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ChangeLog
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2024-08-22 Sebastian Meyer <[email protected]>
* R/corStruct.R (print.summary.corNatural):
failed from wrong coef() method.
2024-08-21 Sebastian Meyer <[email protected]>
* src/nlmefit.c (mixed_fcn): guard against non-finite results
of 'internal_loglik', potentially causing infinite looping in
'optif9'; reported for simulate.lme() in PR#17955 and PR#18433.
* tests/predict.lme.R: add corresponding regression test.
2024-08-16 Sebastian Meyer <[email protected]>
* tests/corFactor.R, tests/corMatrix.R: rename and add test of
spatial correlation with groups.
* src/corStruct.c (corStruct_recalc): fix iterating over 'Xy' to
be compatible with spatial correlation structures, avoiding memory
errors from nlme() (PR#18192) and gnls() (PR#17227).
Thanks to Laurens Bogaardt for the useful reproducible example and to
Mikko Korpela, Benjamin Tyner, and Ivan Krylov for initial debugging.
* tests/nlme.R: add corresponding regression test.
2024-08-13 Kurt Hornik <[email protected]>
* DESCRIPTION (Version): 3.1-166 (released)
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]>