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CVS log for pkgsrc/math/R-lme4/Makefile

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Revision 1.10: download - view: text, markup, annotated - select for diffs
Sat Jan 27 10:22:20 2024 UTC (9 months ago) by mef
Branches: MAIN
CVS tags: pkgsrc-2024Q3-base, pkgsrc-2024Q3, pkgsrc-2024Q2-base, pkgsrc-2024Q2, pkgsrc-2024Q1-base, pkgsrc-2024Q1, HEAD
Diff to: previous 1.9: preferred, colored
Changes since revision 1.9: +5 -4 lines
(math/R-lme4) Uppdate 1.1.34 to 1.1.35.1

CHANGES IN VERSION 1.1-35.1:

  USER-VISIBLE CHANGES:

         * 'lFormula' and 'glFormula' once again _do_ allow
           matrix-valued responses (for use in downstream packages like
           'galamm')

CHANGES IN VERSION 1.1-35 (2023-11-03):

  NEW FEATURES:

         * 'predict.merMod' now has a 'se.fit' method, which computes
           the standard errors of the predictions, conditional on the
           estimated 'theta' (variance-covariance) parameters

  USER-VISIBLE CHANGES:

         * using 'lmer' with a matrix-valued response now throws a more
           informative error message, directing the user to '?refit'

Revision 1.9: download - view: text, markup, annotated - select for diffs
Sat Jul 8 06:06:17 2023 UTC (15 months, 3 weeks ago) by mef
Branches: MAIN
CVS tags: pkgsrc-2023Q4-base, pkgsrc-2023Q4, pkgsrc-2023Q3-base, pkgsrc-2023Q3
Diff to: previous 1.8: preferred, colored
Changes since revision 1.8: +2 -2 lines
(math/R-lme4) Updated 1.1.33 to 1.1.34

(R CMD Rdconv -t txt    /tmp/math/R-lme4/work/lme4/inst/NEWS.Rd)
CHANGES IN VERSION 1.1-34:

  BUG FIXES:

         * 'summary(<merMod>)' now records if 'correlation' was
           specified explicitly and to what; and its 'print()' method
           takes it into account; notably summary(<merMod>,
           correlation=TRUE) will by default print the correlation
           (matrix of the fixed effects) fixing GH #725

  NEW FEATURES:

         * 'refit' gains a 'newweights' argument

Revision 1.8: download - view: text, markup, annotated - select for diffs
Tue Jun 13 13:55:59 2023 UTC (16 months, 2 weeks ago) by mef
Branches: MAIN
CVS tags: pkgsrc-2023Q2-base, pkgsrc-2023Q2
Diff to: previous 1.7: preferred, colored
Changes since revision 1.7: +2 -2 lines
(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)

Revision 1.7: download - view: text, markup, annotated - select for diffs
Thu Sep 16 23:47:51 2021 UTC (3 years, 1 month ago) by mef
Branches: MAIN
CVS tags: pkgsrc-2023Q1-base, pkgsrc-2023Q1, pkgsrc-2022Q4-base, pkgsrc-2022Q4, pkgsrc-2022Q3-base, pkgsrc-2022Q3, pkgsrc-2022Q2-base, pkgsrc-2022Q2, pkgsrc-2022Q1-base, pkgsrc-2022Q1, pkgsrc-2021Q4-base, pkgsrc-2021Q4, pkgsrc-2021Q3-base, pkgsrc-2021Q3
Diff to: previous 1.6: preferred, colored
Changes since revision 1.6: +13 -3 lines
(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)

Revision 1.6: download - view: text, markup, annotated - select for diffs
Thu Aug 8 19:53:50 2019 UTC (5 years, 2 months ago) by brook
Branches: MAIN
CVS tags: pkgsrc-2021Q2-base, pkgsrc-2021Q2, pkgsrc-2021Q1-base, pkgsrc-2021Q1, pkgsrc-2020Q4-base, pkgsrc-2020Q4, pkgsrc-2020Q3-base, pkgsrc-2020Q3, pkgsrc-2020Q2-base, pkgsrc-2020Q2, pkgsrc-2020Q1-base, pkgsrc-2020Q1, pkgsrc-2019Q4-base, pkgsrc-2019Q4, pkgsrc-2019Q3-base, pkgsrc-2019Q3
Diff to: previous 1.5: preferred, colored
Changes since revision 1.5: +4 -6 lines
Update all R packages to canonical form.

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

- 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

Revision 1.5: download - view: text, markup, annotated - select for diffs
Wed Jul 31 19:49:55 2019 UTC (5 years, 3 months ago) by brook
Branches: MAIN
Diff to: previous 1.4: preferred, colored
Changes since revision 1.4: +6 -7 lines
R-lme4: update to version 1.1.21.

Update to the canonical form of an R package and fix the LICENSE
field.

Revision 1.4: download - view: text, markup, annotated - select for diffs
Fri Dec 21 12:53:49 2018 UTC (5 years, 10 months ago) by wen
Branches: MAIN
CVS tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4
Diff to: previous 1.3: preferred, colored
Changes since revision 1.3: +2 -2 lines
Update to 1.1.19

Upstream changes:
CHANGES IN VERSION 1.1-19
NEW FEATURES

    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 structures

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

USER-VISIBLE CHANGES

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

    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 isSingular)

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)
USER-VISIBLE CHANGES

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

NEW FEATURES

    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

BUG FIXES

    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)
BUG FIXES

    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, #457)

USER-VISIBLE CHANGES

    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

Revision 1.3: download - view: text, markup, annotated - select for diffs
Sat Jul 28 14:40:49 2018 UTC (6 years, 3 months ago) by brook
Branches: MAIN
CVS tags: pkgsrc-2018Q3-base, pkgsrc-2018Q3
Diff to: previous 1.2: preferred, colored
Changes since revision 1.2: +1 -2 lines
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.

Revision 1.2: download - view: text, markup, annotated - select for diffs
Mon Jan 22 03:27:45 2018 UTC (6 years, 9 months ago) by wen
Branches: MAIN
CVS tags: pkgsrc-2018Q2-base, pkgsrc-2018Q2, pkgsrc-2018Q1-base, pkgsrc-2018Q1
Diff to: previous 1.1: preferred, colored
Changes since revision 1.1: +1 -2 lines
Remove an unneeded line

Revision 1.1: download - view: text, markup, annotated - select for diffs
Mon Jan 22 03:16:11 2018 UTC (6 years, 9 months ago) by wen
Branches: MAIN
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".

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