2023-07-08 08:06:17 by Makoto Fujiwara | Files touched by this commit (2) |
Log message: (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 |
2023-06-13 15:55:59 by Makoto Fujiwara | Files touched by this commit (2) |
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) |
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 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) |
2019-08-08 21:53:58 by Brook Milligan | Files touched by this commit (189) | |
Log message: 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 |
2018-12-21 13:53:49 by Wen Heping | Files touched by this commit (2) |
Log message: 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 |
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. |