./math/R-lme4, Linear mixed-effects models using Eigen and S4

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Branch: CURRENT, Version:, Package name: R-lme4-, Maintainer: pkgsrc-users

Fit linear and generalized linear mixed-effects models. The models
and their components are represented using S4 classes and methods.
The core computational algorithms are implemented using the Eigen
C++ library for numerical linear algebra and RcppEigen "glue".

Required to run:
[math/R] [devel/R-Rcpp] [math/R-minqa] [math/R-nloptr] [math/R-RcppEigen]

Required to build:

Master sites: (Expand)

Version history: (Expand)

CVS history: (Expand)

   2021-10-26 12:56:13 by Nia Alarie | Files touched by this commit (458)
Log message:
math: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 16:28:36 by Nia Alarie | Files touched by this commit (458)
Log message:
math: Remove SHA1 hashes for distfiles
   2021-09-17 01:47:51 by Makoto Fujiwara | Files touched by this commit (2)
Log message:
(math/R-lme4) Updated 1.1.21 to



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

         * cleaned up performance vignette


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

         * 'influence.merMod' now works with 'glmer' models using

         * '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):


         * 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


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

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


         * '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


         * '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

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


         * '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

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


         * '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.


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

         * '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):


         * 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 \ 
           "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
           optCtrl=list(xtol_abs=1e-6, ftol_abs=1e-6))'.)


         * 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)

         * 'level' argument is now honoured by 'confint(...,
           type="boot", level=...)' (GH #543)
   2019-08-08 21:53:58 by Brook Milligan | Files touched by this commit (189) | Package updated
Log message:
Update all R packages to canonical form.

The canonical form [1] of an R package Makefile includes the

- The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as
  needed), and CATEGORIES.

- HOMEPAGE is not present but defined in math/R/Makefile.extension to
  refer to the CRAN web page describing the package.  Other relevant
  web pages are often linked from there via the URL field.

This updates all current R packages to this form, which will make
regular updates _much_ easier, especially using pkgtools/R2pkg.

[1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html
   2018-12-21 13:53:49 by Wen Heping | Files touched by this commit (2)
Log message:
Update to 1.1.19

Upstream changes:

    influence measure code from car rolled in (see ?influence.merMod)

    mkReTrm gets new arguments reorder.terms, reorder.vars to control \ 
arrangement of RE terms and individual effects with RE terms within model \ 

    adding material from the RePsychLing package (on GitHub; see Bates et al \ 
2015 arXiv:1506.04967) to show orthogonal variance components.


    as.data.frame.merMod finds conditional variance information stored either as \ 
attr(.,"postVar") or attr(.,"condVar") (for glmmTMB \ 

    change to defaults of [g]lmerControl to print a message when fits are singular

    new utility isSingular() function for detecting singular fits; by default a \ 
message is printed for singular fits

    allFit function/methods have been moved to the main package, rather than \ 
being included in an auxiliary source file

    post-fitting convergence checks based on estimated gradient and Hessian (see \ 
troubleshooting) are no longer performed for (nearly-)singular fits (see \ 

CHANGES IN VERSION 1.1-18-1 (2018-08-17)

    This is a minor release; the only change is to roll back (unexport) the \ 
influence.merMod method, pending resolution of conflicts with the car package

CHANGES IN VERSION 1.1-18 ((2018-08-16)

    ranef(.,condVar=TRUE) now works when there are multiple random effects terms \ 
per factor


    rstudent and influence methods are available for merMod objects

    devfun2 function (for generating a deviance function that works on the \ 
standard deviation/correlation scale) is now exported


    lmList now obeys its pool argument (instead of always using what currently \ 
is the default, GH #476)

CHANGES IN VERSION 1.1-17 (2018-04-03)

    This is a maintenance release only (fixes CRAN problems with cross-platform \ 
tests and examples)

CHANGES IN VERSION 1.1-16 (2018-03-28)

    lmList no longer ignores the subset argument (John Fox)

    fixed several minor issues with predicting when (1) grouping variables have \ 
different levels from original model (e.g. missing levels/factor levels not \ 
explicitly specified in newdata) or (2) re.form is a subset of the original RE \ 
formula and some (unused) grouping variables are omitted from newdata (GH #452, \ 


    lmList tries harder to collect errors and pass them on as warnings

    documented as.function method (given a merMod object, returns a function \ 
that computes the deviance/REML criterion for specified parameters)

    print method for summary.merMod objects no longer collapses small values of \ 
the t-statistic to zero
   2018-07-28 16:40:53 by Brook Milligan | Files touched by this commit (126)
Log message:
Remove MASTER_SITES= from individual R package Makefiles.

Each R package should include ../../math/R/Makefile.extension, which also
defines MASTER_SITES.  Consequently, it is redundant for the individual
packages to do the same.  Package-specific definitions also prevent
redefining MASTER_SITES in a single common place.
   2018-01-22 04:27:45 by Wen Heping | Files touched by this commit (1)
Log message:
Remove an unneeded line
   2018-01-22 04:16:11 by Wen Heping | Files touched by this commit (3)
Log message:
Import lme4-1.1.15 as math/R-lme4.

Fit linear and generalized linear mixed-effects models. The models
and their components are represented using S4 classes and methods.
The core computational algorithms are implemented using the Eigen
C++ library for numerical linear algebra and RcppEigen "glue".