2018-02-16 Brian Ripley * DESCRIPTION (Version): 3.1-131.1 2018-01-23, 2018-02-16 Brian Ripley * tests/predict.lme.R: increase tolerance. 2018-01-01 Brian Ripley * tests/anova.gls.R: increase tolerance. 2017-12-24 Brian Ripley * tests/anova.gls.R: increase tolerance. 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 2017-01-17 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 messsages. * po/{R-pl,pl}.po: update. 2014-03-19 Brian Ripley * tests/missing.{R,Rout.save}: reduce 'digits' for cleaner results on platforms without extended-precision hardware. * po/R-de.po: Update from Detlef Steuer. 2014-03-09 Brian Ripley * DESCRIPTION: version is 3.1-115 * R/{gls,gnls,lme,nmle}.R, man/{lmeScale,*Control}.Rd: remove msScale and nlmStepMax arguments which were used for nlm(), where that is not longer used. 2014-03-08 Brian Ripley * DESCRIPTION: version is 3.1-114 * R/new-methods.R: labeling from fitted() was sometimes wrong as the 'groups' component lost row names. (PR#15678) * tests/fitted.R: add regression test. * R/lme.R: clean up * man/{lmeControl,lmeScale}.Rd: update.. 2013-11-17 Brian Ripley * DESCRIPTION: version is 3.1-113 * src/{matrix,nlOptimizer}.h: typos in guard names (clang 3.4) 2013-10-21 Martin Maechler * R/gls.R, man/gls-internal.Rd: remove redundant parentheses. 2013-10-03 Brian Ripley * man/{gls,lme}.Rd: add links, warn on no-covariate formulae. 2013-09-30, 2013-10-02 Brian Ripley * DESCRIPTION: version is 3.1-112 * R/gls.R, man/glsControl.Rd, man/Initialize.glsStruct.Rd. Remove 'qrTol', which was unused and set to the non-existent .Machine$single.eps, that is to NULL. * NAMESPACE, man/gls-internal.Rd: export glsApVar and glsEstimate for use in package rms. * R/gls.R, lme.R: more use of integer constants. * man/*.Rd: classes in quotes, more links, remove CVS lines. * R/lme.R, R/newFunc.R, tests/predict.lme.R: fix asOneFormula and predict.lme for y ~ 0. (see https://stat.ethz.ch/pipermail/r-devel/2013-September/067600.html) * R/lme.R: Several of the return components were incorrect for a model of the form fixed = resp ~ 0. 2013-08-17 Brian Ripley * add start on ko translations. 2013-08-15 Brian Ripley * DESCRIPTION: version is 3.1-111 * R/lmList.R: Adjust to cope with failed fits and fits with fewer coefficients returned by lm(). (Contributed by Ruth Ripley.) 2013-07-02 Brian Ripley * DESCRIPTION: version is 3.1-110, * R/{gls,gnls,lme}.R: Replace as.name() calls by quote(stats::nls) etc. * inst/LICENCE: remove. 2013-03-21 Brian Ripley * inst/CITATION: modernize. 2013-03-11 Brian Ripley * LICENCE: remove (it was not a licence file). 2013-01-26 Brian Ripley * DESCRIPTION: version is 3.1-109, depends on R (>= 3.0.0). 2013-01-26 Brian Ripley * DESCRIPTION: version is 3.1-108, depends on R (< 3.0.0) and has chol.f and rs.f in .Rbuildignore. 2013-01-23 Brian Ripley * man/[n]lme.Rd: add a note about the need to scale the response. * man/lmeControl.Rd: correct description of 'msTol' argument. * man/[n]lmeControl.Rd: correct description of 'opt' argument (it is a character string). * man/*.Rd: s/Jose/José/ * R/[n]lme.R, man/[n]lmeControl.Rd: allow '...' for further control arguments to be based though to nlminb() and optim(). 2013-01-13 Brian Ripley * DESCRIPTION: add accent on JCP's first name (and declare UTF-8 encoding). Add EISPACK authors. * src/rs.f: minimal version of eigen.f containing just RS and ancillaries (replacing eigen.f). 2013-01-12 Brian Ripley * DESCRIPTION: version is 3.1-107 * src/{chol,eigen}.f: port files from R (where they are deprecated/defunct). 2012-12-06 Kurt Hornik * DESCRIPTION: version is 3.1-106, add roles to Authors@R. 2012-11-28 Brian Ripley * NAMESPACE: import selectively from lattice and stats. 2012-09-24 Brian Ripley * DESCRIPTION: version is 3.1-105 * R: improve messages for translation. 2012-09-01 Brian Ripley * po: add Polish translations. 2012-08-30 Brian Ripley * src/init.c: force use of registered symbols in R >= 2.16.0 2012-05-23 Brian Ripley * 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 * src/nlmefit.c: type mismatch shown by clang's -Wconversion 2012-03-29 Brian Ripley * src/nlOptimizer.c: increase PROTECTion (reported by Andrew Runnalls). 2012-02-15 Brian Ripley * inst/CITATION: protect against TRE bug in UTF-8 locales. 2012-01-14 Brian Ripley * DESCRIPTION: version is 3.1-103 2011-12-25 Brian Ripley * DESCRIPTION: needs Suggests: MASS for data(package=) 2011-07-19 Brian Ripley * 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 * COPYING: rename to GPL-2 * LICENCE, inst/LICENCE: adjust wording accordingly 2011-05-30 Brian Ripley * R/newFunc.R: name arguments to lapply() when ... is present. 2011-05-06 Brian Ripley * DESCRIPTION: version is 3.1-101 2011-04-23 Martin Maechler 2011-04-14 Martin Maechler * 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 * src/{nlmefit,pdMat}.c: remove unused variables detected by -Wunused-but-set-variable 2011-03-11 Brian Ripley * Release 3.1-100 for R 2.13.0 * NAMESPACE: no longer re-export BIC * man/BIC.Rd: removed. 