The R Project SVN R-packages

2015-11-25 Bert van Willigen
    * DESCRIPTION: version 3.1-123
    * man/*Control.Rd: Fixed residual error added.
    * R/gls.R, R/gnls.R, R/lme.R, R/nlme.R, R/reStruct.R: Fixed residual error added.
    * src/init.c, src/nlme.c, src/nlmefit.?:
    * tests/example_[1-9]_wequantify.R: 9 files added.
    * README: Credentials added.

2015-08-18 Luke Tierney
    * Description: version 3.1-122
    * src/nlmefit.c: Added PROTECT/UNPROTECT calls.

2015-06-29  Brian Ripley

    * DESCRIPTION: version is 3.1-121

    * NAMESPACE: tweak imports.

2015-02-20  Brian Ripley

    * DESCRIPTION: version is 3.1-120

2015-02-07  Brian Ripley

    * man/bdf.Rd: change markup for a dead URL

2015-01-29  Brian Ripley

    * po/*.de.po: updates.

2015-01-23  Brian Ripley

    * NAMESPACE: register lme method for simulate()

2015-01-10  Martin Maechler

    * remove non-useful legacy "code":  q(); emacs "Mode: S" etc

2015-01-09  Brian Ripley

    * DESCRIPTION: version is 3.1-119

    * man/bdf.Rd: update URL.

2014-10-20  Brian Ripley

    * R/*.R: remove unused assignments.

2014-10-07  Brian Ripley

    * DESCRIPTION: version is 3.1-118

2014-09-30 Brian Ripley

    * R/nlme.R: nlme with self-starting model incorrectly required 'start'.

    * tests/nlme2.R: regression test for above.

    * R/*, src/* correct copyright information.


2014-03-31  Brian Ripley

    * DESCRIPTION: version is 3.1-117

    * po/R-fr.po: update.

2014-03-28  Brian Ripley

    * DESCRIPTION: version is 3.1-116

    * R/{lme,newMethods,nlsList}.R: modify messsages.
    * po/{R-pl,pl}.po: update.

2014-03-19  Brian Ripley

    * tests/missing.{R,Rout.save}: reduce 'digits' for cleaner results
    on platforms without extended-precision hardware.

    * po/R-de.po: Update from Detlef Steuer.

2014-03-09  Brian Ripley

    * DESCRIPTION: version is 3.1-115

    * R/{gls,gnls,lme,nmle}.R, man/{lmeScale,*Control}.Rd:
    remove msScale and nlmStepMax arguments which were used for nlm(),
    where that is not longer used.

2014-03-08  Brian Ripley

    * DESCRIPTION: version is 3.1-114

    * R/new-methods.R: labeling from fitted() was sometimes wrong as
    the 'groups' component lost row names. (PR#15678)

    * tests/fitted.R: add regression test.

    * R/lme.R: clean up

    * man/{lmeControl,lmeScale}.Rd: update..

2013-11-17  Brian Ripley

    * DESCRIPTION: version is 3.1-113

    * src/{matrix,nlOptimizer}.h: typos in guard names (clang 3.4)

2013-10-21  Martin Maechler

    * R/gls.R, man/gls-internal.Rd: remove redundant parentheses.

2013-10-03  Brian Ripley

    * man/{gls,lme}.Rd: add links, warn on no-covariate formulae.

2013-09-30, 2013-10-02  Brian Ripley

    * DESCRIPTION: version is 3.1-112

    * R/gls.R, man/glsControl.Rd, man/Initialize.glsStruct.Rd.
    Remove 'qrTol', which was unused and set to the non-existent
    .Machine$single.eps, that is to NULL.

    * NAMESPACE, man/gls-internal.Rd: export glsApVar and glsEstimate
    for use in package rms.

    * R/gls.R, lme.R: more use of integer constants.

    * man/*.Rd: classes in quotes, more links, remove CVS lines.

    * R/lme.R, R/newFunc.R, tests/predict.lme.R:
    fix asOneFormula and predict.lme for y ~ 0.
    (see https://stat.ethz.ch/pipermail/r-devel/2013-September/067600.html)

    * R/lme.R: Several of the return components were incorrect for a
    model of the form fixed = resp ~ 0.

2013-08-17  Brian Ripley

    * add start on ko translations.

2013-08-15  Brian Ripley

    * DESCRIPTION: version is 3.1-111
    * R/lmList.R: Adjust to cope with failed fits and fits with
    fewer coefficients returned by lm().  (Contributed by Ruth Ripley.)

2013-07-02  Brian Ripley

    * DESCRIPTION: version is 3.1-110,
    * R/{gls,gnls,lme}.R: Replace as.name() calls by quote(stats::nls) etc.
    * inst/LICENCE: remove.

2013-03-21  Brian Ripley

    * inst/CITATION: modernize.

