Update citations and manual with the JSS publication.
tramME 1.0.7 (2024-11-29)
New vignette: “Mixed-effects Additive Transformation Models with the
R Package tramME”
tramME 1.0.6 (2024-07-01)
Bugfix: some arguments passed as variables were not found. This was
introduced by moving away from NSE and not exporting some internal
functions.
Bugfix: error with printing models called with
tramME::.
Documentation: Clarify that the print method of
VarCorr.tramME shows the random effect standard deviations
by default.
New functionality: coef.tramME now has a
complete argument that returns all coefficients (baseline,
fixed, random) of the model as a named vector
New functionality: Access variances and covariances of penalized
parameters (coefficients of smooth terms and random effects) through the
parm argument of vcov.tramME.
New functionality/change of behavior: The new
ok_warnings argument of optim_control provides
control over what warning messages are reported during optimization.
summary.tramME doesn’t report the number of warnings during
optimization anymore.
New functionality: New scales are available in
predict.tramME and plot.tramME.
New functionality: confband.tramME calculates
confidence bands and pointwise confidence intervals for various scales
of the conditional outcome distribution.
Documentation: Update documentation of the model functions with
additional details, examples and references.
Processing random effects formula elements with
reformulas.
tramME 1.0.5 (2023-06-28)
Refactor code, clean up documentation, unexport internal
functions.
New vignette with examples of mixed-effects transformation models
with smooth shift terms.
Some methods have been moved to development branch for proper
testing and refactoring (Aareg, lpterms,
simulate, parboot, trafo). These
features may eventually find their way back to the package, probably in
a slightly changed form.
tramME 0.1.3 (2022-03-08)
Fixed duplicate.tramTMB method to work with TMB
1.8.0.
tramME 0.1.2 (2021-08-16)
Added R-Forge URL
tramME 0.1.1 (2021-04-05)
Fixed uninitialized value problem indicated by valgrind
tramME 0.1.0 (2021-03-29)
Updated internal functions for estimation transformation models with
TMB:
Fixed effects only models can be estimated
Exported functions (coef, logLik)
communicate with the TMB model more smoothly
Updated internal structure to help future development (not exported
currently)
Fixing coefficients with the argument
fixed = c(name = value)
New model classes in SurvregME using the parameter
fixing option
AaregME extends the (parametric) Aalen regression model
of tram with mixed-effects.
Out-of-sample log-likelihoods using the newdata
argument of logLik
Score residuals with the resid method. When frequently
recalculated (e.g. in boosting), setting resid = TRUE in
model definition increases efficiency.
Updating models via the update method
Setting observation weights and offsets efficiently (activated with
do_update = TRUE). Currently, only possible through
directly manipulating the tmb_obj of the model.
Parametric bootstrap with the parboot method
New optimization options (e.g. internal scaling of fixed effects
design matrix to improve convergence, more sensible initial values) and
improved control over the optimization process with
optim_control()
Various methods (including analytical in the case of
fixed effects only models) to calculate the Hessian; trying harder to
invert the Hessian in numerically unstable cases.
Calculate the linear predictor with type = "lp" in
predict
Several additional methods to help the user working with
tramME objects: model.frame,
model.matrix, fitmod,
duplicate.
Improved unit testing
Improved documentation
Demo for IPD meta-analysis
tramME 0.0.4 (2021-02-04)
fixed bug in setting error distributions of ‘dummy’ ctms for predict
and simulate methods
updated Figure 6 in vignette, because the bug above affected predict
in the case of CorlME
fixed bug in unit test for simulate that caused error with mlt
1.2-1
fixed simulate output structure with what = "joint"
option