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tramME (version 1.0.3)

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

1.0.3

License

GPL-2

Maintainer

Balint Tamasi

Last Published

September 5th, 2022

Functions in tramME (1.0.3)

VarCorr.LmME

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

Mixed-effects version of Survreg
LmME

Mixed-effects version of Lm
ColrME

Mixed-effects version of Colr
LehmannME

Mixed-effects version of Lehmann
PolrME

Mixed-effects version of Polr
CoxphME

Mixed-effects version of Coxph
BoxCoxME

Mixed-effects version of BoxCox
anova.tramME

Comparison of nested tramME models.
VarCorr.tramME

Variances and correlation matrices of random effects
duplicate

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

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

Confidence intervals for LmME model parameters
coef.tramME

Extract the coefficients of the fixed effects terms.
confint.tramME

Confidence intervals for tramME model parameters
duplicate.tramTMB

Create a duplicate of the tramTMB object
coef<-.tramME

Set coefficients of a tramME model.
coef.SurvregME

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

EDFs of smooth shift terms
logLik.tramME

Get the log-likelihood of the tramME model
model.matrix.tramME

Model matrices for tramME models
predict.tramME

Predict method for tramME objects
plot.smooth.tramME

Plot smooth terms of a tramME model.
optim_control

Set up and control optimization parameters
print.anova.tramME

Printing anova.tramME table
print.summary.tramME

Print method for tramME model summary
model.frame.tramME

Extract model frame from a tramME model
print.VarCorr.tramME

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

Post-estimation calculations in a tramTMB model
plot.tramME

Plotting method for tramME objects
tramME

General function to define and fit tramME models
summary.tramME

Summary method for tramME model
ranef.tramME

Point estimates and conditional variances of random effects.
residuals.LmME

Residuals of a LmME model
residuals.tramME

Residuals of a tramME model
sigma.LmME

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

Print tramME model
ranef.LmME

Extract the conditional modes of random effects of an LmME model
smooth_terms.LmME

Evaluate smooth terms of a LmME model.
smooth_terms.tramME

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

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

Calculate the variance-covariance matrix of the parameters
varcov

Generic method for varcov
varcov.tramME

Extract the variance-covariance matrix of the random effects
tramTMB

Create a tramTMB object
tramME_model

Create an object that defines a tramME_model
vcov.LmME

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

Return variable names.
varcov<-

Generic method for "varcov<-"
varcov.LmME

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

Variance-covariance matrix of the parameters