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(this page) 2024-11-04 01:37:07 by Makoto Fujiwara | Files touched by this commit (2) |  |
Log message:
(math/R-lme4) Updated 1.1.35.1 to 1.1.35.5
CHANGES IN VERSION 1.1-35.5:
USER-VISIBLE CHANGES:
* in 'predict', the synonyms 'ReForm', 'REForm', and 'REform'
of 're.form' are now hard-deprecated, giving an error (after
10 years of soft deprecation)
OTHER CHANGES:
* minor adjustments in test tolerances
* correct Matrix dependency to >= 1.2-3
CHANGES IN VERSION 1.1-35.4 (2024-06-19):
BUG FIXES:
* 'predict(., re.form=...)' works in a wider range of cases
(GH #691)
* Gamma simulation now uses correct shape parameter (GH #782)
* Avoid triggering RcppEigen UBSAN bug(?) in the case of
profiling fixed effects in a 'merMod' object with a single
fixed effect parameter (GH #794: lots of help from Dirk
Eddelbuettel and Mikael Jagan)
* fix bug in plot methods (cbind'ing zero-length objects)
CHANGES IN VERSION 1.1-35.3 (2024-04-16):
BUG FIXES:
* bug-fix for ASAN/memory access problem in
CholmodDecomposition (Mikael Jagan)
CHANGES IN VERSION 1.1-35.2 (2024-03-28):
* This is primarily a 'bump' release to ensure that package
repositories rebuild binaries with the latest version of the
'Matrix' package.
BUG FIXES:
* 'simulate' works (again) with 're.form=NULL' when 'NA'
values are present in the data (GH #737, @frousseu)
USER-VISIBLE CHANGES:
* updated tests of upstream 'Matrix' version; should now warn
only on ABI incompatibility, not on package version mismatch
alone
|
| 2024-01-27 11:22:20 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(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'
|
| 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)
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| 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)
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| 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
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| 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. |
New packages: