CVS commit: pkgsrc/math/R-lme4

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Thu Sep 16 23:47:51 UTC 2021

Modified Files:
        pkgsrc/math/R-lme4: Makefile distinfo

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)


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/math/R-lme4/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/math/R-lme4/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-lme4/Makefile
diff -u pkgsrc/math/R-lme4/Makefile:1.6 pkgsrc/math/R-lme4/Makefile:1.7
--- pkgsrc/math/R-lme4/Makefile:1.6     Thu Aug  8 19:53:50 2019
+++ pkgsrc/math/R-lme4/Makefile Thu Sep 16 23:47:51 2021
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.6 2019/08/08 19:53:50 brook Exp $
+# $NetBSD: Makefile,v 1.7 2021/09/16 23:47:51 mef Exp $
 
 R_PKGNAME=     lme4
-R_PKGVER=      1.1-21
-CATEGORIES=    math
+R_PKGVER=      1.1-27.1
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Linear mixed-effects models using Eigen and S4
@@ -11,6 +10,17 @@ LICENSE=     gnu-gpl-v2 OR gnu-gpl-v3
 DEPENDS+=      R-minqa>=1.1.15:../../math/R-minqa
 DEPENDS+=      R-nloptr>=1.0.4:../../math/R-nloptr
 
+# Packages suggested but not available:
+#  'PKPDmodels', 'MEMSS', 'mlmRev', 'optimx', 'gamm4', 'HSAUR3',
+#  'dfoptim', 'rr2', 'semEff'
+TEST_DEPENDS+= R-markdown-[0-9]*:../../textproc/R-rmarkdown
+TEST_DEPENDS+= R-testthat-[0-9]*:../../devel/R-testthat
+TEST_DEPENDS+= R-ggplot2-[0-9]*:../../graphics/R-ggplot2
+TEST_DEPENDS+= R-numDeriv-[0-9]*:../../math/R-numDeriv
+TEST_DEPENDS+= R-statmod-[0-9]*:../../math/R-statmod
+TEST_DEPENDS+= R-car-[0-9]*:../../math/R-car
+TEST_DEPENDS+= R-pbkrtest-[0-9]*:../../math/R-pbkrtest
+
 USE_LANGUAGES= c c++
 
 .include "../../math/R/Makefile.extension"

Index: pkgsrc/math/R-lme4/distinfo
diff -u pkgsrc/math/R-lme4/distinfo:1.3 pkgsrc/math/R-lme4/distinfo:1.4
--- pkgsrc/math/R-lme4/distinfo:1.3     Wed Jul 31 19:49:55 2019
+++ pkgsrc/math/R-lme4/distinfo Thu Sep 16 23:47:51 2021
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.3 2019/07/31 19:49:55 brook Exp $
+$NetBSD: distinfo,v 1.4 2021/09/16 23:47:51 mef Exp $
 
-SHA1 (R/lme4_1.1-21.tar.gz) = 489052d369d8cfb8d69807f480e4be33eb64955a
-RMD160 (R/lme4_1.1-21.tar.gz) = eb6bc5ff9a2aebe1554dd839d7fef41a94d31806
-SHA512 (R/lme4_1.1-21.tar.gz) = 6aa61c032731b585e262f52d2051aa2e9c424ec6f797a0073d4b6fb254a2fea28daeadb24e2e0e3522bd9929a4ce50a9899444570ccbd156ddcea9063cac2d13
-Size (R/lme4_1.1-21.tar.gz) = 4124154 bytes
+SHA1 (R/lme4_1.1-27.1.tar.gz) = 4f2fc7666af41670f3de7dc88f943707cfc37a7c
+RMD160 (R/lme4_1.1-27.1.tar.gz) = 3b00bd9f3569ca6f40e3e735b7927b9b214256ae
+SHA512 (R/lme4_1.1-27.1.tar.gz) = 24af458973e4b6cbfb24c8add55438fb5f9b5338a9195f2ea87531fa3c783cd0a2f3a7591fe601af5dd9332b34b116da0f01043cb1d931ec502c88c944106df9
+Size (R/lme4_1.1-27.1.tar.gz) = 3311365 bytes