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tramME (version 0.0.1)

Transformation Models with Mixed Effects

Description

Likelihood-based estimation of mixed-effects transformation models using the Template Model Builder (TMB). The technical details of transformation models are given in Hothorn et al. (2018) . 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 (AD).

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Version

Install

install.packages('tramME')

Monthly Downloads

684

Version

0.0.1

License

GPL-2

Maintainer

Balint Tamasi

Last Published

March 21st, 2020

Functions in tramME (0.0.1)

LehmannME

ME version of tram::Lehmann
VarCorr.LmME

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

ME version of tram::BoxCox
anova.tramME

Comparison of nested tramME models.
VarCorr.tramME

Variances and correlation matrices of random effects
CoxphME

ME version of tram::Coxph
SurvregME

ME version of tram::Survreg
LmME

ME version of tram::Lm
PolrME

ME version of tram::Polr
ColrME

ME version of tram::Colr
coef<-.tramME

Set coefficients of a tramME model.
.mlt_data

Extract information from an mlt model
.model_name

Create name for a specific tramME model
coef.tramME

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

Confidence intervals for LmME model parameters
.re_format

Reshape unformatted random effects vectors
.re_size

Calculates the size of the random effect vector implied by the model and the data
.check_coef

Check the validity of a vector of coefficients
confint.tramME

Confidence intervals for tramME model parameters
.paridx

Match parameters with parameter groups and indeces
.check_varcov

Check the validity of a vector of coefficients
ranef.tramME

Extract the conditional modes and conditional variances of random effects
ranef.LmME

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

Refit the model with a new response vector
coef.LmME

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

Printing anova.tramME table
.parallel_default

Boilerplate parallel-handling function, copied from lme4
.subbars

My own version of lme4::subbar
print.tramME

Print tramME model
print.VarCorr.tramME

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

Remove random effects terms
.dummy_ctm

Dummy ctm model with random effects as offsets
.renames

Return names for random effects parameters
logLik.tramME

Get the log-likelihood of the model
summary.tramME

Summary method for tramME model
plot.trafo.tramME

Plotting method for trafo.tramME objects
trafo

Generic method for extracting baseline transformations
.tramME

General ME tram model
sigma.LmME

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

Create RE data
plot.tramME

Plotting method for tramME objects
.sim_re

Simulates random effects vector from a tramME object
simulate.tramME

Simulate outcome variable from an estimated model
trafo.tramME

Get the baseline transformation function and its confidence interval
vcov.LmME

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

Predict method for tramME objects
varcov<-.tramME

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

Generic method for "varcov<-"
print.simulate.tramME

Print method for simulate.tramME objects
print.summary.tramME

Print method for tramME model summary
vcov.tramME

Calculate the variance-covariance matrix of the parameters
variable.names.tramME

Return variable names.
varcov.tramME

Extract the variance-covariance matrix of the random effects
varcov

Generic method for varcov