# Transformation Models with Mixed Effects

## Documentation for package ‘tramME’ version 1.0.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

anova.tramME | Comparison of nested tramME models.
BoxCoxME | Non-normal (Box-Cox-type) Linear Mixed-effects Additive Regression Model
coef.LmME | Extract the coefficients of an 'LmME' model
coef.SurvregME | Extract the coefficients of the fixed effects terms of an SurvregME model.
coef.tramME | Extract the coefficients of a 'tramME' model
coef<-.tramME | Set coefficients of a tramME model.
ColrME | Mixed-effects Additive Continuous Outcome Logistic Regression Model
confband.tramME | Confidence intervals and bands from a 'tramME' model
confint.LmME | Confidence intervals for LmME model parameters
confint.tramME | Confidence intervals for tramME model parameters
CoxphME | Mixed-effects Additive Parametric Cox Regression Model
edf_smooth | EDFs of smooth shift terms
edf_smooth.tramME | EDFs of smooth shift terms
format.Resp | Response objects
is.na.Resp | Response objects
LehmannME | Mixed-effects Additive Lehmann-alternative Linear Regression Model
length.Resp | Response objects
LmME | Mixed-effects Additive Normal Linear Regression Model
logLik.tramME | Get the log-likelihood of the tramME model
model.frame.tramME | Extract model frame from a tramME model
model.matrix.tramME | Model matrices for 'tramME' models
optim_control | Set up and control optimization parameters
plot.confband.tramME | Plot confidence bands from 'tramME' models
plot.smooth.tramME | Plot smooth terms of a tramME model.
plot.tramME | Plotting method for tramME objects
plot_ci | Plot confidence bands from 'tramME' models
PolrME | Mixed-effects Additive Transformation Models for Ordered Categorical Responses
predict.tramME | Predict method for tramME objects
predict.tramTMB | Post-estimation calculations in a tramTMB model
print.anova.tramME | Printing 'anova.tramME' table
print.Resp | Response 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
R.Resp | Response objects
ranef | Point estimates and conditional variances of 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.
residuals.LmME | Residuals of a LmME model
residuals.tramME | Residuals of a tramME model
Resp | Response objects
sigma.LmME | Extract the SD of the error term of an LmME model.
simulate.tramME | Simulate from a 'tramME' model
smooth_terms | Extract and evaluate the smooth terms 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
summary.tramME | Summary method for tramME model
SurvregME | Mixed-effects Additive Parametric Survival Models
tramME | Mixed-effects Additive transformation models
tramTMB | Create a tramTMB object
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.LmME | Extract the variance-covariance matrix of the random effects of an LmME model
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
[.Resp | Response objects