2013-03-11  Brian Ripley

    * LICENCE: remove (it was not a licence file).

2013-01-26  Brian Ripley

    * DESCRIPTION: version is 3.1-109,
    depends on R (>= 3.0.0).

2013-01-26  Brian Ripley

    * DESCRIPTION: version is 3.1-108,
    depends on R (< 3.0.0) and has chol.f and rs.f in .Rbuildignore.

2013-01-23  Brian Ripley

    * man/[n]lme.Rd: add a note about the need to scale the response.
    * man/lmeControl.Rd: correct description of 'msTol' argument.
    * man/[n]lmeControl.Rd: correct description of 'opt' argument (it is
    a character string).
    * man/*.Rd: s/Jose/José/
    * R/[n]lme.R, man/[n]lmeControl.Rd: allow '...' for further
    control arguments to be based though to nlminb() and optim().


2013-01-13  Brian Ripley

    * DESCRIPTION: add accent on JCP's first name (and declare
    UTF-8 encoding). Add EISPACK authors.
    * src/rs.f: minimal version of eigen.f containing just RS and
    ancillaries (replacing eigen.f).

2013-01-12  Brian Ripley

    * DESCRIPTION: version is 3.1-107
    * src/{chol,eigen}.f: port files from R (where they are
      deprecated/defunct).

2012-12-06  Kurt Hornik

    * DESCRIPTION: version is 3.1-106, add roles to Authors@R.

2012-11-28  Brian Ripley <Brian.Ripley@R-project.org>

    * NAMESPACE: import selectively from lattice and stats.

2012-09-24  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: version is 3.1-105
    * R: improve messages for translation.

2012-09-01  Brian Ripley <Brian.Ripley@R-project.org>

    * po: add Polish translations.

2012-08-30  Brian Ripley <Brian.Ripley@R-project.org>

    * src/init.c: force use of registered symbols in R >= 2.16.0

2012-05-23  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: version is 3.1-104
    * src/gnls.c, src/nlme.c, src/nlmefit.[ch]:
    type mismatches shown by clang's -Wconversion

2012-04-25  Brian Ripley <Brian.Ripley@R-project.org>

    * src/nlmefit.c: type mismatch shown by clang's -Wconversion

2012-03-29  Brian Ripley <Brian.Ripley@R-project.org>

    * src/nlOptimizer.c: increase PROTECTion (reported by Andrew Runnalls).

2012-02-15  Brian Ripley <Brian.Ripley@R-project.org>

    * inst/CITATION: protect against TRE bug in UTF-8 locales.

2012-01-14  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: version is 3.1-103

2011-12-25  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: needs Suggests: MASS for data(package=)

2011-07-19  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: version is 3.1-102
    * R/newMethods.R: getData.nls (aka getData.lme) used the na.action
    of the call on the whole data and not on the model frame: should
    have used the na.action component of the result.
    * tests/{lme.R,lme.Rout.save,ss2.rda}: test for above.
    * man/simulate.lme: document as method.

2011-07-11  Brian Ripley <Brian.Ripley@R-project.org>

    * COPYING: rename to GPL-2
    * LICENCE, inst/LICENCE: adjust wording accordingly

2011-05-30  Brian Ripley <Brian.Ripley@R-project.org>

    * R/newFunc.R: name arguments to lapply() when ... is present.

2011-05-06  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: version is 3.1-101

2011-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2011-04-14  Martin Maechler  <maechler@stat.math.ethz.ch>

    * man/augPred.Rd, R/groupedData.R, R/gls.R, R/lme.R, R/simulate.R
    Changes he failed to document.

2011-03-26  Brian Ripley <Brian.Ripley@R-project.org>

    * src/{nlmefit,pdMat}.c: remove unused variables detected by
    -Wunused-but-set-variable

2011-03-11  Brian Ripley <Brian.Ripley@R-project.org>

    * Release 3.1-100 for R 2.13.0

    * NAMESPACE: no longer re-export BIC

    * man/BIC.Rd: removed.

2011-02-23  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: version is 3.1-100, require R >= 2.13

    * man/BIC.Rd: make a stub referring to stats::BIC()

    * Everywhere: remove obsolete email addresses of former authors

2011-02-23  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: version is 3.1-99 (unreleased, used for R-devel),
    remove email addresses of former authors (and JCP has moved).

    * R/{new,zz}Methods.R:
    Put all BIC() methods in one place, as the default method.

    * man/BIC.Rd: remove aliases to methods (not all of which actually
    existed)

    * man/BIC.logLik.Rd: merge into BIC.Rd

    * tests/lme.Rout.save: update for R 2.13.0.

    * NAMESPACE, R/newMethods.R: prepare for migration of BIC() to stats.

