2024-08-13  Kurt Hornik  <[email protected]>

	* DESCRIPTION (Version): 3.1-166.

2024-08-12  Sebastian Meyer  <[email protected]>

	* R/corStruct.R (Initialize.corARMA): catch unsupported values of
	'p' and 'q' (PR#18777, thanks to Liming Li).
	* tests/corStruct.R: added, with regression test.

2024-06-18  Sebastian Meyer  <[email protected]>

	* tests/deviance.R, tests/nlme.R, tests/updateLme.R:
	use 'MASS' conditionally.

2024-06-16  Kurt Hornik  <[email protected]>

	* man/pairs.compareFits.Rd:
	* man/pairs.lmList.Rd:
	* man/pairs.lme.Rd:
	* man/plot.ACF.Rd:
	* man/plot.Variogram.Rd:
	* man/plot.augPred.Rd:
	* man/plot.gls.Rd:
	* man/plot.lmList.Rd:
	* man/plot.lme.Rd:
	* man/plot.nfnGroupedData.Rd:
	Add package anchors for links to targets from package 'lattice'.

2024-06-05  Sebastian Meyer  <[email protected]>

	* DESCRIPTION (Depends): update to real minimum R version (R >= 3.6.0).

	* po, inst/po: update (installed) translations

	* man/simulate.lme.Rd, man/summary.lme.Rd: drop unneeded \donttest.

2024-04-29  Sebastian Meyer  <[email protected]>

	* R/nlme.R (nlme.nlsList): fix scoping issue for nlsList() and
	self-starting nlme() calls with a preconstructed formula.

2024-04-28  Sebastian Meyer  <[email protected]>

	* R/corStruct.R (corARMA): corARMA() no longer returns the
	dysfunctional/undocumented corIdent() structure, with a clear
	error message when neither 'p' nor 'q' are set > 0 (PR#17988).

2024-04-23  Sebastian Meyer  <[email protected]>

	* R/VarCov.R (getVarCov.lme, getVarCov.gls): support
	'individual[s]' with only one observation (PR#16806).
	* tests/getVarCov.R: add corresponding regression tests.

2024-04-17  Sebastian Meyer  <[email protected]>

	* R/lme.R (predict.lme): use formula() instead of
	re-evaluating the call (with the wrong scope), similar to PR#15892.

	* R/nlme.R (nlme.formula): nlme() finally works with fixed
	variance weights (PR#17712), thanks to the pointers by Bill
	Denney, Benjamin Tyner, and Ben Bolker.
	* tests/varFixed.R: added, based on BD's example.

	* R/varFunc.R (varIdent): warn about misguided varIdent(~1|g)

2023-12-08  Martin Maechler  <[email protected]>

	* tests/augPred_lab.R: manually do Hmisc  label(.) <- ..
	* DESCRIPTION (Version): 3.1-165; no longer suggesting 'Hmisc'.

2023-11-27  Martin Maechler  <[email protected]>

	* src/nlmefit.c: 2 x format 'int': s/%ld/%d/
	* DESCRIPTION (Version): 3.1-164

2023-07-31  Martin Maechler  <[email protected]>

	* R/nlme.R (nlme.formula, formula.nlme):
	* R/gnls.R (gnls, formula.gnls): store 'model' argument as 'formula'
	==> trivial formula() methods, fixing PR#18559 by Ben Bolker.

2023-04-06  Martin Maechler  <[email protected]>

	* tests/sigma-fixed-etc.R (nlme): loosen tol for sM4$tTable[,"Std.Error"]
	* DESCRIPTION (Version): 3.1-163

2023-01-28  Martin Maechler  <[email protected]>

	* DESCRIPTION (Version): 3.1-162 (to be released)

	* R/corStruct.R (corIdent, *.corIdent): deprecated corIdent() and
	some of the "corIdent" methods.
	* man/nlme-deprecated.Rd: deprecation

2023-01-26  Sebastian Meyer  <[email protected]>

	* src/matrix.h: fix return value in C declaration of Fortran
	subroutine 'RS'.  (PR#18438 by Lionel Henry.)

2023-01-23  Sebastian Meyer  <[email protected]>

	* R/groupedData.R (nfGroupedData, nmGroupedData):
	fix deprecation logic to give a warning when not called
	internally.

