# Transformation Models with Mixed Effects

## Documentation for package ‘tramME’ version 1.0.0

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

## Help Pages

.cctm | Create a 'conditional' ctm model with random effects as offsets
.idx | Get parameter indices of various structures
.parallel_default | Boilerplate parallel-handling function, modified from 'glmmTMB'
anova.tramME | Comparison of nested tramME models.
BoxCoxME | Mixed-effects version of 'BoxCox'
coef.LmME | Extract the coefficients of the fixed effects terms of an LmME model.
coef.SurvregME | Extract the coefficients of the fixed effects terms of an SurvregME model.
coef.tramME | Extract the coefficients of the fixed effects terms.
coef<-.tramME | Set coefficients of a tramME model.
ColrME | Mixed-effects version of 'Colr'
confint.LmME | Confidence intervals for LmME model parameters
confint.tramME | Confidence intervals for tramME model parameters
CoxphME | Mixed-effects version of 'Coxph'
duplicate | Generic for copying objects that are (partly) modified in place
duplicate.tramTMB | Create a duplicate of the tramTMB object
edf_smooth | Calculate edf for smooth terms
edf_smooth.tramME | EDFs of smooth shift terms
fitmod | Fit the model.
fitmod.tramME | Call the optimizer on a tramME object
is.pd | Check positive definiteness
LehmannME | Mixed-effects version of 'Lehmann'
LmME | Mixed-effects version of 'Lm'
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
offset | Generic method for '"offset"'
offset.default | Default method for '"offset"'
offset.tramME | Get the offset vector of a tramME object.
offset<- | Generic method for '"offset<-"'
offset<-.tramME | Set the values of the offsets of a tramME model.
optim_control | Set up and control optimization parameters
optim_tramTMB | Optimize the tramTMB object
plot.smooth.tramME | Plot smooth terms of a tramME model.
plot.tramME | Plotting method for tramME objects
PolrME | Mixed-effects version of 'Polr'
predict.tramME | Predict method for tramME objects
predict.tramTMB | Post-estimation calculations in a tramTMB model
print.anova.tramME | Printing 'anova.tramME' table
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 | 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
sigma.LmME | Extract the SD of the error term of an LmME model.
smooth_terms | Get smooth terms.
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 version of 'Survreg'
tramME | General function to define and fit tramME models
tramME_model | Create an object that defines a tramME_model
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
vcov.tramTMB | Variance-covariance matrix of the parameters
weights.tramME | Get the observation weight vector of a tramME object.
weights<- | Generic method for '"weights<-"'
weights<-.tramME | Set the values of the observation weights of a tramME model.