574 lines
18 KiB
Plaintext
574 lines
18 KiB
Plaintext
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% Check from R:
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% news(db = tools:::.build_news_db_from_package_NEWS_Rd("~/R/Pkgs/cluster/inst/NEWS.Rd"))!
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\name{NEWS}
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\title{News for \R Package \pkg{cluster}}% MM: look into ../svn-log-from.all
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\encoding{UTF-8}
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%% NB: The date (yyyy-mm-dd) is the "Packaged:" date in ../DESCRIPTION
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\section{Changes in version 2.1.6 (2023-11-30, svn r8311)}{
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\subsection{Bug Fixes}{
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\itemize{
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\item \code{clara(*, metric="gower")} is too buggy, and hence
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\bold{removed} for now, see below (2.1.5).
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}
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}
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\subsection{Misc}{
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\itemize{
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\item tweak \file{tests/fanny-ex.\{R,Rout.save\}} for less "diffs".
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}
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}
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}
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\section{Changes in version 2.1.5 (2023-11-27, svn r8301)}{
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\subsection{New Features}{
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\itemize{
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\item \code{pam()} and \code{clara()} also accept a
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\code{\link{logical}} matrix as input.
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\item \code{clara()} gets new \code{metric = "gower"} donated by
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Kasper Fischer-Rasmussen.
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--- was removed in 2.1.6 because of valgrind-detected memory leaks
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(and problems/bugs found earlier in R experiments).
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}
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}
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\subsection{Misc}{
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\itemize{
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\item renamed internal function \code{silhouette.default.R} to \code{silhouetteR}.
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\item \file{CITATION} switched from old \code{citEntry()} to \code{bibentry()}.
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\item \code{clara(*, trace = <pos>)} prints slightly better info.
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\item \file{DESCRIPTION} gets \kbd{Enhances: } for packages
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cross-referenced in \file{man/*.Rd}.
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}
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}
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}
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\section{Changes in version 2.1.4 (2022-08-19, svn r8119)}{
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\subsection{New Features}{
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\itemize{
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\item New \code{medoids()} to compute \code{pam}-consistent medoids,
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given a clustering (and data).
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item \code{help(dissimilarity.object)} % ../man/dissimilarity.object.Rd
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now correctly describes the meaning of a \code{method = "gower"}
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result type \code{"T"}.
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Also, \code{help(daisy)} now extensively documents the different
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options for \code{type = *}, notably \code{"ordratio"} and
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\code{"logratio"}.
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\item \code{pam(x, diss=TRUE)} uses \code{inherits(x, "dissimilarity")} instead
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of semi-deprecated \code{data.class(x) == "dissimilarity")} to check.
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\item Using \code{deparse1()} from \R version 4.0.0 and newer (even
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when \pkg{cluster} is installed into an older versions of R),
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e.g., in plot default titles.
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}
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}
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}
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\section{Changes in version 2.1.3 (2022-03-28, svn r8062)}{
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\subsection{New Features}{
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\itemize{
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\item \code{as.data.frame(<silhouette>)} now works; suggested by
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Jonathan Marshall (@Massey, NZ).
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}
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}
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\subsection{Translations}{
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\itemize{
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\item Updated German translations (Detlef Steuer)
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}
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}
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\subsection{Tweaks}{
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\itemize{
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\item use explicit cast, quieting \code{-Wconversion}.
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}
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}
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}
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\section{Changes in version 2.1.2 (2021-04-16, svn r7959)}{% CRAN published 2021-04-17; R 4.1.0
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\subsection{New Features}{
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\itemize{
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\item Updated the Italian translations (by Daniele Medri), the
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French (by Philippe Grosjean) and the German (by Detlef Steuer).
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New Lithuanian translations by Gabriele Stupuriene & Rimantas Zakauskas.
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}
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}
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}
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\section{Changes in version 2.1.1 (2021-02-11, svn r7925)}{
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\subsection{New Features}{
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\itemize{
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\item Added Italian translations from Daniele Medri, and updated the
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French ones from Philippe Grosjean.
