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 withtramME::.
Documentation: Clarify that the print method ofVarCorr.tramME shows the random effect standard deviations by default.
New functionality: coef.tramME now has acomplete 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 theparm argument of vcov.tramME.
New functionality/change of behavior: The newok_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 inpredict.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 withreformulas.
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 argumentfixed = 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 newdataargument 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 withdo_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 withoptim_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" inpredict
Several additional methods to help the user working withtramME 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