	* R/groupedData.R (balancedGrouped): suppress spurious warning
	from testing for numeric row names.

2022-11-17  Martin Maechler <[email protected]>

	* DESCRIPTION (Version): 3.1-161 (released)

	* R/pdMat.R (str.pdMat): new method, fixing error for
	   un-initialized, and misleading e.g., in `pdDiag` case.

2022-10-10  Brian Ripley

	* DESCRIPTION (Version): 3.1-160 (released)

2022-08-24  Brian Ripley

	* src/nlmefit.c: Fix for -Wstrict-prototypes.

2022-07-28  Martin Maechler  <[email protected]>

	* DESCRIPTION (Version): 3.1-159

	* R/gnls.R (gnls): 'if (deparse(params[[nm]][[3]]) != "1")' fails
	for long formulas (R-help list, thanks to Bill Dunlap, Jul 24)

2022-07-05  Brian Ripley

	* man/{gls,lme}: document the prohibition on  (rather than
	ignoring of) offset() terms.

2022-06-13  Brian Ripley

	* DESCRIPTION (Version): 3.1-158 (released)
	* R/lme.R (formula.lme): get the formula from the terms instead of
	re-evaluating the call (with the wrong scope), fixing PR#15892.
	* tests/scoping.R: add corresponding regression test.
	* R/nlsList.R: use inherits() instead of comparing class to string.

2022-03-25  Brian Ripley

	* DESCRIPTION (Version): 3.1-157 (released)

2022-03-24  Sebastian Meyer  <[email protected]>

	* R/nlme.R (nlme.formula):
	* R/gnls.R (gnls): revert check for offset() terms in non-linear
	models (avoid symbolic interpretation of arithmetic expressions).
	* R/lme.R (formula.lme): defer fix for scoping issue to give more
	time to update reverse dependencies

2022-03-22  Brian Ripley

	* DESCRIPTION (Version): 3.1-156 (unreleased)

2022-03-18  Sebastian Meyer  <[email protected]>

	* R/gls.R: keep "terms" from gls() for use in predict.gls(),
	fixing PR#18283.
	* R/zzMethods.R, NAMESPACE: drop formula-based terms.gls().
	* tests/gls.R: add corresponding regression test.

	* R/gls.R (formula.gls):
	* R/lme.R (formula.lme): get the formula from the terms instead of
	re-evaluating the call (with the wrong scope), fixing PR#15892.
	* tests/scoping.R: add corresponding regression test.

2022-03-17  Sebastian Meyer  <[email protected]>

	* R/lme.R (lme.formula):
	* R/nlme.R (nlme.formula):
	* R/gls.R (gls):
	* R/gnls.R (gnls): stop() at offset() terms, fixing PR#17880.
	(They were previously ignored.)

2022-03-08  Sebastian Meyer  <[email protected]>

	Improve handling of factor variables in predict() methods.

	* R/gls.R (predict.gls):
	* R/gnls.R (predict.gnls):
	* R/lme.R (predict.lme):
	* R/nlme.R (predict.nlme):
	call model.frame() with 'xlev' to make sure factor levels are
	compatible with the employed contrasts (fixing PR#17226),
	including to warn for numeric 'newdata' for factor variables,
	and to support character input (cf. PR#18312).
	* tests/gls.R:
	* tests/nlme2.R:
	* tests/predict.lme.R: add corresponding regression tests.

	* R/gnls.R (gnls): always return contrast _matrices_ not just names
	of contrast functions. Needed for the above fix and for
	consistency with the other modelling functions in nlme.

2022-03-05  Sebastian Meyer  <[email protected]>

	* inst/CITATION: use citation(auto=meta) and add NLME book.

	* DESCRIPTION (Depends): finally require R >= 3.5.0.
	* R/lmList.R: drop old warnErrList() code, part of utils >= 3.5.0.

	* man/reStruct.Rd: late doc update for the pdClass default changed
	2000-07-07 (PR#17740).

2022-03-04  Sebastian Meyer  <[email protected]>

	* R/lme.R (predict.lme): fix predictions for character-type newdata.
	The example in ch04.R produced wrong results with R >= 4.0.0 (PR#18312).
	* tests/predict.lme: add corresponding regression test.

