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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)

Revision | Action | file |

1.7 | modify | pkgsrc/math/R-lme4/Makefile |

1.4 | modify | pkgsrc/math/R-lme4/distinfo |