NEWS | R Documentation |
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