20240127 11:22:20 by Makoto Fujiwara  Files touched by this commit (2) 
Log message:
(math/Rlme4) Uppdate 1.1.34 to 1.1.35.1
CHANGES IN VERSION 1.135.1:
USERVISIBLE CHANGES:
* 'lFormula' and 'glFormula' once again _do_ allow
matrixvalued responses (for use in downstream packages like
'galamm')
CHANGES IN VERSION 1.135 (20231103):
NEW FEATURES:
* 'predict.merMod' now has a 'se.fit' method, which computes
the standard errors of the predictions, conditional on the
estimated 'theta' (variancecovariance) parameters
USERVISIBLE CHANGES:
* using 'lmer' with a matrixvalued response now throws a more
informative error message, directing the user to '?refit'

20230708 08:06:17 by Makoto Fujiwara  Files touched by this commit (2) 
Log message:
(math/Rlme4) Updated 1.1.33 to 1.1.34
(R CMD Rdconv t txt /tmp/math/Rlme4/work/lme4/inst/NEWS.Rd)
CHANGES IN VERSION 1.134:
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

20230613 15:55:59 by Makoto Fujiwara  Files touched by this commit (2) 
Log message:
(math/Rlme4) Updated 1.1.27 to 1.1.33
CHANGES IN VERSION 1.133:
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 1.132 (20230314):
USERVISIBLE 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 1.131 (20221101):
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 1.130 (20220708):
USERVISIBLE CHANGES:
* 'nl' (term names) component added to output list of
'mkReTrms (GH #679)'
* eliminate partialmatching of 'eta' (for 'etastart') (GH
#686: not actually "uservisible" 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 1.129)
* 'maxfun' argument to 'allFit' controls max function
evaluations for every optimizer type (GH#685)
CHANGES IN VERSION 1.129 (20220407):
USERVISIBLE 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 1.128 (20220204):
USERVISIBLE 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
* singularfit 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 1.41 which has
'names(diag(<sparse>))'
BUG FIXES:
* 'reOnly' preserves environment (GH #654, Mikael Jagan)
* backwardcompatibility hooks changed to evaluate at runtime
(i.e., in '.onLoad()') rather than at build time (GH #649)
* 'lmList' no longer warns when 'data' is a tibble (GH #645)

20211026 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 doublechecked against existing RMD160 and
SHA512 hashes

20211007 16:28:36 by Nia Alarie  Files touched by this commit (458) 
Log message:
math: Remove SHA1 hashes for distfiles

20210917 01:47:51 by Makoto Fujiwara  Files touched by this commit (2) 
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)

20190808 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://mailindex.netbsd.org/techpkg/2019/08/02/msg021711.html

20181221 13:53:49 by Wen Heping  Files touched by this commit (2) 
Log message:
Update to 1.1.19
Upstream changes:
CHANGES IN VERSION 1.119
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

20180728 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. Packagespecific definitions also prevent
redefining MASTER_SITES in a single common place.

20180122 04:27:45 by Wen Heping  Files touched by this commit (1) 
Log message:
Remove an unneeded line
