2016-10-07, svn r7278)

New Features

• clusGap() gets a new option scaleH0, and scaleH0 = "original" is an alternative to the default PCA rotation.

• clusGap() now also stores its call and uses that for print()ing and (by default in the main title) for plot()ing "clusGap" objects.

• __ MOSTLY NOT IMPLEMENTED yet __

  diana() gets new optional argument stop.at.k. When a positive integer, the DIANA algorithm will stop early, as much desirable for large n.

Bug Fixes

• daisy() gets 3+1 new options warn* which allow to suppress three different kind of warnings, as these are undesirable in some cases. With thanks to Kirill Müller for the convincing context.

• pam() now signals an error when there are more than 65536 observational units (whereas it could segfault previously), thanks to a patch from Mikko Korpela, Helsinki.

Changes in version 2.0.4 (2016-04-16, svn r7186)

New Features

• clusGap() gets a new option d.power = 1 allowing to choose the basic weight statistic as it was originally proposed, namely squared distances by setting d.power = 2.

Bug Fixes

• fix small glitch in silhouette's help page.

• Finally fixed a bug (in the original Fortran code from Rousseeuw!) in clara's distance computation when there are NAs in the data. As the fix is not backward compatible, a warning is produced (for the time being) if there are NAs and the user does not explicitly use clara(*, correct.d = TRUE).

Changes in version 2.0.3 (2015-07-20, svn r6985)

New Features

• This new ‘NEWS.Rd’ file – going to replace ‘ChangeLog’ eventually.

Bug Fixes

• import all we need (but not more) from the "base" pkgs (stats, graphics, ...).

Changes in version 2.0.2 (2015-06-18, svn r6955)

New Features

• using new anyNA() where appropriate.

• New Korean translations, thanks to Chel Hee Lee.

• plotpart(): cmdscale() tweaks.

Bug Fixes

• valgrind detected missing allocation (nisol["1"] for k=1).

• typo R/daisy.q (R bug PR#16430).

Changes in version 2.0.1 (2015-01-31, svn r6877)

Bug Fixes

• Fix silhouette( obj ) for obj <- pam(x, k = 1).

Changes in version 2.0.0 (2015-01-29, svn r6874)

New Features

• pam() now using .Call() instead of .C() is potentially considerably more efficient.

• agnes() has improved trace behaviour; also, some invalid par.method = * settings now give an early and understandable error message.

• lower.to.upper.tri.inds() (etc) now returns integer.

Bug Fixes

• .C(..) and .Fortran(..): no longer using DUP=FALSE as that has become deprecated.

Changes in version 1.15.3 (2014-09-04, svn r6804)

New Features

• agnes() and diana() finally get, respectively work with a trace.lev option.

• plot.(agnes|diana)() now deals well with long calls, by using multiple title lines.

• Message translations now also for C level error messages.

Bug Fixes

• agnes(*, method="flexible", par.method = c(a1, a2, b, c)), i.e., length(alpha) == 4, finally works correctly.

Changes in version 1.15.2 (2014-03-31, svn r6724)

New Features

• Rewrote parts of the R level messages so they are more easily translatable, thanks to proposals by Lukasz Daniel.

• French translations from Philippe Grosjean.

Changes in version 1.15.1 (2014-03-13, svn r6676)

Bug Fixes

• mona example not working in R < 3.0.x.

Changes in version 1.15.0 (2014-03-11, svn r6672)

New Features

• agnes(*, method = "gaverage") contributed by Pierre Roudier.

• documentation improvements;

• better translatable messages and translation updates.

Changes in version 1.14.4 (2013-03-26, svn r6469)

Tweaks

• 2 de translations; update ‘mona.Rout.save’

Changes in version 1.14.3 (2012-10-14, svn r6318)

New Features

• Polnish translations from Lukasz Daniel.

Misc

• Tweaks for translations.

• Improve clusGap() examples.

Changes in version 1.14.2 (2012-02-06, svn r6069)

New Features

• New clusGap() to compute the “cluster Gap” goodness-of-fit statistic.

• Export coefHier()

• as.dendrogram() now for "twins", not just "agnes".

Changes in version 1.14.1 (2011-10-16, svn r5928)

New Features

• First translations (into German, thanks to Detlef Steuer).

• better citation("cluster")

Bug Fixes

• plot.silhouette(..., col = <one per cluster>) had ordering bug.

Changes in version 1.14.0 (2011-06-07, svn r5842)

New Features

• Make clara() more pam()-like; provide pamLike = * option.

• clusplot.default() re-factored; use new mkCheckX(); new args add = FALSE, cex, cex.txt.

Bug Fixes

• agnes( <n=1> ): correct error now.

Version 1.2-1 – 1.13-3

Many historical releases

• 60 more CRAN releases of the package cluster from Dec 1999 to Feb 2011, see also the ‘ChangeLog’ file and svn log.

Version 1.2-0 (1999-04-11)

First CRAN release of the cluster package, by Kurt Hornik

• Martin Maechler had its own version independently.

• Both closely modeled after clus the tarball off JSS.

R Functions – Fortran Files

• agnes() – ‘twins.f’ for the “twins” agnes and diana.

• clara() – clara.f

• daisy() – ‘daisy.f’ (and ‘meet.f’)

• diana() – (twins.f)

• fanny() – ‘fanny.f’

• mona() – ‘mona.f’

• pam() – ‘pam.f’

Data Sets

• agriculture

• animals

• flower

• ruspini

• votes.repub

Further Features

• all Examples in ‘man/*.Rd’ hand edited to become executable.

• summary(), print() (and print.summary.**() methods) for the six basic R functions above.

Version 1.1-2 (1998-06-16)

Renamed previous clus to cluster

• .

Version 1.1-1 (1998-06-15)

New Features

• started ‘ChangeLog’