CVS commit: pkgsrc/math/R-lme4

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Tue Jun 13 13:55:59 UTC 2023

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

Log Message:
(math/R-lme4) Updated 1.1.27 to 1.1.33

CHANGES IN VERSION 1.1-33:

  BUG FIXES:

         * a boundary check could fail occasionally when large data
           produced an NA value in a computed gradient; now warns
           instead (GH #719, Mathias Ambuehl)

         * 'allFit' now works better when 'optimx' and 'dfoptim'
           packages are not installed (GH #724)

         * 'refit' reset internal degrees of freedom component
           incorrectly for REML fits (resulted in incorrect reported
           REML criteria, but otherwise harmless: side effect of GH
           #678)

  NEW FEATURES:

         * 'dotplot' and 'qqmath' methods gain a 'level' argument to
           set the width of confidence intervals

         * 'dotplot' method is now more flexible, using ".v" options
           ('lty.v', 'col.line.v', 'lwd.v') to set appearance of
           vertical lines (Iago Gin<c3><a9> V<c3><a1>zquez)

         * 'refit' gains a 'newweights' argument (GH #678)

CHANGES IN VERSION 1.1-32 (2023-03-14):

  USER-VISIBLE CHANGES:

         * 'formatVC()' gets a new optional argument 'corr' indicating
           if correlations or covariances should be used for vector
           random effects; this corresponds to 'print(<merMod>,
           ranef.corr = ...)' .  By default, it is FALSE for 'comp =
           "Variance"', fixing (GH #707).

         * 'qqmath.merMod' adds a (useless) 'data' argument for S3
           compatibility. Going forward, the 'id' and 'idLabels'
           arguments should always be specified by name.  We have added
           code to try to detect/warn when this is not done.

  BUG FIXES:

         * 'nobars' now retains the environment of its formula argument
           (GH #713, Mikael Jagan)

CHANGES IN VERSION 1.1-31 (2022-11-01):

  BUG FIXES:

         * 'confint(fm, <single string>)' now works (after years of
           being broken) again.

         * simulating from binomial model with a factor response, when
           the simulated response contains only a single factor level,
           now works (Daniel Kennedy)

CHANGES IN VERSION 1.1-30 (2022-07-08):

  USER-VISIBLE CHANGES:

         * 'nl' (term names) component added to output list of
           'mkReTrms (GH #679)'

         * eliminate partial-matching of 'eta' (for 'etastart') (GH
           #686: not actually "user-visible" unless
           'getOption("warnPartialMatchDollar")' is 'TRUE')

         * 'summary' method doesn't break for GLMMs other than
           binomial/Poisson when 'merDeriv''s 'vcov.glmerMod' method is
           attached (GH #688)

  BUG FIXES:

         * better handling of 'simulate(., re.form = NULL)' when model
           frame contains derived components (e.g. 'offset()',
           'log(x)')
           (<https://github.com/florianhartig/DHARMa/issues/335>)

         * 'bootMer' works with 'glmmTMB' again (broken in 1.1-29)

         * 'maxfun' argument to 'allFit' controls max function
           evaluations for every optimizer type (GH#685)

CHANGES IN VERSION 1.1-29 (2022-04-07):

  USER-VISIBLE CHANGES:

         * prediction with new levels (when not allowed) returns a more
           informative error message (displays a list of unobserved
           levels)

  BUG FIXES:

         * 'glmer.nb' now works when 'lme4' is not loaded (GH #658,
           @brgew)

         * tests for singularity ('check.conv.singular') now run
           independently of derivative computation (e.g., when
           'calc.derivs=FALSE') (GH #660, @palday)

         * 'influence.merMod' now works when data were originally
           specified as a tibble

         * fixed bug in 'cooks.distance' method for 'influence.merMod'
           (i.e., objects created via 'influence(fitted_model)') (John
           Fox) (GH #672)

         * 'predict' works for formulas containing . when 'newdata' is
           specified (GH #653)

         * 'bootMer' now correctly inherits control settings from
           original fit

CHANGES IN VERSION 1.1-28 (2022-02-04):

  USER-VISIBLE CHANGES:

         * construction of interacting factors (e.g. when 'f1:f2' or
           'f1/f2' occur in random effects terms) is now more efficient
           for partially crossed designs (doesn't try to create all
           combinations of 'f1' and 'f2') (GH #635 and #636)

         * 'mkNewReTrms' is exported

         * singular-fit message now refers to 'help("isSingular")'
           rather than '?isSingular'

  TESTS:

         * fix 'all.equal(p1,p2,p3)' and similar 'expect_equal()'
           thinkos

         * fix some tests only run when 'lme4:::testLevel() > 1'; adapt
           tests for upcoming Matrix 1.4-1 which has
           'names(diag(<sparse>))'

  BUG FIXES:

         * 'reOnly' preserves environment (GH #654, Mikael Jagan)

         * backward-compatibility hooks changed to evaluate at run-time
           (i.e., in '.onLoad()') rather than at build time (GH #649)

         * 'lmList' no longer warns when 'data' is a tibble (GH #645)


To generate a diff of this commit:
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/R-lme4/Makefile
cvs rdiff -u -r1.6 -r1.7 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:1.7 pkgsrc/math/R-lme4/Makefile:1.8
--- pkgsrc/math/R-lme4/Makefile:1.7     Thu Sep 16 23:47:51 2021
+++ pkgsrc/math/R-lme4/Makefile Tue Jun 13 13:55:59 2023
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.7 2021/09/16 23:47:51 mef Exp $
+# $NetBSD: Makefile,v 1.8 2023/06/13 13:55:59 mef Exp $
 
 R_PKGNAME=     lme4
-R_PKGVER=      1.1-27.1
+R_PKGVER=      1.1-33
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Linear mixed-effects models using Eigen and S4

Index: pkgsrc/math/R-lme4/distinfo
diff -u pkgsrc/math/R-lme4/distinfo:1.6 pkgsrc/math/R-lme4/distinfo:1.7
--- pkgsrc/math/R-lme4/distinfo:1.6     Tue Oct 26 10:55:28 2021
+++ pkgsrc/math/R-lme4/distinfo Tue Jun 13 13:55:59 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.6 2021/10/26 10:55:28 nia Exp $
+$NetBSD: distinfo,v 1.7 2023/06/13 13:55:59 mef Exp $
 
-BLAKE2s (R/lme4_1.1-27.1.tar.gz) = 7aeb93259e978af60580b74588af45f06ff012a17b2d00bdcd54a1022751ac88
-SHA512 (R/lme4_1.1-27.1.tar.gz) = 24af458973e4b6cbfb24c8add55438fb5f9b5338a9195f2ea87531fa3c783cd0a2f3a7591fe601af5dd9332b34b116da0f01043cb1d931ec502c88c944106df9
-Size (R/lme4_1.1-27.1.tar.gz) = 3311365 bytes
+BLAKE2s (R/lme4_1.1-33.tar.gz) = f5ca8fed4ed84378060351f1b04bfd55eacd9c7dac045268072d30c17d52ef03
+SHA512 (R/lme4_1.1-33.tar.gz) = e28d95c8690c7da09839b9ac4db2d2016f8a10f8ea2925b33c63ab146f0209faccfba7e23e16ccf90612097c31bb74a2d096aa28c55ced4035839662cdf7682e
+Size (R/lme4_1.1-33.tar.gz) = 2940865 bytes