Log message:
(math/Rlme4) Updated 1.1.21 to 1.1.27.1
HANGES IN VERSION 1.127.1:
USERVISIBLE CHANGES:
* 'influence.merMod' allows userspecified 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 1.127 (20210515):
USERVISIBLE 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 outofbounds linear
predictors from nonconstraining link functions such as
identitylink 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 1.126 (20201130):
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 1.125 (20201023):
* Set more tests to run only if environment variable
'LME4_TEST_LEVEL'>1
CHANGES IN VERSION 1.124 (never on CRAN):
USERVISIBLE CHANGES:
* 'anova()' now returns a pvalue 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 nonNA 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 longstanding UBSAN issues (GH #561)
CHANGES IN VERSION 1.123 (20200306):
This is primarily for CRAN compliance (previous submission was
retracted to allow time for downstream package adjustments).
* Some PROTECT/UNPROTECT fixes
CHANGES IN VERSION 1.122 (never on CRAN):
USERVISIBLE 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 201306.
* '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 '1e5' to '1e4', 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 inverseGaussian models (GH #284
revisited, @nahorp/Florian Hartig)
* singlemodel 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 1e6, now 1e8).
(To revert to former tolerances, use
'control=lmerControl(optimizer="nloptwrap",
optCtrl=list(xtol_abs=1e6, ftol_abs=1e6))'.)
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)

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://mailindex.netbsd.org/techpkg/2019/08/02/msg021711.html

Log message:
Update to 1.1.19
Upstream changes:
CHANGES IN VERSION 1.119
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.
USERVISIBLE 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
postfitting convergence checks based on estimated gradient and Hessian (see \
troubleshooting) are no longer performed for (nearly)singular fits (see \
isSingular)
CHANGES IN VERSION 1.1181 (20180817)
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 1.118 ((20180816)
USERVISIBLE 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 1.117 (20180403)
This is a maintenance release only (fixes CRAN problems with crossplatform \
tests and examples)
CHANGES IN VERSION 1.116 (20180328)
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)
USERVISIBLE 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 tstatistic to zero

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. Packagespecific definitions also prevent
redefining MASTER_SITES in a single common place.