	* R/newFunc.R (asOneFormula, getCovariateFormula, getResponseFormula):
	* R/newMethods.R (getGroupsFormula.default):
	fix environment of created formula (was local envir, now .GlobalEnv),
	in line with stats::asOneSidedFormula() in R 4.2.0.

	* inst/scripts/ch06.R: increase maxiter for nlsList() of Soybean data
	to only fail for a single plot, consistent with the book (p. 289).

2022-03-03  Sebastian Meyer  <[email protected]>

	Setup extra tests conditional on nlme:::doExtras()

	* DESCRIPTION: add SASmixed to Suggests (used in code from NLME book)
	* inst/scripts: arrange for cleaner Rdiff() (drop proc.time(), tag
	platform-dependent output via ## IGNORE_RDIFF_*, reduce digits in tests)
	* tests/extras: added, including test scripts to run the full code
	from the installed book chapters (with reference output)
	* tests/nlme-stall.R: moved to extras

2022-03-02  Sebastian Meyer  <[email protected]>

	* R/lmList.R (coef.lmList, summary.lmList): fix finding unique
	coefficient names when the set of estimated coefficients varies
	between subgroups (PR#16542); based on a patch by Ben Bolker.
	* tests/lmList.R: add corresponding regression test

2022-02-28  Sebastian Meyer  <[email protected]>

	Clean up license information

	* DESCRIPTION (Authors@R): "R Core Team" rather than "R-core"
	* DESCRIPTION (License): dropped redundant "| file LICENCE"
	* LICENCE: removed (copy of GPL-2)
	* LICENSE.note: created from README
	* README: removed

2022-02-26  Sebastian Meyer  <[email protected]>

	* R/VarCov.R (getVarCov.lme):
	* R/corStruct.R (Variogram.corSpatial):
	* R/lmList.R (predict.lmList):
	* R/lme.R (plot.ranef.lme): fix partial matching issues.

2022-02-25  Sebastian Meyer  <[email protected]>

	Fix more scoping issues (detected by sourcing the installed
	chapter scripts in a local environment)

	* R/simulate.R (simulate.lme): evaluate constructed calls in the
	parent frame.
	* R/lme.R (augPred.lme): look for data in the parent frame.
	* R/gls.R (augPred.gls): (ditto)

2022-02-23  Sebastian Meyer  <[email protected]>

	* R/simulate.R (simulate.lme): fix `useGen = TRUE` branch.

2022-01-13  Brian Ripley

	* DESCRIPTION (Version): 3.1-155 (released)
	* src: Use R_Calloc, R_Free.

2021-11-02  Sebastian Meyer  <[email protected]>

	* R/nlme.R (nlme.nlsList, nlme.formula): fix more scoping issues
	with self-starting models by evaluating calls in the parent frame.
	* R/nlsList.R (nlsList.selfStart): (ditto)
	* tests/scoping.R: add corresponding regression tests.

2021-10-21  Sebastian Meyer  <[email protected]>

	* R/gnls.R (gnls), tests/scoping.R: fix evaluation environment of
	the internal `nls` call used for self-starting models (PR#18157).

	* R/nlme.R (nlme.formula), tests/nlme.R: fix "unused argument" error
	when explicitly specifying `groups` in a self-starting model.

2021-09-23  Martin Maechler  <[email protected]>

	* DESCRIPTION (Version): 3.1-154 (unreleased)

	* R/gls.R (print.intervals.gls): do not print `attr(., "label")` twice;
	ditto in R/lme.R, PR#18196, with thanks to Johannes Ranke.

2021-09-07  Martin Maechler  <[email protected]>

	* R/groupedData.R ("[.groupedData"): change the default of `drop` to
	to FALSE for the case of `x[j]`, fixing PR#18177.

	* R/lme.R (print.summary.lme): change partial match to
	`x$coefficients`, PR#18184.

	* DESCRIPTION: Release 3.1-154

2021-08-05  Martin Maechler  <[email protected]>

	* R/zzMethods.R (.onLoad), R/VarCorr.R: remove code used only
	if(getRversion() < "3.3"); from Sebastian Meyer.