    * R/{gls,gnls,lme}.R, NAMESPACE: add nobs() methods.

2011-02-10  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-98

2011-02-04  Brian Ripley <Brian.Ripley@R-project.org>

    * data/{MathAchieve,bdf}.rda: resave with xz compression.
    * DESCRIPTION: depend on R (>= 2.10).

2010-10-01  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-97

2010-09-22  Brian Ripley <Brian.Ripley@R-project.org>

    * man/residuals.gls.Rd: incorrect default, see
    https://stat.ethz.ch/pipermail/r-devel/2010-September/058487.html

2009-12-22  Brian Ripley <Brian.Ripley@R-project.org>

    * man/ACF.gls.Rd: has \seealso to itself: seems ACF.lme was meant.

2009-12-18  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: add BugReports field.

2009-10-12,16  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-96
    * po/R-de.po, po/de.po: update

2009-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version, Date): 3.1-95
    * R/nlme.R (nonlinModel): use unname() instead of clearNames()

2009-09-02  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-94
    * man/*.Rd: remove unnecessarily anchored links, including several
    incorrect ones.

2009-08-16  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-93
    * R/lmList.R, tests/lmList.R: bug fix for predict.lmList (PR#13788)
    * R/gls.R, tests/anova.gls.R: bug fix for anova.gls (PR#13567)

2009-05-30  Brian Ripley <Brian.Ripley@R-project.org>

    * R/gnls.R, R/corStruct.Rd: minor message wording changes from
    Debian 'bug' report.
    * R/R-de.po: add

    [ Missing entries for 3.1-9[12] which were concerned with German
    translations. ]

2009-01-16  Brian Ripley <Brian.Ripley@R-project.org>

    * man/*.Rd: expand tabs

2008-12-30  Brian Ripley <Brian.Ripley@R-project.org>

    * man/summary.pdMat.Rd: avoid embedded newlines in \code strings.

2008-12-27  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-90
    * R/gls.R: call dist correctly (PR#13418)

2008-12-19  Brian Ripley <Brian.Ripley@R-project.org>

    * man/*.Rd: clean up some reference formats and misuse of $...$.

2008-12-11  Brian Ripley <Brian.Ripley@R-project.org>

    * man/*.Rd: spelling
    * src/nlOptimizer.c: missing PROTECT

2008-06-07  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-89
    * R/lme.R: fitted.lme() always dropped, when it should drop for
    one column but not for one row.
    * tests/lme.R, lme.Rout.save: add regression test for
    single-row predictions.

2008-04-10  Brian Ripley <Brian.Ripley@R-project.org>

    * R/zzMethods.R: add .onUnload() to unload the DLL.

2008-03-30  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-88

2008-02-19  Brian Ripley <Brian.Ripley@R-project.org>

    * man/logLik.lme.Rd, man/logLik.gnls.Rd: correct description of
    'REML' argument.

2008-02-19  Brian Ripley <Brian.Ripley@R-project.org>

    * inst/CITATION: add file (essentially what citation() would
    produce, without the warning).

2008-02-18  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-87
    * R/gnls.R, tests/gls.R: fix for PR#10364, missing row names
    on predict.gnls.

2008-02-11  Duncan Murdoch <murdoch@stats.uwo.ca>

    * R/*.R: Return invisible(x) from numerous print methods.

2007-12-30  Douglas Bates <bates@stat.wisc.edu>

    * [r4884] man/plot.nffGroupedData.Rd: Correct malformed link reported
      by Yihui Xie <xieyihui@gmail.com>. Remove reference to nonexistent
      URL.
    * [r4885] Initialize.reStruct.Rd, collapse.groupedData.Rd,
      fitted.lmeStruct.Rd, lme.Rd, lme.groupedData.Rd, lme.lmList.Rd,
      logLik.reStruct.Rd, nlme.nlsList.Rd, plot.nfnGroupedData.Rd,
      plot.nmGroupedData.Rd, recalc.reStruct.Rd, residuals.lme.Rd,
      residuals.lmeStruct.Rd: Remove reference to nonexistent URL

2007-10-04  Kurt Hornik

    * DESCRIPTION (Version, Date): 3.1-86

2007-10-04  Brian Ripley <Brian.Ripley@R-project.org>

    * R/corStruct.R: check for uninitialized corARMA structures.

2007-09-17  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-85
    Also, use approved form of GPL (>=2).
    * R/varFunc.R: fix for PR#9831.
    * tests/coef.R: test for the above.
    * tests/lme.Rout.save: update format for R >= 2.6.0.
    * man/corRatio.Rd: wrong formula, reported to R-devel by
    Ben Bolker on 2007-09-03.

