Navigation:
Browse pkgsrc
(this page)
math R-lme4
CVSweb ] [ 
Homepage ] [ 
RSS ] [ 
Required by ] | 2026-06-13 13:04:42 by Makoto Fujiwara | Files touched by this commit (3) |
Log message: (math/R-lme4) Fix build against R 4.6.0 |
| 2025-02-15 05:29:47 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(math/R-lme4) Updated 1.1.35.5 to 1.1.36
(R CMD Rd2txt /tmp/math/R-lme4/work/lme4/inst/NEWS.Rd | head -30)
lme4 News
CHANGES IN VERSION 1.1-36:
NEW FEATURES:
The full (joint) conditional covariance matrix of fixed
effects and conditional modes is now available via
vcov(fitted_model, full = TRUE)
Random effects formulas are now processed by code from the
reformulas package, meaning that some extended random
effects formulas (such as (1|f*g) for crossed random
effects) will now work
USER-VISIBLE CHANGES:
simulate with newparams no longer prints a message
if the individual parameter vectors are unnamed
BUG FIXES:
floating-point errors leading to slightly negative deviances
could lead to NaN deviance residuals (Wolfgang Viechtbauer,
GH #812)
|
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)
|
| 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 |
New packages: