Subject: CVS commit: pkgsrc/math/R-lme4
From: Makoto Fujiwara
Date: 2021-09-17 01:47:51
Message id: 20210916234751.3F34CFA97@cvs.NetBSD.org

Log Message:
(math/R-lme4) Updated 1.1.21 to 1.1.27.1

HANGES IN VERSION 1.1-27.1:

  USER-VISIBLE CHANGES:

         * 'influence.merMod' allows user-specified starting parameters

         * cleaned up performance vignette

  BUG FIXES:

         * 'cooks.distance' now works with objects computed by
           'influence' method

         * 'influence.merMod' now works with 'glmer' models using
           'nAGQ=0'

         * 'predict' (with new data) and 'simulate' methods now work
           for models with >100 levels in a random effect grouping
           variable (GH #631)

CHANGES IN VERSION 1.1-27 (2021-05-15):

  USER-VISIBLE CHANGES:

         * improvements from Lionel Henry (via
           https://github.com/lme4/lme4/pull/587) to fix corner cases
           in data checking; also resolves GH #601 (allFit scoping)

         * 'getME(., "lower")' now has names (request of GH #609)

         * improved detection of 'NaN' in internal calculations
           (typically due to underflow/overflow or out-of-bounds linear
           predictors from non-constraining link functions such as
           identity-link Gamma models)

         * 'influence.merMod' allows parallel computation

         * the 'statmod' package is no longer required unless
           attempting to simulate results from a model with an inverse
           Gaussian response

  BUG FIXES:

         * long formulas work better in 'anova' headings (GH #611)

CHANGES IN VERSION 1.1-26 (2020-11-30):

  BUG FIXES:

         * 'predict', 'model.frame(.,fixed.only=TRUE)' work with
           variable names containing spaces (GH #605)

         * 'simulate' works when original response variable was logical

         * 'densityplot' handles partly broken profiles more robustly

  NEW FEATURES:

         * 'thpr' method for 'densityplot()' (for plotting profiles
           scaled as densities) gets new arguments

CHANGES IN VERSION 1.1-25 (2020-10-23):

        * Set more tests to run only if environment variable
          'LME4_TEST_LEVEL'>1

CHANGES IN VERSION 1.1-24 (never on CRAN):

  USER-VISIBLE CHANGES:

         * 'anova()' now returns a p-value of 'NA' if the df difference
           between two models is 0 (implying they are equivalent
           models) (GH#583, @MetaEntropy)

         * speedup in 'coef()' for large models, by skipping
           conditional variance calculation (Alexander Bauer)

         * 'simulate.formula' machinery has changed slightly, for
           compatibility with the 'ergm' package (Pavel Krivitsky)

         * informational messages about (non-)convergence improved (GH
           #599)

         * improved error messages for 0 non-NA cases in data (GH #533)

  NEW FEATURES:

         * 'getME(.,"devfun")' now works for 'glmer' objects.
           Additionally, 'profile'/'confint' for GLMMs no longer depend
           on objects in the fitting environment remaining unchanged
           (GH #589). This change also affects likelihood profiling
           machinery; results of 'glmer' profiling/CIs may not match
           results from previous versions exactly.

  BUG FIXES:

         * improved handling/documentation of 'glmer.nb' controls (GH
           #556)

         * 'predict' works better for 'gamm4' objects (GH #575)

         * resolved some long-standing UBSAN issues (GH #561)

CHANGES IN VERSION 1.1-23 (2020-03-06):

     This is primarily for CRAN compliance (previous submission was
     retracted to allow time for downstream package adjustments).

        * Some PROTECT/UNPROTECT fixes

CHANGES IN VERSION 1.1-22 (never on CRAN):

  USER-VISIBLE CHANGES:

         * prediction now works better for factors with many levels
           (GH#467, solution by @sihoward)

         * minor changes to argument order in '[g]lmerControl'; default
           tolerance for convergence checks increased from 0.001 to
           0.002 for 'glmerControl' (now consistent with 'lmerControl')

         * 'lmer(*, family="<fam>")' is no longer valid; it had been
           deprecated since 2013-06.

         * 'lmer()', 'glmer()', and 'nlmer()' no longer have a formal
           '...' argument.  This defunctifies the use of a 'sparseX =
           .' argument and will reveal some user errors, where
           extraneous arguments were previously disregarded.

         * In 'isSingular(x, tol)', the default tolerance ('tol') has
           been increased from '1e-5' to '1e-4', the default of
           'check.conv.singular' in 'g?lmerControl()'.

         * for clarity and consistency with base R methods, some column
           names of 'anova()' output are changed: "Df" becomes \ 
"npar",
           "Chi Df" becomes "Df" (GH #528)

         * 'simulate()' now works with inverse-Gaussian models (GH #284
           revisited, @nahorp/Florian Hartig)

         * single-model mode of 'anova()' now warns about unused
           arguments in ...  (e.g. 'type="III"')

         * default tolerances for 'nloptwrap'/BOBYQA optimizer
           tightened ('xtol_abs' and 'ftol_abs' were 1e-6, now 1e-8).
           (To revert to former tolerances, use
           'control=lmerControl(optimizer="nloptwrap",
           optCtrl=list(xtol_abs=1e-6, ftol_abs=1e-6))'.)

  BUG FIXES:

         * improved checking for missing data (@lionel-)

         * internal 'checkZrank()' should be able to deal with
           ('Matrix' package) 'rankMatrix()' returning 'NA'.

         * 'allFit(fm)' now works for a model that had an explicit
           'control = lmerControl(..)' call.

         * internal 'getStart()' now works when model's 'start' was
           specified as a list, and when called from 'drop1()' on a
           submodel, fixing GH #521.

         * internal function 'mkdevfun' now works even if there is an
           extraneous 'getCall' function defined in the global
           environment (GH #535)

         * 'allFit()' works even if a variable with symbol 'i' is used
           somewhere in the original model call (GH #538, reported by
           Don Cohen); generally more robust

         * 'glmer.nb' works even if an alternative version of
           'negative.binomial' (other than the one from 'MASS') is
           loaded in the workspace (e.g. by the 'GLMMadaptive' package)
           (GH#516)

         * 'level' argument is now honoured by 'confint(...,
           type="boot", level=...)' (GH #543)

Files:
RevisionActionfile
1.7modifypkgsrc/math/R-lme4/Makefile
1.4modifypkgsrc/math/R-lme4/distinfo