2007-07-26  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-84
    * LICENCE, inst/LICENCE: clarify this is licensed under GPL >= 2.
    * README, R/*.R, src/*.[ch]: Update source for GPL.
    * man/*.Rd: add header with licence conditions

2007-07-02  Brian Ripley <Brian.Ripley@R-project.org>

    * R/varFunc.R: varIdent did not look at its 'fixed' arg, PR#9765
    * tests/varIndent.R: test for the above.

2007-06-13  Brian Ripley <Brian.Ripley@R-project.org>

    * R/VarCov.R: correct getVarCov.gls, PR#9752

2007-06-13  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-83
    Also, update authors and email addresses where known.
    * R/lme.R: called quantile on potentially missing values.
    * tests/missing.{R,Rout.save}: test summary methods

2007-06-12  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-82
    Also, R >= 2.4.0 because of seq_along.
    * tests/lme.Rout.save: back to 2.5.1 layout.

2007-05-29  Brian Ripley <Brian.Ripley@R-project.org>

    * R/{gls,lme,pdMat}.R: qualify uses of nchar() by 'type'.
    * R/lme.R: layout of over-long error message.
    * tests/lme.Rout.save: update for above and for 2.6.0 layout.
    * R/{gls,gnls,lme,nlme}.R: copy row names to fitted values and
    residuals.
    * R/{gls,gnls,lme}.R: support naresid and napredict.
    * man/{residuals,fitted}.lme.Rd: document this.
    * tests/missing.{R,Rout.save}: tests of missing-value support.

2007-05-20,24  Brian Ripley <Brian.Ripley@R-project.org>

    * R/*.R: partial matching issues, switch to seq_along.

2007-05-15  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-81
    * NAMESPACE, R/zzMethods.R: migrate vcov methods from stats to here.

2007-05-04  Brian Ripley <Brian.Ripley@R-project.org>

    * man/{Extracr.pdMat,getdata.*,summary.varFunc}.Rd: remove
    surplus }.

2007-03-30  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-80
    * R/nlme.R (contrMat): Allow for expressions in 'fixed'.
    * tests/contrMat.R: regression test for above.
    * R/gls.R: bug fix for the case of y ~ 0.
    * tests/gls.R: regression test for above.
    * R/{lme,lmList,newMethods}.R: patch for lattice 0.15-x.

2007-01-30  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Title): Capitalize for consistency.

2006-12-29  Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION (Version, Date): 3.1-79

    * R/corStruct.R, R/pdMat.R, R/reStruct.R, man/corStruct.Rd,
    man/pdMat.Rd, man/reStruct.Rd: add '...' argument to as.matrix()
    methods. (Needed for 2.5.0, but works in earier versions.)

2006-12-10  Douglas Bates  <bates@stat.wisc.edu>

    * DESCRIPTION (Version, Date): 3.1-78

2006-12-06  Douglas Bates  <bates@stat.wisc.edu>

    * R/nlme.R (contrMat): Ensure that the contrasts component is a
    list of matrices by expanding function names if necessary.

2006-11-29  Douglas Bates  <bates@stat.wisc.edu>

    * DESCRIPTION: Prepare for new version.
    * R/newMethods.R (getData.nls): getData.nls for R's nls objects
    * inst/scripts/ch*.R: update Pinheiro and Bates (2000) scripts

2006-11-29  Brian Ripley <Brian.Ripley@R-project.org>

    * R/reStruct.R: fix PR#9262, multiple-line deparse.
    * R/gls.R, groupedData.R, lme.R, lmList.R, newMethods,R, nlme.R:
    more deparse width issues.

2006-09-28  Douglas Bates  <bates@stat.wisc.edu>

    * R/nlme.R (getParsNlme): backed out change that caused failure
    reported by Christian Ritz.

2006-09-18  Douglas Bates  <bates@stat.wisc.edu>

    * R/VarCorr.R (VarCorr): Clean up problems in this file and
    several others detected by codetools.

2006-09-11  Douglas Bates  <bates@R-project.org>

    * R/nlme.R (getParsNlme): '[[' not '[' in case start$fixed is a list
    * R/gls.R,gnls.R,newMethods.R,nlme.R,pdMat,Rsimulate.R: fix
    problems exposed by codetools.

2006-07-31  Douglas Bates  <Douglas.Bates@R-project.org>

    * man/ranef.lme.Rd: Modified the description of the `standard'
    argument to more clearly describe its effect.

2006-07-24  Douglas Bates  <Douglas.Bates@R-project.org>

    * R/lme.R: Patch by Andrew Robinson <A.Robinson@ms.unimelb.edu.au>
    and Berwin Turlach <berwin@maths.uwa.edu.au> to set maximum number
    of function calls in nlminb.

