| NEWS | R Documentation |
fix documentation links for CRAN checks
the refit() function is now re-exported (i.e., you no
longer need to load lme4 to use it)
a modelparm.glmmTMB method is now provided (so that
multcomp::glht should work out of the box with
glmmTMB objects)
new sparseX argument to specify sparse fixed-effect
model matrices for one or more components
summary and model printing now work if
control=glmmTMBControl(optimizer=optim) is used (GH #589)
structured covariance models now work in zero-inflation and dispersion components (GH #579)
documentaion of formula for variance in beta family (GH #595)
updated for R-devel changes (R 4.0.0 will set stringsAsFactors=FALSE by default)
The 1.0.0 release does not introduce any major changes or incompatibilities, but signifies that glmmTMB is considered stable and reliable for general use.
new map argument to glmmTMB allows for some
parameter values to be fixed
(see ?TMB::MakeADFun for details)
new optimizer and
optArgs arguments to glmmTMBControl allow use of
optimizers other than nlminb
predict can make population-level predictions
(i.e., setting all random effects to zero).
See ?predict.glmmTMB for details.
beta_family now allows zero-inflation;
new ziGamma family (minor modification of
stats::Gamma) allows zero-inflation
(i.e., Gamma-hurdle models)
vcov(., full=TRUE) (and hence profiling) now work for models with dispformula=~0
Documentation fix: when family=genpois, the
index of dispersion is known as phi^2.
Anova now respects the component argument (GH
#494, from @eds-slim)
predict now works when contrasts are set on factors
in original data (GH #439, from @cvoeten)
bootMer now works with models with Bernoulli
responses (even though simulate() returns a two-column
matrix in this case) (GH #529, @frousseu)
better support for emmeans applied to zero-inflation
or dispersion models (correct link functions) (Russ Lenth)
sigma(.) now returns NA for models with
non-trivial dispersion models (i.e. models with more than one
dispersion parameter) (raised by GH #533, from @marek-tph)
VarCorr no longer prints residual variances for
models with dispformula=~0
the model.matrix() and terms() methods
for glmmTMB objects have been slightly modified
ranef now returns information about conditional variances (as
attributes of the individual random effects terms) by default;
this information can easily be retrieved by
as.data.frame(ranef(.)).
coef method now available: as in lme4, returns
sum of fixed + random effects for each random-effects
level. (Conditional variances for coef not yet available.)
simulate works for models with genpois family
parametric bootstrapping should work, using
bootMer from the lme4 package as a front end.
models with multiple types of RE (e.g. ar1 and us) may have failed previously (GH #329)
predict was not handling data-dependent predictors (e.g. poly, spline, scale) correctly
profile now works for models without random effects
The value returned from simulate for binomial models
is now a non-standard data frame where each element contains a
two-column matrix (as in the base-R simulate method for
binomial GLMS).
REML is now an option (GH #352). It is typically only for Gaussian response variables, but can also be useful for some non-Gaussian response variables if used with caution (i.e. simulate a test case first).
Because family functions are now available for all
families that have been implemented in the underlying TMB
code, specifying the family argument as a raw list (rather than as a family
function, the name of a family function, or the output of such a
function) is now deprecated.
likelihood profiles (via profile) and likelihood
profile confidence intervals (via confint(profile(.)))
can now be computed;
confint(fitted,method="profile") and
confint(fitted,method="uniroot") (find CIs by using
a root-finding algorithm on the likelihood profile)
offsets are now allowed in the zero-inflation and dispersion
formulas as well as in the main (conditional-mean) formula
(if offset is specified as a separate argument, it applies
only to the conditional mean)
zero-truncated generalized Poisson family=truncated_genpois
zero-truncated Conway-Maxwell-Poisson
family=truncated_compois
predict now allows type ("link", "response",
"conditional", "zprob", "zlink")
built-in betar() family for Beta regression fixed
(and name changed to beta_family()) (GH #278)
fixed segfault in predict method when response is specified as two columns (GH #289)
fixed summary-printing bug when some random effects have covariance terms and others don't (GH #291)
fix bugs in binomial residuals and prediction (GH #307)
in predict.glmmTMB,
the zitype argument has been rolled into the new
type argument: default prediction type is now
"link" instead of "response", in order to match glm() default