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\item \code{clara()} gains a \code{cluster.only} argument, entirely
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\dQuote{in parallel} to \code{pam()}.
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\item the \code{silhouette()} method for \code{clara} now allows
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\code{full} to be a number in [0,1] instead of just a logical and it gains
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gains new optional argument \code{subset} to specify the indices of
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observations for which silhouette values shold be computed.
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\item Faster \code{pam()} - \sQuote{fasterPAM} from Erich Schubert.
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New optional arguments \code{medoids = "random"}, \code{nstart}, and
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\code{variant}, notably \code{variant = "faster"}.
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}
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}
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}
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\section{Changes in version 2.1.0 (2019-06-14, svn r7675)}{
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\subsection{Bug Fixes}{
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\itemize{
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\item \code{volume(obj)} is now correct also for ellipsoids of
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dimension \eqn{d > 2}.
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\item \command{--enable-lto} compilation revealed missing
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\code{weights} argument in \file{src/cluster.h}'s declaration of
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\code{cldaisy()}.
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}
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}
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\subsection{Tweaks}{
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\itemize{
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\item Replaced many \dQuote{old style} \verb{`<word>'} quotations.
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}
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}
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}
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\section{Changes in version 2.0.9 (2019-05-01, svn r7663)}{
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\subsection{Tweaks}{
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\itemize{
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\item \file{src/mona.c} now uses correct \emph{void} \code{F77_NAME}
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and source cleaned.
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}
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}
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}
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\section{Changes in version 2.0.8 (2019-04-02, svn r7643)}{
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\subsection{New Features}{
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\itemize{
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\item \code{pam()} gets new \code{pamonce} options, for values 3,
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4, or 5, choosing versions of \command{fastpam}, contributed by Erich
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Schubert, Univ. Dortmund.
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\item update \file{tests/*} to work with R >= 3.6.0 (sample.kind)
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item correct thinko in \code{?clusGap}, the help page.
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}
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}
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}
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\section{Changes in version 2.0.7 (2018-03-29, svn r7509)}{
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\subsection{New Features}{
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\itemize{
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\item \code{clara()} gets new option \code{metric = "jaccard"},
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contributed by Kamil Kozlowski and Kamil Jadszko.
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%% FIXME: Also add for pam() !!
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\item \code{pam()} and \code{clara()} use \code{match.arg(metric)}
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and hence \code{metric} can be abbreviated (and invalid strings
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give an error instead of being interpreted as \code{"euclidean"}).
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item The bug fix of \code{clara(*, correct.d = TRUE)} (from
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version 2.0.4) for the NA-data case now also applies to the
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internal C function \code{selec()}.
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}
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}
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}
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\section{Changes in version 2.0.6 (2017-03-10, svn r7332)}{
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\subsection{New Features}{
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\itemize{
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\item \code{mona()} now C- instead of Fortran-based (having used
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f2c etc) and now has a \code{trace.lev} option which allows
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progress reporting
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\dQuote{remembers} if the original data had missing values.
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item \code{mona(<1-column>)} no longer loops infinitely but signals
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an error.
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}
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}
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}
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\section{Changes in version 2.0.5 (2016-10-07, svn r7278)}{
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\subsection{New Features}{
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\itemize{
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\item \code{clusGap()} gets a new option \code{scaleH0}, and
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\code{scaleH0 = "original"} is an alternative to the default PCA
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rotation.%% still see ../TODO-MM !
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\item \code{clusGap()} now also stores its \code{call} and uses
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that for \code{print()}ing and (by default in the \code{main} title)
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for \code{plot()}ing \code{"clusGap"} objects.
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\item
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__ MOSTLY NOT IMPLEMENTED yet __ %%% TODO !!!
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\code{diana()} gets new optional argument \code{stop.at.k}.
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When a positive integer, the DIANA algorithm will stop early, as
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much desirable for large \eqn{n}.
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item \code{daisy()} gets 3+1 new options \code{warn*} which allow
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to suppress three different kind of warnings, as these are
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undesirable in some cases. With thanks to Kirill Müller for the
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convincing context.
