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
	ZZ* 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  <saikat@stat.wisc.edu>

	* 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 <saikat@stat.wisc.edu>

	* 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 <saikat@stat.wisc.edu>

	* 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