2011-02-23 Brian Ripley * 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 * 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 * DESCRIPTION (Version, Date): 3.1-98 2011-02-04 Brian Ripley * data/{MathAchieve,bdf}.rda: resave with xz compression. * DESCRIPTION: depend on R (>= 2.10). 2010-10-01 Brian Ripley * DESCRIPTION (Version, Date): 3.1-97 2010-09-22 Brian Ripley * man/residuals.gls.Rd: incorrect default, see https://stat.ethz.ch/pipermail/r-devel/2010-September/058487.html 2009-12-22 Brian Ripley * man/ACF.gls.Rd: has \seealso to itself: seems ACF.lme was meant. 2009-12-18 Brian Ripley * DESCRIPTION: add BugReports field. 2009-10-12,16 Brian Ripley * DESCRIPTION (Version, Date): 3.1-96 * po/R-de.po, po/de.po: update 2009-09-16 Martin Maechler * DESCRIPTION (Version, Date): 3.1-95 * R/nlme.R (nonlinModel): use unname() instead of clearNames() 2009-09-02 Brian Ripley * DESCRIPTION (Version, Date): 3.1-94 * man/*.Rd: remove unnecessarily anchored links, including several incorrect ones. 2009-08-16 Brian Ripley * 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 * 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 * man/*.Rd: expand tabs 2008-12-30 Brian Ripley * man/summary.pdMat.Rd: avoid embedded newlines in \code strings. 2008-12-27 Brian Ripley * DESCRIPTION (Version, Date): 3.1-90 * R/gls.R: call dist correctly (PR#13418) 2008-12-19 Brian Ripley * man/*.Rd: clean up some reference formats and misuse of $...$. 2008-12-11 Brian Ripley * man/*.Rd: spelling * src/nlOptimizer.c: missing PROTECT 2008-06-07 Brian Ripley * 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 * R/zzMethods.R: add .onUnload() to unload the DLL. 2008-03-30 Brian Ripley * DESCRIPTION (Version, Date): 3.1-88 2008-02-19 Brian Ripley * man/logLik.lme.Rd, man/logLik.gnls.Rd: correct description of 'REML' argument. 2008-02-19 Brian Ripley * inst/CITATION: add file (essentially what citation() would produce, without the warning). 2008-02-18 Brian Ripley * 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 * R/*.R: Return invisible(x) from numerous print methods. 2007-12-30 Douglas Bates * [r4884] man/plot.nffGroupedData.Rd: Correct malformed link reported by Yihui Xie . 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 * R/corStruct.R: check for uninitialized corARMA structures. 2007-09-17 Brian Ripley * 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 * 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 * 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 * R/VarCov.R: correct getVarCov.gls, PR#9752 2007-06-13 Brian Ripley * 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 * 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 * 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 * R/*.R: partial matching issues, switch to seq_along. 2007-05-15 Brian Ripley * DESCRIPTION (Version, Date): 3.1-81 * NAMESPACE, R/zzMethods.R: migrate vcov methods from stats to here. 2007-05-04 Brian Ripley * man/{Extracr.pdMat,getdata.*,summary.varFunc}.Rd: remove surplus }. 2007-03-30 Brian Ripley * 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 * DESCRIPTION (Title): Capitalize for consistency. 2006-12-29 Brian Ripley * 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 * DESCRIPTION (Version, Date): 3.1-78 2006-12-06 Douglas Bates * 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 * 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 * 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 * R/nlme.R (getParsNlme): backed out change that caused failure reported by Christian Ritz. 2006-09-18 Douglas Bates * R/VarCorr.R (VarCorr): Clean up problems in this file and several others detected by codetools. 2006-09-11 Douglas Bates * R/nlme.R (getParsNlme): '[[' not '[' in case start$fixed is a list * R/gls.R,gnls.R,newMethods.R,nlme.R,pdMat,Rsimulate.R: fix problems exposed by codetools. 2006-07-31 Douglas Bates * man/ranef.lme.Rd: Modified the description of the `standard' argument to more clearly describe its effect. 2006-07-24 Douglas Bates * R/lme.R: Patch by Andrew Robinson and Berwin Turlach to set maximum number of function calls in nlminb. 2006-07-03 Douglas Bates * DESCRIPTION: Version is 3.1-75 * man/{many files}: Documentation changes contributed by Spencer Graves . Most of the changes add Pinheiro and Bates (2000) as a reference or add additional \seealso{} entries. Some examples from Pinheiro and Bates (2000) have also been added. * R/nlme.R: reformat the code, typo. 2006-07-03 Martin Maechler * R/lme.R (lme.formula): when control()$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 * DESCRIPTION: Version is 3.1-74 2006-05-31 Brian Ripley * 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 * 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 * DESCRIPTION: Version is 3.1-73 2006-05-21 Brian Ripley * LICENCE, inst/LICENCE: add and install a licence file. 2006-05-18 Brian Ripley * 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 * 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 * R/newMethods.R: as.list() did not work on symbols in R. 2006-03-14 Brian Ripley * R/lme.R, man/Variogram.Rd: make example work (na.omit in the wrong place). 