2021-03-09  Martin Maechler  <[email protected]>

	* R/varFunc.R (print.varFunc): use full 'unconstrained' argument
	name, fixing PR#17767, thanks to Sebastian Meyer.

	* DESCRIPTION (Version, Date): 3.1-153 (*not* yet for release)

2021-02-12 Brian Ripley

	* po: update fr translations.

2020-02-03  Brian Ripley

	* DESCRIPTION (Version, Date): 3.1-152 for 4.0.4.

2020-12-09  Martin Maechler  <[email protected]>

	* nlme/man/Remifentanil.Rd: change 2 URLs to 'moved to' locations.

2020-12-07  Martin Maechler  <[email protected]>

	* R/corStruct.R (print.corCompSymm, print.summary.corCompSymm): new,
	thanks to patch in PR#17990 by Sebastian Meyer; also fixing typo
	("Uninitialized").

2020-10-29  Martin Maechler  <[email protected]>

	* DESCRIPTION (Version): 3.1-151
	* R/varFunc.R (varConstProp): constructor and methods, from
	PR#17954 by Johannes Ranke.

2020-10-02  Brian Ripley

	* DESCRIPTION (Version, Date): Prepare to release 3.1-150.

2020-09-24  Peter Dalgaard

        * R/VarCov.R tests/getVarCov.R: Patch set from Sebastian Meyer
          to fix group order issues PR#16744
        * tests/corFactor.R: missed commit from patch for PR#16110
        * INDEX: removed as it was out of date and autobuilt anyway

2020-08-21  Brian Ripley

	* R/pdMat.R: use parent.frame not sys.parent for data= args
	* DESCRIPTION (Version, Date): Prepare to release 3.1-149.

2020-08-20 Peter Dalgaard

	* NAMESPACE, R/corStruct.R, man/corFactor.corStruct.Rd,
	  man/corMatrix.corStruct.Rd, tests/corFactor.R: Applied patch set
	  from Sebastian Meyer to fix misnamed
	  corFactor.compSymm -> corFactor.corCompSymm PR#16110

2020-07-20 Deepayan Sarkar

	* R/lme.R: Applied patch from Johannes Ranke to fix PR#17761

	* DESCRIPTION: update version / date (unreleased)

2020-05-13  Martin Maechler  <[email protected]>

	* DESCRIPTION (Contact, MailingList): R-help (*not* R-core)

2020-04-21  Martin Maechler  <[email protected]>

	* DESCRIPTION (Version): 3.1-148 (not yet released)

	* man/nlsList.Rd: fix stopifnot(.) check in examples.

2020-03-03  Brian Ripley

	* src/nlmefit.c: clean up code.

2020-03-03  Brian Ripley

	* DESCRIPTION (Version): 3.1-147 (released)

	* po: update, including updated German translations from Detlef Steuer

2020-03-11  Martin Maechler  <[email protected]>

	* DESCRIPTION (Version): 3.1-146 (unreleased)

	* man/Remifentanil.Rd: more information incl references.

2020-03-03  Brian Ripley

	* DESCRIPTION (Version): 3.1-145 (released)

	* src/nlmefit.c: avoid clang-UBSAN warning.

2020-02-06

	* DESCRIPTION (Version): 3.1-144 (released)

2020-02-02  Kurt Hornik  <[email protected]>

	* man/gnls.Rd: Drop docs for argument not in usage.

2019-12-10  Brian Ripley

	* DESCRIPTION (Version): 3.1-143 (released)

	* tests/augPred_lab.R: change yet another 'plucked from air' tolerance.

2019-11-07  Martin Maechler  <[email protected]>

	* DESCRIPTION (Version): 3.1-142 (released)

	* R/nlme.R: use vapply and is.matrix.
	* man/pairs.compareFits.Rd: change example.

2019-09-26  Brian Ripley

	* src/nlmefit.c: suppress warning from clang trunk.

2019-08-01  Kurt Hornik  <[email protected]>

	* DESCRIPTION (Version): 3.1-141 (released)

2019-07-27  Kurt Hornik  <[email protected]>

	* R/lme.R:
	* tests/nlme2.R:
	Robustify against using stringsAsFactors = FALSE by default.

