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tramME (version 1.0.4)

Transformation Models with Mixed Effects

Description

Likelihood-based estimation of mixed-effects transformation models using the Template Model Builder ('TMB', Kristensen et al., 2016) . The technical details of transformation models are given in Hothorn et al. (2018) . Likelihood contributions of exact, randomly censored (left, right, interval) and truncated observations are supported. The random effects are assumed to be normally distributed on the scale of the transformation function, the marginal likelihood is evaluated using the Laplace approximation, and the gradients are calculated with automatic differentiation (Tamasi & Hothorn, 2021) . Penalized smooth shift terms can be defined using 'mgcv'.

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Version

Install

install.packages('tramME')

Monthly Downloads

684

Version

1.0.4

License

GPL-2

Maintainer

Balint Tamasi

Last Published

April 4th, 2023

Functions in tramME (1.0.4)

duplicate.tramTMB

Create a duplicate of the tramTMB object

Generic for copying objects that are (partly) modified in place

Mixed-effects version of Coxph

Mixed-effects version of Lehmann

Comparison of nested tramME models.

Set coefficients of a tramME model.

Plotting method for tramME objects

Predict method for tramME objects

Confidence intervals for tramME model parameters

Mixed-effects version of Colr

Create a corresponding ctm model for a tramME model

plot.smooth.tramME

Plot smooth terms of a tramME model.

Set up and control optimization parameters

predict.tramTMB

Post-estimation calculations in a tramTMB model

model.matrix.tramME

Model matrices for tramME models

Mixed-effects version of Lm

model.frame.tramME

Extract model frame from a tramME model

print.anova.tramME

Printing anova.tramME table

print.VarCorr.tramME

Print method for the variance-correlation parameters of a tramME object

print.summary.tramME

Print method for tramME model summary

Extract the coefficients of the fixed effects terms of an LmME model.

Print tramME model

Extract the conditional modes of random effects of an LmME model

residuals.tramME

Residuals of a tramME model

Extract the coefficients of the fixed effects terms of an SurvregME model.

Get the log-likelihood of the tramME model

edf_smooth.tramME

EDFs of smooth shift terms

Mixed-effects version of Polr

Confidence intervals for LmME model parameters

Extract the coefficients of the fixed effects terms.

simulate.tramME

Simulate from a tramME model

Calculate the variance-covariance matrix of the parameters

smooth_terms.tramME

Extract and evaluate the smooth terms of a tramME model

Extract the SD of the error term of an LmME model.

Summary method for tramME model

Point estimates and conditional variances of random effects.

Extract the variance-covariance matrix of the random effects of an LmME model

Generic method for "varcov<-"

General function to define and fit tramME models

variable.names.tramME

Return variable names.

Get the variance-covariance matrix of the parameters of an LmME model

Create a tramTMB object

Residuals of a LmME model

varcov<-.tramME

Set the values of the random effects covariance matrices of a tramME model.

Create an object that defines a tramME_model

Generic method for varcov

smooth_terms.LmME

Evaluate smooth terms of a LmME model.

Extract the variance-covariance matrix of the random effects

Variances and correlation matrices of random effects of an LmME object

Mixed-effects version of BoxCox

Response objects

Mixed-effects version of Survreg

Variances and correlation matrices of random effects