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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'

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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

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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)

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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)

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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

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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.

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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

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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.

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Remove an unneeded line

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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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