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\item \code{pam()} now signals an error when there are more than
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65536 observational units (whereas it could segfault previously),
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thanks to a patch from Mikko Korpela, Helsinki.
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}
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}
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}
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\section{Changes in version 2.0.4 (2016-04-16, svn r7186)}{
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\subsection{New Features}{
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\itemize{
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\item \code{clusGap()} gets a new option \code{d.power = 1}
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allowing to choose the basic weight statistic as it was originally
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proposed, namely \emph{squared} distances by setting \code{d.power = 2}.
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%% ~/R/MM/Pkg-ex/cluster/Gonzalez-on-clusGap.R <--
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item fix small glitch in silhouette's help page.
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\item Finally fixed a bug (in the original Fortran code from
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Rousseeuw!) in clara's distance computation when there are
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\code{NA}s in the data. As the fix is not backward compatible,
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a warning is produced (for the time being) if there \emph{are}
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\code{NA}s and the user does not explicitly use \code{clara(*, correct.d = TRUE)}.
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}
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}
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}
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\section{Changes in version 2.0.3 (2015-07-20, svn r6985)}{
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\subsection{New Features}{
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\itemize{
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\item This new \file{NEWS.Rd} file -- going to replace \file{ChangeLog}
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eventually.
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item import all we need (but not more) from the "base" pkgs
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(stats, graphics, ...).
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}
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}
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}
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\section{Changes in version 2.0.2 (2015-06-18, svn r6955)}{
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\subsection{New Features}{
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\itemize{
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\item using new \code{anyNA()} where appropriate.
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\item New Korean translations, thanks to Chel Hee Lee.
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\item \code{plotpart()}: \code{cmdscale()} tweaks.
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item valgrind detected missing allocation (\code{nisol["1"]} for k=1).
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\item typo R/daisy.q (R bug %once we require R >= 3.2.0: \PR{16430}
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\Sexpr[results=rd]{tools:::Rd_expr_PR(16430)}).
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}
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}
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}
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\section{Changes in version 2.0.1 (2015-01-31, svn r6877)}{
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\subsection{Bug Fixes}{
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\itemize{
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\item Fix \code{silhouette( obj )} for \code{obj <- pam(x, k = 1)}.
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}
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}
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}
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\section{Changes in version 2.0.0 (2015-01-29, svn r6874)}{
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\subsection{New Features}{
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\itemize{
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\item \code{pam()} now using \code{.Call()} instead of
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\code{.C()} is potentially considerably more efficient.
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\item \code{agnes()} has improved \code{trace} behaviour; also,
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some invalid \code{par.method = *} settings now give an early and
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understandable error message.
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\item \code{lower.to.upper.tri.inds()} (etc) now returns \code{integer}.
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item \code{.C(..)} and \code{.Fortran(..)}: no longer using
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\code{DUP=FALSE} as that has become deprecated.
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}
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}
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}
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\section{Changes in version 1.15.3 (2014-09-04, svn r6804)}{
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\subsection{New Features}{
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\itemize{
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\item \code{agnes()} and \code{diana()} finally get, respectively
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work with a \code{trace.lev} option.
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\item \code{plot.(agnes|diana)()} now deals well with long
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\code{call}s, by using multiple title lines.
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\item Message translations now also for C level error messages.
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}
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}
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\subsection{Bug Fixes}{
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\itemize{
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\item \code{agnes(*, method="flexible", par.method = c(a1, a2, b, c))},
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i.e., \code{length(alpha) == 4}, finally works \emph{correctly}.
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}
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}
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}
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\section{Changes in version 1.15.2 (2014-03-31, svn r6724)}{
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\subsection{New Features}{
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\itemize{
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\item Rewrote parts of the R level messages so they are more
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easily translatable, thanks to proposals by Lukasz Daniel.
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\item French translations from Philippe Grosjean.
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}
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}
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}
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\section{Changes in version 1.15.1 (2014-03-13, svn r6676)}{
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\subsection{Bug Fixes}{
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\itemize{
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\item \code{mona} example not working in \R < 3.0.x.