2006-07-03  Douglas Bates  <Douglas.Bates@R-project.org>

    * DESCRIPTION: Version is 3.1-75

    * man/{many files}: Documentation changes contributed by Spencer
    Graves <spencer.graves@pdf.com>.  Most of the changes add Pinheiro
    and Bates (2000) as a reference or add additional \seealso{}
    entries.  Some examples from Pinheiro and Bates (2000) have also
    been added.

    * R/nlme.R: reformat the code, typo.

2006-07-03  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/lme.R (lme.formula): when control()$returnObject is TRUE, only
    warn instead of stop() in the case of non-convergence.
    * tests/lme.R: test the above
    * tests/lme.Rout.save:

2006-06-02 Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: Version is 3.1-74

2006-05-31 Brian Ripley <Brian.Ripley@R-project.org>

    * R/lme.R: Keep terms and optional model frame in lme.formula.
    Use terms for prediction (get safe prediction that way).
    Add keep.data argument to lme and methods.
    * man/lme*.Rd: update for keep.data argument.
    * R/newMethods.R: make use of saved data in getData methods.
    * tests/getData.R, tests/predict.lme.R: new tests.

2006-05-24 Brian Ripley <Brian.Ripley@R-project.org>

    * R/gls.R, man/comparePred.Rd:  'minimum' and 'maximum' were
    evaluated on a formula in the comparePred methods.  Instead,
    evaluate 'primary' in the 'data' used to fit object1, and document
    what is done.  (Reported by Mark Difford.)

2006-05-22 Brian Ripley <Brian.Ripley@R-project.org>

    * DESCRIPTION: Version is 3.1-73

2006-05-21 Brian Ripley <Brian.Ripley@R-project.org>

    * LICENCE, inst/LICENCE: add and install a licence file.

2006-05-18 Brian Ripley  <Brian.Ripley@r-project.org>

    * R/groupedData.R: adjust method of as.data.frame.
    * R/newFunc.R: fix bug in gsummary with objects that have
    classes, e.g. Hmisc labels.  (Reported by Mark Difford, in a
    private followup to
    https://stat.ethz.ch/pipermail/r-help/2006-May/094549.html.)
    * tests/augPred_lab.R: tests for the above fix.

2006-05-12 Brian Ripley  <Brian.Ripley@r-project.org>

    * R/gls.R, R/gnls.R, R/nlme.R: missing data=data in terms calls,
    needed to resolve '.' on rhs of formulae.

    * DESCRIPTION: Version is 3.1-72

2006-03-29 Brian Ripley  <Brian.Ripley@r-project.org>

    * R/newMethods.R: as.list() did not work on symbols in R.

2006-03-14 Brian Ripley  <Brian.Ripley@r-project.org>

    * R/lme.R, man/Variogram.Rd: make example work (na.omit in
    the wrong place).

2006-03-10 Brian Ripley  <Brian.Ripley@r-project.org>

    * DESCRIPTION: Version is 3.1-71

2006-02-17 Brian Ripley  <Brian.Ripley@r-project.org>

    * R/nlsList.R: need to allow for multi-line deparse.
    * tests/deparse.R: add regression test

2006-01-05  Brian Ripley  <Brian.Ripley@r-project.org>

    * DESCRIPTION: Version is 3.1-70
    * src/init.c, src/Makevars: make use of gcc4 visibility where supported
    * inst/mlbook/ch0[45].R: remove unnecessary use of data()
    * inst/scripts/ch0[58].R: all allowed versions of R have nlminb
    * R/gls.R: element 'optimMethod' in the return value for
    glsControl was unnamed.
    * R/{gls,ngls,lme,nlme}.R, man/{gls,ngls,lme,nlme}Control.Rd:
    let the user (rather than the version of R) choose the optimizer
    to be used.

2006-01-05  Brian Ripley  <Brian.Ripley@r-project.org>

    * src/init.c: missing registration for ARMA_constCoef
    * inst/scripts/ch02.R: correct argument names in simulate.lme call

2005-12-31  Brian Ripley  <Brian.Ripley@r-project.org>

    * DESCRIPTION: Version is 3.1-69, require 2.3.0.
    * NAMESPACE: use registration.
    * R/*.R: use registered symbols.

2005-12-31  Brian Ripley  <Brian.Ripley@r-project.org>

    * DESCRIPTION: Version is 3.1-68.
    * src/init.c: new file to register symbols
    * R/corStruct.R: corrected one use of PACKAGE="base"
    * R/lmList.R: remove attempted use of 'frame = 1'

2005-12-09  Deepayan Sarkar  <deepayan@stat.wisc.edu>

    * R/newMethods.R, R/groupedData.R: fix for problem described in
    https://stat.ethz.ch/pipermail/r-help/2005-December/082890.html
    (superpose.line/symbol components were being truncated to length
    of an arbitrary component).


