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tramME (version 1.0.7)

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

1.0.7

License

GPL-2

Maintainer

Balint Tamasi

Last Published

November 29th, 2024

Functions in tramME (1.0.7)

optim_control

Set up and control optimization parameters
print.VarCorr.tramME

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

Extract the coefficients of the fixed effects terms of an SurvregME model.
coef<-.tramME

Set coefficients of a tramME model.
plot.tramME

Plotting method for tramME objects
confint.tramME

Confidence intervals for tramME model parameters
model.frame.tramME

Extract model frame from a tramME model
model.matrix.tramME

Model matrices for tramME models
coef.tramME

Extract the coefficients of a tramME model
plot.smooth.tramME

Plot smooth terms of a tramME model.
summary.tramME

Summary method for tramME model
simulate.tramME

Simulate from a tramME model
predict.tramTMB

Post-estimation calculations in a tramTMB model
sigma.LmME

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

Predict method for tramME objects
confband.tramME

Confidence intervals and bands from a tramME model
plot_ci

Plot confidence bands from tramME models
tramME

Mixed-effects Additive transformation models
print.anova.tramME

Printing anova.tramME table
edf_smooth.tramME

EDFs of smooth shift terms
smooth_terms.LmME

Evaluate smooth terms of a LmME model.
varcov

Generic method for varcov
varcov.tramME

Extract the variance-covariance matrix of the random effects
ranef.LmME

Extract the conditional modes of random effects of an LmME model
ranef.tramME

Point estimates and conditional variances of random effects.
print.summary.tramME

Print method for tramME model summary
tramTMB

Create a tramTMB object
varcov<-.tramME

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

Print tramME model
logLik.tramME

Get the log-likelihood of the tramME model
residuals.LmME

Residuals of a LmME model
smooth_terms.tramME

Extract and evaluate the smooth terms of a tramME model
varcov<-

Generic method for "varcov<-"
varcov.LmME

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

Residuals of a tramME model
variable.names.tramME

Return variable names.
vcov.LmME

Get the variance-covariance matrix of the parameters of an LmME model
vcov.tramME

Calculate the variance-covariance matrix of the parameters
BoxCoxME

Non-normal (Box-Cox-type) Linear Mixed-effects Additive Regression Model
VarCorr.tramME

Variances and correlation matrices of random effects
LehmannME

Mixed-effects Additive Lehmann-alternative Linear Regression Model
VarCorr.LmME

Variances and correlation matrices of random effects of an LmME object
PolrME

Mixed-effects Additive Transformation Models for Ordered Categorical Responses
SurvregME

Mixed-effects Additive Parametric Survival Models
CoxphME

Mixed-effects Additive Parametric Cox Regression Model
Resp

Response objects
LmME

Mixed-effects Additive Normal Linear Regression Model
ColrME

Mixed-effects Additive Continuous Outcome Logistic Regression Model
coef.LmME

Extract the coefficients of an LmME model
confint.LmME

Confidence intervals for LmME model parameters
anova.tramME

Comparison of nested tramME models.