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}
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}
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}
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|
|
|
||
|
|
\section{Changes in version 1.15.0 (2014-03-11, svn r6672)}{
|
||
|
|
\subsection{New Features}{
|
||
|
|
\itemize{
|
||
|
|
\item \code{agnes(*, method = "gaverage")} contributed by Pierre
|
||
|
|
Roudier.
|
||
|
|
\item documentation improvements;
|
||
|
|
\item better translatable messages and translation updates.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
%% ============================== FIXME ===========================
|
||
|
|
%% ~~~~~~~~~
|
||
|
|
%% use ../ChangeLog
|
||
|
|
%% ~~~~~~~~~
|
||
|
|
%% and then
|
||
|
|
%%
|
||
|
|
%% use ../svn-log-from.all
|
||
|
|
%% ~~~~~~~~~~~~~~~~
|
||
|
|
%% and ../../cluster_Archive.lst {~= CRAN src/contrib/Archive/cluster/ :
|
||
|
|
%%
|
||
|
|
\section{Changes in version 1.14.4 (2013-03-26, svn r6469)}{
|
||
|
|
\subsection{Tweaks}{
|
||
|
|
\itemize{
|
||
|
|
\item 2 de translations; update \file{mona.Rout.save}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 1.14.3 (2012-10-14, svn r6318)}{
|
||
|
|
\subsection{New Features}{
|
||
|
|
\itemize{
|
||
|
|
\item Polnish translations from Lukasz Daniel.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\subsection{Misc}{
|
||
|
|
\itemize{
|
||
|
|
\item Tweaks for translations.
|
||
|
|
\item Improve \code{clusGap()} examples.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
\section{Changes in version 1.14.2 (2012-02-06, svn r6069)}{
|
||
|
|
\subsection{New Features}{
|
||
|
|
\itemize{
|
||
|
|
\item New \code{clusGap()} to compute the \dQuote{cluster Gap}
|
||
|
|
goodness-of-fit statistic.
|
||
|
|
\item Export \code{coefHier()}
|
||
|
|
\item \code{as.dendrogram()} now for \code{"twins"}, not just
|
||
|
|
\code{"agnes"}.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 1.14.1 (2011-10-16, svn r5928)}{
|
||
|
|
\subsection{New Features}{
|
||
|
|
\itemize{
|
||
|
|
\item First translations (into German, thanks to Detlef Steuer).
|
||
|
|
\item better \code{citation("cluster")}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\subsection{Bug Fixes}{
|
||
|
|
\itemize{
|
||
|
|
\item \code{plot.silhouette(..., col = <one per cluster>)} had
|
||
|
|
ordering bug.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\section{Changes in version 1.14.0 (2011-06-07, svn r5842)}{
|
||
|
|
\subsection{New Features}{
|
||
|
|
\itemize{
|
||
|
|
\item Make \code{clara()} more \code{pam()}-like;
|
||
|
|
provide \code{pamLike = *} option.