2005-12-09  Brian Ripley  <Brian.Ripley@r-project.org>

    * DESCRIPTION: Version is 3.1-67.
    * R/gls.R: Replace do.call by eval.parent on massaged call.
    * po/fr.R, po/R-fr.R, inst/po: add French translation by
    Philippe Grosjean and automated en@quot translation.

2005-08-25  Douglas Bates  <bates@stat.wisc.edu>

    * R/gls.R: Added option "optimMethod" to gls, gnls, and lme.

2005-08-24  Douglas Bates  <bates@wisc.edu>

    * R/lme.R (print.intervals.lme): Replace calls to print.matrix by
    print(as.matrix()).

2005-07-25  Douglas Bates  <bates@bates1-home>

    * inst/scripts/ch08.R: Cleaned up examples in ch04, ch06, ch08.

    * src/matrix.h: Include R_Ext/Linpack.h in addition to R_Ext/Applic.h

2005-07-19  Douglas Bates  <bates@stat.wisc.edu>

    * R/gnls.R: Added definition of convIter when using nlminb or when
    using optim.  Reindented this and other R source files.

2005-07-12  Douglas Bates  <bates@bates1-home>

    * inst/scripts/ch01.R: Clean up and check these scripts

    * src/nlmefit.c (gls_loglik): re-write contributed by ?? (I
    accidently deleted the email message).

    * R/lme.R (lme.formula): Use nlminb if available.


2005-06-08  Douglas Bates  <bates@bates1-home>

    * R/lme.R (predict.lme): Fixed bug when using a name for a formula
    in original fit. (Reported by Arne.Mueller@sanofi-aventis.com)

2005-05-20  Douglas Bates  <bates@bates1-home>

    * man/contr.SAS.Rd: Removed

2005-04-04  Douglas Bates  <bates@bates1-home>

    * R/newFunc.R: Removed contr.SAS definition as it has been revised
    and moved into the stats package for R-2.1.0

2005-03-02  Douglas Bates  <bates@bates1-home>

    * src/nlmefit.c (gls_loglik): Replaced rnkm1 by p.

    * po/,inst/po/: Added localization support.

2004-11-04  Douglas Bates  <bates@bates1-home>

    * src/nlmefit.c (dimFree): Fix memory leak reported by Brian Ripley.

2004-11-03  Douglas Bates  <bates@bates1-home>

    * man/varWeights.Rd: Remove all calls to data()

    * man/corExp.Rd: Remove all references to the mva package

2004-08-10  Douglas Bates  <bates@bates1-home>

    * man/pairs.compareFits.Rd: fix syntax errors (new check available
    in R CMD check)

2004-01-14  Douglas Bates  <bates@stat.wisc.edu>

    * man/getCovariate.varFunc.Rd: Syntax correction from Kurt.

2003-12-16  Douglas Bates  <bates@stat.wisc.edu>

    * install.R: Create stored image

2003-08-29  Douglas Bates  <bates@stat.wisc.edu>

    * tests/lme.Rout.save (Coefficients): Now consistent with
    i386-linux result.

    * src/base.h: Replace R_ext/Mathlib.h by Rmath.h

2003-08-09  Douglas Bates  <bates@stat.wisc.edu>

    * man/Covariate.varFunc.Rd, man/Matrix.pdMat.Rd, man/Matrix.reStruct.Rd, man/Names.pdMat.Rd, man/Names.reStruct.Rd, man/coef.corStruct.Rd, man/coef.modelStruct.Rd, man/coef.pdMat.Rd, man/coef.reStruct.Rd, man/coef.varFunc.Rd, man/getData.lmList.Rd, man/gnls.Rd:
    Use \method for replacement method documentation as per Rd changes

    * R/lme.R:
    Changed check for intercept-like column in getFixDF (PR#2418)

2003-06-12  Douglas Bates  <bates@stat.wisc.edu>

    * DESCRIPTION: New release

    * man/ranef.lmList.Rd, man/nlme.Rd: Overdocumented arguments

2003-06-10  Douglas Bates  <bates@stat.wisc.edu>

    * man/MathAchSchool.Rd, man/MathAchieve.Rd, ChangeLog, DESCRIPTION, R/groupedData.R, inst/scripts/ch03.R, inst/scripts/ch04.R:
    Release 3.1-42

    * inst/scripts/ch01.R: Protecting power in formula

2003-06-10  Douglas Bates  <bates@stat.wisc.edu>

    * R/groupedData.R: Fixed bug in groupedData constructor when outer
    is not missing.

2003-05-16  Douglas Bates  <bates@stat.wisc.edu>

    * src/nlmefit.c (internal_EM): Fix by Peter Dalgaard for compound
    symmetry EM calculations (PR#2985)

2003-05-05  Douglas Bates  <bates@stat.wisc.edu>

    * R/lmList.R (update.lmList): Changed this and several other
    update methods.

