# Transformation Models with Mixed Effects

## Documentation for package ‘tramME’ version 0.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.check_coef | Check the validity of a vector of coefficients
.check_varcov | Check the validity of a vector of coefficients
.dummy_ctm | Dummy ctm model with random effects as offsets
.mlt_data | Extract information from an mlt model
.model_name | Create name for a specific tramME model
.nobars | Remove random effects terms
.parallel_default | Boilerplate parallel-handling function, copied from 'lme4'
.paridx | Match parameters with parameter groups and indeces
.renames | Return names for random effects parameters
.re_data | Create RE data
.re_format | Reshape unformatted random effects vectors
.re_size | Calculates the size of the random effect vector implied by the model and the data
.sim_re | Simulates random effects vector from a tramME object
.subbars | My own version of lme4::subbar
.tramME | General ME tram model
anova.tramME | Comparison of nested tramME models.
BoxCoxME | ME version of tram::BoxCox
coef.LmME | Extract the coefficients of the fixed effects terms of an LmME model.
coef.tramME | Extract the coefficients of the fixed effects terms.
coef<-.tramME | Set coefficients of a tramME model.
ColrME | ME version of tram::Colr
confint.LmME | Confidence intervals for LmME model parameters
confint.tramME | Confidence intervals for tramME model parameters
CoxphME | ME version of tram::Coxph
LehmannME | ME version of tram::Lehmann
LmME | ME version of tram::Lm
logLik.tramME | Get the log-likelihood of the model
plot.trafo.tramME | Plotting method for 'trafo.tramME' objects
plot.tramME | Plotting method for tramME objects
PolrME | ME version of tram::Polr
predict.tramME | Predict method for tramME objects
print.anova.tramME | Printing 'anova.tramME' table
print.simulate.tramME | Print method for 'simulate.tramME' objects
print.summary.tramME | Print method for tramME model summary
print.tramME | Print tramME model
print.VarCorr.tramME | Print method for the variance-correlation parameters of a tramME object
ranef | Extract the conditional modes and conditional variances of random effects
ranef.LmME | Extract the conditional modes of random effects of an LmME model
ranef.tramME | Extract the conditional modes and conditional variances of random effects
refit.tramME | Refit the model with a new response vector
sigma.LmME | Extract the SD of the error term of an LmME model.
simulate.tramME | Simulate outcome variable from an estimated model
summary.tramME | Summary method for tramME model
SurvregME | ME version of tram::Survreg
trafo | Generic method for extracting baseline transformations
trafo.tramME | Get the baseline transformation function and its confidence interval
VarCorr | Variances and correlation matrices of random effects
VarCorr.LmME | Variances and correlation matrices of random effects of an LmME object
VarCorr.tramME | Variances and correlation matrices of random effects
varcov | Generic method for 'varcov'
varcov.tramME | Extract the variance-covariance matrix of the random effects
varcov<- | Generic method for '"varcov<-"'
varcov<-.tramME | Set the values of the random effects covariance matrices 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