|
||
|
|
\item \code{clusplot.default()} re-factored; use new
|
||
|
|
\code{mkCheckX()}; new args \code{add = FALSE}, \code{cex},
|
||
|
|
\code{cex.txt}.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\subsection{Bug Fixes}{
|
||
|
|
\itemize{
|
||
|
|
\item \code{agnes( <n=1> )}: correct error now.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
%% -> /sfs/w/ftp/CRAN/src/contrib/Archive/cluster/
|
||
|
|
|
||
|
|
%% 214765 Feb 21 2011 cluster_1.13.3.tar.gz
|
||
|
|
%% 213663 Nov 10 2010 cluster_1.13.2.tar.gz
|
||
|
|
%% 214083 Jun 25 2010 cluster_1.13.1.tar.gz
|
||
|
|
%% 214677 Apr 2 2010 cluster_1.12.3.tar.gz
|
||
|
|
%% 214577 Oct 6 2009 cluster_1.12.1.tar.gz
|
||
|
|
%% 215041 May 13 2009 cluster_1.12.0.tar.gz
|
||
|
|
%% 211085 Mar 31 2009 cluster_1.11.13.tar.gz
|
||
|
|
%% 321990 Jan 7 2009 cluster_1.11.12.tar.gz
|
||
|
|
%% 245055 Jun 16 2008 cluster_1.11.11.tar.gz
|
||
|
|
%% 243446 Feb 29 2008 cluster_1.11.10.tar.gz
|
||
|
|
%% 216573 Oct 2 2007 cluster_1.11.9.tar.gz
|
||
|
|
%% 215257 Sep 4 2007 cluster_1.11.8.tar.gz
|
||
|
|
%% 216815 Jun 5 2007 cluster_1.11.7.tar.gz
|
||
|
|
%% 216729 Apr 27 2007 cluster_1.11.6.tar.gz
|
||
|
|
%% 211615 Mar 31 2007 cluster_1.11.5.tar.gz
|
||
|
|
%% 211634 Dec 12 2006 cluster_1.11.4.tar.gz
|
||
|
|
%% 203692 Dec 2 2006 cluster_1.11.3.tar.gz
|
||
|
|
%% 210927 Sep 7 2006 cluster_1.11.2.tar.gz
|
||
|
|
%% 210091 Aug 25 2006 cluster_1.11.1.tar.gz
|
||
|
|
%% 210215 May 18 2006 cluster_1.11.0.tar.gz
|
||
|
|
%% 195962 Mar 21 2006 cluster_1.10.5.tar.gz
|
||
|
|
%% 197577 Jan 26 2006 cluster_1.10.4.tar.gz
|
||
|
|
%% 197853 Jan 26 2006 cluster_1.10.3.tar.gz
|
||
|
|
%% 190839 Aug 31 2005 cluster_1.10.2.tar.gz
|
||
|
|
%% 190975 Jul 3 2005 cluster_1.10.1.tar.gz
|
||
|
|
%% 189042 Jun 13 2005 cluster_1.10.0.tar.gz
|
||
|
|
%% 179723 Apr 4 2005 cluster_1.9.8.tar.gz
|
||
|
|
%% 176832 Jan 24 2005 cluster_1.9.7.tar.gz
|
||
|
|
%% 174742 Aug 24 2004 cluster_1.9.6.tar.gz
|
||
|
|
%% 174218 Aug 4 2004 cluster_1.9.5.tar.gz
|
||
|
|
%% 175565 Jun 26 2004 cluster_1.9.4.tar.gz
|
||
|
|
%% 173097 Jun 18 2004 cluster_1.9.3.tar.gz
|
||
|
|
%% 173251 Jun 13 2004 cluster_1.9.2.tar.gz
|
||
|
|
%% 169773 Apr 12 2004 cluster_1.9.1.tar.gz
|
||
|
|
%% 170071 Mar 14 2004 cluster_1.8.1.tar.gz
|
||
|
|
%% 165322 Jan 22 2004 cluster_1.8.0.tar.gz
|
||
|
|
%% 161548 Sep 24 2003 cluster_1.7.6.tar.gz
|
||
|
|
%% 161359 Sep 3 2003 cluster_1.7.5.tar.gz
|
||
|
|
%% 161257 Jul 18 2003 cluster_1.7.4.tar.gz
|
||
|
|
%% 160252 Jun 11 2003 cluster_1.7.3.tar.gz
|
||
|
|
%% 158265 Jun 4 2003 cluster_1.7.2.tar.gz
|
||
|
|
%% 157386 May 1 2003 cluster_1.7.1.tar.gz
|
||
|
|
%% 155161 Mar 26 2003 cluster_1.7.0.tar.gz
|
||
|
|
%% 154089 Dec 31 2002 cluster_1.6-4.tar.gz
|
||
|
|
%% 154987 Dec 5 2002 cluster_1.6-3.tar.gz
|
||
|
|
%% 154261 Oct 23 2002 cluster_1.6-2.tar.gz
|
||
|
|
%% 147063 Sep 10 2002 cluster_1.6-1.tar.gz
|
||
|
|
%% 131808 Jul 30 2002 cluster_1.5-2.tar.gz
|
||