2019-05-10  Brian Ripley

	* DESCRIPTION (Version): 3.1-140 (released)

2019-05-01  Brian Ripley

	* src/init.c: correct declaration of fit_nlme

2019-04-10  Brian Ripley

	* src/nlmefit.c: remove clang warning.

2019-04-08  Brian Ripley

	* DESCRIPTION (Version): 3.1-139 (released)

2019-04-08  Brian Ripley

	* R/groupedData.R: *GroupedData are exported, so use :: not :::

2019-04-07  Martin Maechler  <[email protected]>

	* Release 3.1-138.

2019-04-02  Brian Ripley

	* Start preparing to release 3.1-138 for R 3.6.0

2019-04-02  Martin Maechler  <[email protected]>

	* po/{R-de,de}.po: updated

2019-01-23  Martin Maechler  <[email protected]>

	* R/lme.R (lme.formula, lmeControl): new option
	'allow.n.lt.q=FALSE' by default now triggers error
	"fewer observations than random effects in all level <Q> groups".

	* src/nlmefit.c (finite_diff_Hess): prevent integer overflow (and
	later seg.fault) for large 'nTot' (already for npar >= 305).

2018-08-04  Martin Mächler  <[email protected]>

	* DESCRIPTION (Version): 3.1-138 (unreleased)

	* R/groupedData.R: deprecate the *undocumented* functions
	nmGroupedData() and nfGroupedData() in favor of their wrapper
	groupedData() (to allow subsequent code simplification).

2018-08-03  Martin Maechler  <[email protected]>

	* R/lmList.R (plot.intervals.lmList, ..), tests/lmList.R: make
	'xlab', 'ylab', 'strip' regular arguments (instead of wrongly
	trying to use them from `...`).
	* R/lme.R (plot.ranef.lme, ..): (ditto)

2018-05-08  Brian Ripley

	* tests/sigma-fixed-etc.R: increase tolerance for ATLAS run.

2018-04-07  Brian Ripley

	* DESCRIPTION (Version): 3.1-137 for release with R 3.5.0

	* po/*/.pot: updated

	* po/{R-de,de}.po: updated

2018-03-09  Brian Ripley

	* DESCRIPTION: Update Date, release for R-devel.

	* tests/nlme-stall.R: Add comments.

2018-02-27  Martin Mächler  <[email protected]>

	* R/nlme.R, man/nlmeControl.Rd: nlmeControl() gets new
	`msWarnNoConv` option. When it is true, as by default, nlme() now
	warns about non convergence in the LME step of the 'alternating
	algorithm'.  Applies e.g. also to the nlme-stall.R example.

2018-02-27  Brian Ripley

	* DESCRIPTION: Update Date. (Still unreleased.)
	Relax R (>= 3.5.0) to 3.4.0 so it can be released generally once
	3.5.0 is out.

	* src/init.c, src/nlmefit.h: Remove broken utilities added on
	2018-01-31.

	* src/pythag.c: New file, contents moved from init.c.

	* tests/nlme-stall.R: New regression test, optional.

	* tests/sigma-fixed-etc.R: Changed tolerance after win-builder
	run, change t7.fix.REML.lme to use optim() (as done for LME, and
	Solaris has false convergence with nlminb()).  Drop all uses of
	platform-dependent tolerances.

2018-02-26  Brian Ripley

	* src/init.c, src/rs.f: The 2018-01-31 change is broken (passes
	pointers as doubles).  Try a simpler approach, to replace PYTHAG
	in rs.f by a wrapped call to the C99 function hypot().

2018-02-16  Brian Ripley

	* DESCRIPTION (Version): 3.1-131.1, for R 3.4.4.
	(and 3.1-131) are available at
	https://svn.r-project.org/R-packages/branches/R-3-4-branch/nlme

	* tests/deparse.R: comment on failure with macOS's Accelerate.

2018-01-31  Martin Maechler  <[email protected]>

	* src/nlmefit.h, src/init.c (risnan, risfinite, ..): utilities to
	check for NaN, NA, Inf etc from Fortran.  [Since removed.]

	* src/rs.f (PYTHAG): prevent infinite loop checking for finite arg.
	as reported in https://stat.ethz.ch/pipermail/r-devel/2018-January/075459.html .