    * R/groupedData.R: Use eval instead of do.call (Dieter Menne)

2003-04-17  Douglas Bates  <bates@stat.wisc.edu>

    * NAMESPACE: contributed by Brian Ripley

    * man/print.corStruct.Rd: Removed this and many other redundant
    documentation files for S3 methods.

    * R/<many files> Remove redundant GPL notices.

2003-03-25  Douglas Bates  <bates@stat.wisc.edu>

    * R/nlme.R (nonlinModel): Moved definition from AAA.R to here

    * man/summary.nlsList.Rd: Remove references to summary.nls

    * R/newMethods.R: Remove vestigial definitions of AIC.lm

    * R/zzMethods.R: Remove references to AIC.lm

2003-02-08  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R (lme.formula): Removed hessian=TRUE in calls to optim as
    suggested by Brian Ripley.

2003-01-30  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R:
    Incorporate change from Brian Ripley in response to Dieter Menne

    * man/lme.lmList.Rd, man/lme.groupedData.Rd, man/lme.Rd:
    Documentation of the contrasts argument added (Greg Warnes).

2003-01-30  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R (lme.formula): Incorporate Greg Warnes' changes for
    the contrasts argument.

    * R/nlsList.R: Correct check for is.null(class(FUN))

2002-12-27  Douglas Bates  <bates@stat.wisc.edu>

    * R/newFunc.R (gsummary): Fix comparison in check for varying
    columns (PR#1775 - bug report with fix provided by Dieter Menne.

2002-12-11  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R (print.lme): Removed one more as.vector()

    * R/varFunc.R (print.summary.varFixed): changed  instances of
    deparse(as.vector(x)) to deparse(x) here and in many other places.

2002-09-10  Saikat DebRoy

    * nlsList.R (nlsList.formula): Use "try" instead of "restart".

2002-08-09  Douglas Bates  <bates@stat.wisc.edu>

    * R/groupedData.R: Fixed creation of grouped data from a formula
    only

    * R/newGenerics.R: Renamed the initialize generic and all methods
    and calls to Initialize so as not to conflict with the methods
    package.

2002-07-23  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R (update.lme): Fix formula handling in update methods
    (Brian Ripley).

2002-04-20  Douglas Bates  <bates@stat.wisc.edu>

    * R/nlme.R: Bug fix by SDR - convergence criterion was being
    calculated incorrectly.

2002-04-04  Douglas Bates  <bates@stat.wisc.edu>

    * man/getVarCov.Rd: Added an example of the type="marginal"
    Corrected misplaced brace.

    * R/VarCov.R (getVarCov.lme): Added the getVarCov functions
    contributed by Mary Lindstrom <lindstro@biostat.wisc.edu>

2002-03-27  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R (anova.lme): Change strvar != "NA" to !is.na(strvar)

2002-03-05  Douglas Bates  <bates@stat.wisc.edu>

    * man/ACF.gls.Rd: Changed Jose's email address on this and all the
    other man pages.

    * R/varFunc.R: Incorporate fix from Thomas Lumley and from Setzer
    Woodrow for the logic where ifelse(length(el) == 1, is used
    instead of if(length(el) == 1)

    * R/pdMat.R: Change all vestigial instances of T and F to TRUE and
    FALSE.

2001-12-18  Douglas Bates  <bates@stat.wisc.edu>

    * R/corStruct.R: Finally resolved the print.summary.corSymm
    controversy so it prints and it prints the correct value.

2001-12-10  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R: unclassed the logLik component of an lme summary before
    trying to put it into a data frame for printing.

2001-12-01  Douglas Bates  <bates@stat.wisc.edu>

    * R/zzMethods.R: Removed the .Alias calls.

2001-10-30  Douglas Bates  <bates@stat.wisc.edu>

    * man/pairs.lme.Rd: Modified many documentation files to pass the
    codoc checks.

2001-10-23  Douglas Bates  <bates@stat.wisc.edu>

    * man/ACF.lme.Rd: Modified many, many method definitions and
    documentation files to get them to pass the R-1.4.0 (in
    development) package checking process.

2001-10-08  Douglas Bates  <bates@stat.wisc.edu>

    * R/lmList.R: Fixed definition of logLik.lmList to work with R
    (but it is still rather ugly).

    * R/varFunc.R: Changed definition of logLik.varComb to return a
    logLik object.

2001-10-05  Douglas Bates  <bates@stat.wisc.edu>

    * R/lmList.R: Fixed selection of id[subscripts] in the panel
    function of pairs.lmList (and several other functions) so it does
    not produce a warning from evaluating is.na(NULL).

2001-09-17  Douglas Bates  <bates@stat.wisc.edu>

    * R/nlme.R: Incorporated a change from
    Setzer.Woodrow@epamail.epa.gov for using nested grouping factors
    in nlme.