|
|
%% 116292 Jun 19 2002 cluster_1.5-1.tar.gz
|
||
|
|
%% 113972 Mar 31 2002 cluster_1.4-2.tar.gz
|
||
|
|
%% 113889 Mar 7 2002 cluster_1.4-1.tar.gz
|
||
|
|
%% 116698 Jan 24 2002 cluster_1.4-0.tar.gz
|
||
|
|
%% 105552 Dec 19 2001 cluster_1.3-6.tar.gz
|
||
|
|
%% 105390 Nov 7 2001 cluster_1.3-5.tar.gz
|
||
|
|
%% 105275 Aug 24 2001 cluster_1.3-4.tar.gz
|
||
|
|
%% 103626 Jun 8 2001 cluster_1.3-3.tar.gz
|
||
|
|
%% 99698 Jan 4 2001 cluster_1.3-2.tar.gz
|
||
|
|
%% 91608 Feb 18 2000 cluster_1.2-3.tar.gz
|
||
|
|
%% 91736 Dec 29 1999 cluster_1.2-2.tar.gz
|
||
|
|
%% 93048 Dec 5 1999 cluster_1.2-1.tar.gz
|
||
|
|
|
||
|
|
%% ============================== FIXME ===========================
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
\section{Version 1.2-1 -- 1.13-3}{
|
||
|
|
\subsection{Many historical releases}{
|
||
|
|
\itemize{
|
||
|
|
\item 60 more CRAN releases of the package \pkg{cluster}
|
||
|
|
from Dec 1999 to Feb 2011, see also the \file{ChangeLog} file and
|
||
|
|
\command{svn log}.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
% How can I add vertical space ?
|
||
|
|
% \preformatted{} is not allowed, nor is \cr
|
||
|
|
|
||
|
|
|
||
|
|
\section{Version 1.2-0 (1999-04-11)}{
|
||
|
|
\subsection{First CRAN release of the \pkg{cluster} package, by Kurt Hornik}{
|
||
|
|
\itemize{
|
||
|
|
\item Martin Maechler had its own version independently.
|
||
|
|
\item Both closely modeled after \code{clus} the tarball off JSS.
|
||
|
|
}}
|
||
|
|
|
||
|
|
\subsection{R Functions -- Fortran Files}{
|
||
|
|
\itemize{
|
||
|
|
\item \code{agnes()} -- \file{twins.f} for the \dQuote{twins} \code{agnes} and \code{diana}.
|
||
|
|
\item \code{clara()} -- \code{clara.f}
|
||
|
|
\item \code{daisy()} -- \file{daisy.f} (and \file{meet.f})
|
||
|
|
\item \code{diana()} -- (twins.f)
|
||
|
|
\item \code{fanny()} -- \file{fanny.f}
|
||
|
|
\item \code{mona()} -- \file{mona.f}
|
||
|
|
\item \code{pam()} -- \file{pam.f}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\subsection{Data Sets}{
|
||
|
|
\itemize{
|
||
|
|
\item agriculture
|
||
|
|
\item animals
|
||
|
|
\item flower
|
||
|
|
\item ruspini
|
||
|
|
\item votes.repub
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
\subsection{Further Features}{
|
||
|
|
\itemize{
|
||
|
|
\item all Examples in \file{man/*.Rd} hand edited to become
|
||
|
|
executable.
|
||
|
|
\item \code{summary()}, \code{print()} (and
|
||
|
|
\code{print.summary.**()} methods) for the six basic \R functions above.
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
\section{Version 1.1-2 (1998-06-16)}{
|
||
|
|
\subsection{Renamed previous \pkg{clus} to \pkg{cluster}}{
|
||
|
|
\itemize{ \item . }
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\section{Version 1.1-1 (1998-06-15)}{
|
||
|
|
\subsection{New Features}{
|
||
|
|
\itemize{
|
||
|
|
\item started \file{ChangeLog}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|