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tramME (version 1.0.1)

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 and Hothorn, 2021, ). Penalized smooth shift terms can be defined using 'mgcv'.

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Version

Install

install.packages('tramME')

Monthly Downloads

684

Version

1.0.1

License

GPL-2

Maintainer

Balint Tamasi

Last Published

April 25th, 2022

Functions in tramME (1.0.1)

VarCorr.tramME

Variances and correlation matrices of random effects
ColrME

Mixed-effects version of Colr
CoxphME

Mixed-effects version of Coxph
PolrME

Mixed-effects version of Polr
SurvregME

Mixed-effects version of Survreg
BoxCoxME

Mixed-effects version of BoxCox
LmME

Mixed-effects version of Lm
anova.tramME

Comparison of nested tramME models.
LehmannME

Mixed-effects version of Lehmann
VarCorr.LmME

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

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

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

Create a duplicate of the tramTMB object
.parallel_default

Boilerplate parallel-handling function, modified from glmmTMB
confint.LmME

Confidence intervals for LmME model parameters
offset<-

Generic method for "offset<-"
print.summary.tramME

Print method for tramME model summary
offset

Generic method for "offset"
edf_smooth

Calculate edf for smooth terms
coef<-.tramME

Set coefficients of a tramME model.
coef.LmME

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

Print tramME model
coef.tramME

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

Call the optimizer on a tramME object
confint.tramME

Confidence intervals for tramME model parameters
model.matrix.tramME

Model matrices for tramME models
model.frame.tramME

Extract model frame from a tramME model
predict.tramTMB

Post-estimation calculations in a tramTMB model
logLik.tramME

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

Predict method for tramME objects
residuals.LmME

Residuals of a LmME model
residuals.tramME

Residuals of a tramME model
tramME_model

Create an object that defines a tramME_model
.cctm

Create a 'conditional' ctm model with random effects as offsets
.idx

Get parameter indices of various structures
tramTMB

Create a tramTMB object
is.pd

Check positive definiteness
edf_smooth.tramME

EDFs of smooth shift terms
plot.smooth.tramME

Plot smooth terms of a tramME model.
summary.tramME

Summary method for tramME model
tramME

General function to define and fit tramME models
offset.default

Default method for "offset"
offset.tramME

Get the offset vector of a tramME object.
optim_control

Set up and control optimization parameters
ranef.LmME

Extract the conditional modes of random effects of an LmME model
fitmod

Fit the model.
optim_tramTMB

Optimize the tramTMB object
vcov.LmME

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

Variance-covariance matrix of the parameters
ranef.tramME

Point estimates and conditional variances of random effects.
vcov.tramME

Calculate the variance-covariance matrix of the parameters
print.VarCorr.tramME

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

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

Generic method for "weights<-"
weights.tramME

Get the observation weight vector of a tramME object.
varcov

Generic method for varcov
plot.tramME

Plotting method for tramME objects
print.anova.tramME

Printing anova.tramME table
weights<-.tramME

Set the values of the observation weights of a tramME model.
offset<-.tramME

Set the values of the offsets of a tramME model.
varcov<-.tramME

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

Evaluate smooth terms of a LmME model.
smooth_terms.tramME

Extract and evaluate the smooth terms of a tramME model
sigma.LmME

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

Get smooth terms.
variable.names.tramME

Return variable names.
varcov<-

Generic method for "varcov<-"
varcov.tramME

Extract the variance-covariance matrix of the random effects