	* src/nlme.c (nlme_iterate): add R_CheckUserInterrupt()

2018-01-02  Martin Maechler  <[email protected]>

	* R/lmList.R (warnErrList): bug fix.
	Added to the 'utils' package for R-devel, keep here for R <= 3.4.x.

2018-02-16  Brian Ripley

	* DESCRIPTION (Version): 3.1-135.5 (released for R-devel only)

2018-01-23, 2018-02-16 Brian Ripley

	* tests/predict.lme.R: increase tolerance.

2018-01-01  Brian Ripley

	* DESCRIPTION (Version): 3.1-135 (released for R-devel only)
	* tests/anova.gls.R: increase tolerance.

2017-12-24  Brian Ripley

	* tests/anova.gls.R: increase tolerance.

2017-12-01  Brian Ripley

	* DESCRIPTION (Version): 3.1-134, R >= 3.5.0
	* R/VarCorr.R: correct breakage in r7326 (2017-03-07)
	  (broke packages joineR and lme4).

2017-11-28  Brian Ripley

	* DESCRIPTION (Version): 3.1-133 (released for R-devel but withdrawn)
	* tests/coef.Rout.save: update for R-pre-3.5.0 changes to str()

2017-09-18  Martin Maechler

	* tests/nlme2.R: 'tweak and investigate platform dependent results'

2017-03-07  Martin Maechler

	* nlme/R/VarCorr.R, nlme/man/VarCorr.Rd: see below.
	* 'correct default for VarCorr.lme() to what it has really been.'
	* 'Fix print.*()'.
	* 'Cosmetic (not changing any results)'

2017-02-27  Martin Maechler

	* nlme/R/gnls.R, nlme/man/glsControl.Rd, nlme/man/gnlsControl.Rd,
	  nlme/man/lmeControl.R:  'cosmetic'

2017-02-22  Martin Maechler

	* DESCRIPTION (Version): 3.1-132 (unreleased)
	* R/gnls.R, src/gnls.c: 'small cosmetic related to getting closer
	to the root cause of PR#17227'

2017-02-11 Brian Ripley

	* src/nlmefit.c: gcc -Wconversion pointed out misuse of long
	constants '0L' and  '1L'.

2017-02-06  Martin Maechler

	* DESCRIPTION (Version): 3.1-131, tweaked test tolerance to also
	pass openblas 0.2.18, in
	* tests/sigma-fixed-etc.R example 6

2017-01-23  Martin Maechler

	* DESCRIPTION (Version): 3.1-130
	* NAMESPACE, R/zzmethods.R, tests/deviance.R: workaround design
	error in 3.1-129 re deviance.

2017-01-17  Martin Maechler

	* R/groupedData.R (groupedData): must prepend 'nlme::' for call,
	fixing PR #17211.

2016-12-12  Martin Maechler

	* R/lme.R (Variogram.lme): fix PR #17192, with thanks to
	Sebastian Meyer.

2016-07-11 Martin Maechler

	* DESCRIPTION (Version): 3.1-129
	* NAMESPACE, R/zzMethods.R (confint, sigma, deviance) methods (the
	last giving an error).

2016-05-04 Martin Maechler

	* R/lme.R, etc (lmeControl): 'sigma = 0' is now allowed (and
	equivalent to 'sigma = NULL'); this fixes mgcv::gamm()'s use of
	the equivalent of 'do.call(lmeControl, lmeControl())'.

2016-04-26 Martin Maechler

	* DESCRIPTION (Version): 3.1-128
	* R/lme.R (qqnorm.lme): fixed bug introduced in v 3.1-127
	* R/lme.R, R/nlme.R, etc: "fixed sigma" now computes 'apVar'
	correctly; thanks to patches from Siem Heisterkamp
	* R/lme.R, R/gls.R: coef(summary(.)) now also works for "gls", "lme".
	* R/gls.R (anova.gls): fixed a very long standing bug in the F
	statistics for the ML case, thanks to Siem H.

2016-03-21 Martin Maechler

	* R/nlme.R (getParsNlme): wish of PR#16614 : now predict REs as NA
	for non-existing levels instead of signalling error.
	* R/*.R: cosmetics: More vapply(); quote(.) instead of as.name(),
	passing '...' down in print() methods, etc.