2006-03-10 Brian Ripley * DESCRIPTION: Version is 3.1-71 2006-02-17 Brian Ripley * R/nlsList.R: need to allow for multi-line deparse. * tests/deparse.R: add regression test 2006-01-05 Brian Ripley * 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 * src/init.c: missing registration for ARMA_constCoef * inst/scripts/ch02.R: correct argument names in simulate.lme call 2005-12-31 Brian Ripley * DESCRIPTION: Version is 3.1-69, require 2.3.0. * NAMESPACE: use registration. * R/*.R: use registered symbols. 2005-12-31 Brian Ripley * 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 * 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 * 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 * R/gls.R: Added option "optimMethod" to gls, gnls, and lme. 2005-08-24 Douglas Bates * R/lme.R (print.intervals.lme): Replace calls to print.matrix by print(as.matrix()). 2005-07-25 Douglas Bates * 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 * 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 * 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 * 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 * man/contr.SAS.Rd: Removed 2005-04-04 Douglas Bates * 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 * src/nlmefit.c (gls_loglik): Replaced rnkm1 by p. * po/,inst/po/: Added localization support. 2004-11-04 Douglas Bates * src/nlmefit.c (dimFree): Fix memory leak reported by Brian Ripley. 2004-11-03 Douglas Bates * man/varWeights.Rd: Remove all calls to data() * man/corExp.Rd: Remove all references to the mva package 2004-08-10 Douglas Bates * man/pairs.compareFits.Rd: fix syntax errors (new check available in R CMD check) 2004-01-14 Douglas Bates * man/getCovariate.varFunc.Rd: Syntax correction from Kurt. 2003-12-16 Douglas Bates * install.R: Create stored image 2003-08-29 Douglas Bates * 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 * 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 * DESCRIPTION: New release * man/ranef.lmList.Rd, man/nlme.Rd: Overdocumented arguments 2003-06-10 Douglas Bates * 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 * R/groupedData.R: Fixed bug in groupedData constructor when outer is not missing. 2003-05-16 Douglas Bates * src/nlmefit.c (internal_EM): Fix by Peter Dalgaard for compound symmetry EM calculations (PR#2985) 2003-05-05 Douglas Bates * 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 * NAMESPACE: contributed by Brian Ripley * man/print.corStruct.Rd: Removed this and many other redundant documentation files for S3 methods. * R/ Remove redundant GPL notices. 2003-03-25 Douglas Bates * 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 * R/lme.R (lme.formula): Removed hessian=TRUE in calls to optim as suggested by Brian Ripley. 2003-01-30 Douglas Bates * 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 * 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 * 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 * 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 * 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 * R/lme.R (update.lme): Fix formula handling in update methods (Brian Ripley). 2002-04-20 Douglas Bates * R/nlme.R: Bug fix by SDR - convergence criterion was being calculated incorrectly. 2002-04-04 Douglas Bates * 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 2002-03-27 Douglas Bates * R/lme.R (anova.lme): Change strvar != "NA" to !is.na(strvar) 2002-03-05 Douglas Bates * 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 * R/corStruct.R: Finally resolved the print.summary.corSymm controversy so it prints and it prints the correct value. 2001-12-10 Douglas Bates * 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 * R/zzMethods.R: Removed the .Alias calls. 2001-10-30 Douglas Bates * man/pairs.lme.Rd: Modified many documentation files to pass the codoc checks. 2001-10-23 Douglas Bates * 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 * 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 * 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 * R/nlme.R: Incorporated a change from Setzer.Woodrow@epamail.epa.gov for using nested grouping factors in nlme. 2001-06-20 Douglas Bates * 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 * 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 * R/simulate.R: Modified simulate.lme for default pdMat class of pdLogChol. 2001-02-24 Douglas Bates * 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 * DESCRIPTION (Maintainer): Added Maintainer entry to DESCRIPTION. 2000-12-09 Douglas Bates * R/lme.R: (Variogram.lme) Coerced n.pairs to numeric and corrected calls to dist. 2000-12-08 Douglas Bates * 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 * 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 * 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 * 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 * TITLE: Changed the title to nlme