The R Project SVN R-packages

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

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

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

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

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

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

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

    * man/contr.SAS.Rd: Removed

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    * install.R: Create stored image

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

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

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

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

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

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

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

    * DESCRIPTION: New release

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

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

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

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

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

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

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

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

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

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

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

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

    * NAMESPACE: contributed by Brian Ripley
    
    * man/print.corStruct.Rd: Removed this and many other redundant
    documentation files for S3 methods.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2002-09-10  Saikat DebRoy  <saikat@stat.wisc.edu>

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    * src/matrix.c: Removed dependency on S_compat.h by replacing
    calls to dqrdca with the equivalent call to dqrdc2.
    
2000-07-24  Saikat DebRoy <saikat@stat.wisc.edu>

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

2000-07-07  Saikat DebRoy <saikat@stat.wisc.edu>

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

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

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

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

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

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

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

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

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

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

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

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

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

    * added many data sets

    * incorporated patches from Brian Ripley to use optim for the
    optimization rather than nlm
    
    * src/nlmefit.c (internal_loglik): Returned R_NegInf instead of
    generating a error on a singular precision matrix.

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

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

    * TITLE: Changed the title to nlme