2001-06-20  Douglas Bates  <bates@stat.wisc.edu>

    * R/varFunc.R: Changes in calling sequences and in documentation
    so the package passes codoc() checks.  These affect many files in
    both the R and the man directory.  No changes of substance.

2001-05-29  Martin Maechler <maechler@stat.math.ethz.ch>

    * R/zzMethods.R: Use .Alias()

    * R/newGenerics.R:  Generic AIC()
    * R/newMethods.R:   logLik.lm()   moved to "base R"
    * man/AIC.Rd,
    * man/AIC.logLik.Rd: AIC.logLik() and AIC.lm() as well
    * man/logLik.lm.Rd:

2001-03-28  Douglas Bates  <bates@stat.wisc.edu>

    * R/simulate.R: Modified simulate.lme for default pdMat class of
    pdLogChol.

2001-02-24  Douglas Bates  <bates@stat.wisc.edu>

    * R/newFunc.R: Removed the old fake xyplot function.  The new work
    by Murrell and Sarkar will make this superfluous.

    * man/MEestimate.Rd: Added manual pages for MEEM, MEdecomp,
    MEestimate.

    * R/newMethods.R: Revised assignments in plotting methods to be
    compatible with the Murrell/Sarkar preliminary trellis package.

    * src/nlmefit.c (internal_decomp): Corrected an error reported by
    Kathryn Chaloner where Srows >= ZXrows.

2001-01-10  Douglas Bates  <bates@stat.wisc.edu>

    * DESCRIPTION (Maintainer): Added Maintainer entry to
    DESCRIPTION.

2000-12-09  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R: (Variogram.lme) Coerced n.pairs to numeric and
    corrected calls to dist.

2000-12-08  Douglas Bates  <bates@stat.wisc.edu>

    * R/lme.R: Changed all calls to dist in lme.R, gls.R and
    corStruct.R to use the argument "method" rather than "metric".

    * R/pdMat.R: Replaced calls to .Fortran("dbksl", ...) with calls
    to the R function solve() for R-1.2.0 where the S_compat.c file
    has been removed.

    * inst/scripts/ch01.R: Added the chapter scripts from
    "Mixed-Effects Models in S and S-PLUS" to the inst directory.

    * man/formula.nlme.Rd: Modified the examples in this and many
    other .Rd files to use the Loblolly data and the SSasymp
    self-starting function.  There were many occasions where the
    Soybean data was being fit to a default formulation of an nlme
    model just to get things like a formula.  This fit of the Soybean
    data is difficult and time consuming and not very illuminating.

2000-11-30  Douglas Bates  <bates@stat.wisc.edu>

    * src/matrix.c: Removed dependency on S_compat.h by replacing
    calls to dqrdca with the equivalent call to dqrdc2.

2000-07-24  Saikat DebRoy

    * Changed various uses of do.call to eval.  The reason for doing
    this is to allow calls to the function calling eval from within
    another function.  It's the old scoping problem again.

2000-07-07  Saikat DebRoy

    * src/nlme.c, src/nlmefit.c: Added mixed_grad in calls to optif9.

    * src/nlmefit.c : Added handling of pdLogChol objects (pdClass =
    4) in various functions.

    * src/nlmefit.c (mixed_grad): New function giving analytic
    gradient for mixed-effects log-likelihood.

    * R/nlme.R (nlme.formula): Added updating of the pdFactor in the
    PNLS step.

    * R/reStruct.R: Made pdLogChol the default representation for
    reStruct objects.

    * src/pdMat.c (logChol_pd): new function.

    * R/pdMat.R: Added back the pdLogChol class and associated
    methods.


2000-07-03  Douglas Bates  <bates@stat.wisc.edu>

    * man/corFactor.corStruct.Rd: Added an alias for
    corFactor.corNatural

    * src/nlmefit.c (internal_loglik): Changed the return value on
    error from R_NegInf to -DOUBLE_XMAX so the optif[09] optimizers
    will work properly.

    * src/corStruct.c (corStruct_factList): Provided a correct call to
    the R version of F77_CALL(chol) here and everywhere else in this
    source file.

    * R/zzz.R: Removed the deprecated call to provide

2000-03-17  Douglas Bates  <bates@stat.wisc.edu>

    * added many data sets

    * incorporated patches from Brian Ripley to use optim for the
    optimization rather than nlm

    * src/nlmefit.c (internal_loglik): Returned R_NegInf instead of
    generating a error on a singular precision matrix.

    * DESCRIPTION (Depends): Changed Depends to R version 1.0.1
    because of problem with assigning components of lists.

1999-12-23  Douglas Bates  <bates@stat.wisc.edu>

    * TITLE: Changed the title to nlme