2016-03-16 Martin Maechler

	* DESCRIPTION (Version): 3.1-127
	* R/lmList.R, R/nlsList.R: same kind of error catching -> warning
	* */*.R: speedup cosmetics:  seq_along; vapply(); lengths();
	lapply(a, `[[`, i).  Less  eval(parse(text = ....))

2016-03-12 Martin Maechler

	* DESCRIPTION: version 3.1-126
	* R/nlme.R (predict.nlme): fix bug PR#16715; +cosmetic; also in
	* R/lmList.R, R/nlsList.R: better error catching -> warning()

2016-02-27 Brian Ripley

	* DESCRIPTION: version 3.1-125; released
	* tests/coef.Rout.save: update for R 3.3.x

2016-02-13 Brian Ripley

	* src/*.[ch]: remove use of S.h, clean up.
	* src/nls.c: Unused in R, so remove.

2016-01-25 Brian Ripley

	* src/*.c: include directly headers included via R.h.

2016-01-19 Martin Maechler

	* DESCRIPTION: version 3.1-124, and released

2016-01-19 Brian Ripley

	* src/{corStruct,gnls,nlme,nlmefit,nls}.c: Avoid clang warnings on
	implicit conversions.

2016-01-18 Martin Maechler

	* nlme/man/lmeControl.Rd, R/lme.R, etc: in lmeControl() etc,
	currently 'apVar' to FALSE when sigma is fixed, and document that
	somewhat.

2016-01-11  Martin Maechler

	* R/VarCorr.R, man/VarCorr.Rd: add optional '...' and remove 'rdig'
	from the argument list of the generic (for other methods).

2015-11-25 Bert van Willigen --- with modifications by MM
	* DESCRIPTION: version 3.1-123 (released 2016-01-17)
	* man/*Control.Rd: Fixed "sigma" (residual error) added.
	* R/gls.R, R/gnls.R, R/lme.R, R/nlme.R, R/reStruct.R: Fixed sigma 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 messages.
	* 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 <[email protected]>

	* NAMESPACE: import selectively from lattice and stats.

2012-09-24  Brian Ripley <[email protected]>

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

2012-09-01  Brian Ripley <[email protected]>

	* po: add Polish translations.

2012-08-30  Brian Ripley <[email protected]>

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

2012-05-23  Brian Ripley <[email protected]>

	* 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 <[email protected]>

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

2012-03-29  Brian Ripley <[email protected]>

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

2012-02-15  Brian Ripley <[email protected]>

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

2012-01-14  Brian Ripley <[email protected]>

	* DESCRIPTION: version is 3.1-103

2011-12-25  Brian Ripley <[email protected]>

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

2011-07-19  Brian Ripley <[email protected]>

	* 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 <[email protected]>

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

2011-05-30  Brian Ripley <[email protected]>

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

2011-05-06  Brian Ripley <[email protected]>

	* DESCRIPTION: version is 3.1-101

2011-04-23  Martin Maechler  <[email protected]>
2011-04-14  Martin Maechler  <[email protected]>

	* 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 <[email protected]>

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

2011-03-11  Brian Ripley <[email protected]>

	* Release 3.1-100 for R 2.13.0

	* NAMESPACE: no longer re-export BIC

	* man/BIC.Rd: removed.

2011-02-23  Brian Ripley <[email protected]>

	* 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 <[email protected]>

	* 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 <[email protected]>

	* DESCRIPTION (Version, Date): 3.1-98

2011-02-04  Brian Ripley <[email protected]>

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

2010-10-01  Brian Ripley <[email protected]>

	* DESCRIPTION (Version, Date): 3.1-97

2010-09-22  Brian Ripley <[email protected]>

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

2009-12-22  Brian Ripley <[email protected]>

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

2009-12-18  Brian Ripley <[email protected]>

	* DESCRIPTION: add BugReports field.

