| .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. |