2009-10-12,16  Brian Ripley <[email protected]>

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

2009-09-16  Martin Maechler  <[email protected]>

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

2009-09-02  Brian Ripley <[email protected]>

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

2009-08-16  Brian Ripley <[email protected]>

	* 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 <[email protected]>

	* 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 <[email protected]>

	* man/*.Rd: expand tabs

2008-12-30  Brian Ripley <[email protected]>

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

2008-12-27  Brian Ripley <[email protected]>

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

2008-12-19  Brian Ripley <[email protected]>

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

2008-12-11  Brian Ripley <[email protected]>

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

2008-06-07  Brian Ripley <[email protected]>

	* 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 <[email protected]>

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

2008-03-30  Brian Ripley <[email protected]>

	* DESCRIPTION (Version, Date): 3.1-88

2008-02-19  Brian Ripley <[email protected]>

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

2008-02-19  Brian Ripley <[email protected]>

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

2008-02-18  Brian Ripley <[email protected]>

	* 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 <[email protected]>

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

2007-12-30  Douglas Bates <[email protected]>

	* [r4884] man/plot.nffGroupedData.Rd: Correct malformed link reported
	  by Yihui Xie <[email protected]>. 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 <[email protected]>

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

2007-09-17  Brian Ripley <[email protected]>

	* 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 <[email protected]>

	* 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 <[email protected]>

	* 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 <[email protected]>

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

2007-06-13  Brian Ripley <[email protected]>

	* 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 <[email protected]>

	* 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 <[email protected]>

	* 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 <[email protected]>

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

2007-05-15  Brian Ripley <[email protected]>

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

2007-05-04  Brian Ripley <[email protected]>

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

2007-03-30  Brian Ripley <[email protected]>

	* 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 <[email protected]>

	* DESCRIPTION (Title): Capitalize for consistency.

2006-12-29  Brian Ripley <[email protected]>

	* 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  <[email protected]>

	* DESCRIPTION (Version, Date): 3.1-78

2006-12-06  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

	* 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 <[email protected]>

	* 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  <[email protected]>

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

2006-09-18  Douglas Bates  <[email protected]>

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

2006-09-11  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

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

2006-07-24  Douglas Bates  <[email protected]>

	* R/lme.R: Patch by Andrew Robinson <[email protected]>
	and Berwin Turlach <[email protected]> to set maximum number
	of function calls in nlminb.

2006-07-03  Douglas Bates  <[email protected]>

	* DESCRIPTION: Version is 3.1-75

	* man/{many files}: Documentation changes contributed by Spencer
	Graves <[email protected]>.  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  <[email protected]>

	* 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 <[email protected]>

	* DESCRIPTION: Version is 3.1-74

2006-05-31 Brian Ripley <[email protected]>

	* 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 <[email protected]>

	* 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 <[email protected]>

	* DESCRIPTION: Version is 3.1-73

2006-05-21 Brian Ripley <[email protected]>

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

2006-05-18 Brian Ripley	 <[email protected]>

	* 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	 <[email protected]>

	* 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	 <[email protected]>

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

2006-03-14 Brian Ripley	 <[email protected]>

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

2006-03-10 Brian Ripley	 <[email protected]>

	* DESCRIPTION: Version is 3.1-71

2006-02-17 Brian Ripley	 <[email protected]>

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

2006-01-05  Brian Ripley  <[email protected]>

	* 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  <[email protected]>

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

2005-12-31  Brian Ripley  <[email protected]>

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

2005-12-31  Brian Ripley  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

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

2005-08-24  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

	* 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
	accidentally 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 [email protected])

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  <[email protected]>

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

2003-12-16  Douglas Bates  <[email protected]>

	* install.R: Create stored image

2003-08-29  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* DESCRIPTION: New release

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

2003-06-10  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

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

2003-05-16  Douglas Bates  <[email protected]>

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

2003-05-05  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

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

2003-01-30  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

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

2002-04-20  Douglas Bates  <[email protected]>

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

2002-04-04  Douglas Bates  <[email protected]>

	* 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 <[email protected]>

2002-03-27  Douglas Bates  <[email protected]>

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

2002-03-05  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

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

2001-12-10  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

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

2001-10-30  Douglas Bates  <[email protected]>

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

2001-10-23  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* R/nlme.R: Incorporated a change from
	[email protected] for using nested grouping factors
	in nlme.

2001-06-20  Douglas Bates  <[email protected]>

	* 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 <[email protected]>

	* 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  <[email protected]>

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

2001-02-24  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

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

2000-12-09  Douglas Bates  <[email protected]>

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

2000-12-08  Douglas Bates  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* 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  <[email protected]>

	* TITLE: Changed the title to nlme