| .cctm | Create a 'conditional' ctm model with random effects as offsets |
| .check_par | Helper function to check parameter constarints |
| .combine_formulas | Combine a set of formulas into one (similar to nlme::asOneFormula) |
| .constr_adj | Helper function to adjust the constraints consistently with the parameter restrictions |
| .ctm2formula | Create a dummy fromula from a ctm object |
| .gen_param | Generator for param closure |
| .get_cf | Get the coefficient vector |
| .get_par | Helper function to extract formatted parameters |
| .idx | Get parameter indices of various structures |
| .isbars | Check whether formula contains bars (RE parts) |
| .model_name | Generates proper model name for the tramME model |
| .mod_negative | Helper function to figure out if negative = TRUE in a given model |
| .nm2mat | Add names to the vc matrix |
| .nm2vec | Add names to the vector of theta parameters |
| .nobars | Remove random effects terms from full formulas or calls |
| .parallel_default | Boilerplate parallel-handling function, modified from 'glmmTMB' |
| .re_format | Format random effects |
| .re_size | Calculates the size of the random effect vector implied by the model and the data |
| .set_cf | Set the coefficient vector |
| .set_vc | Set the parameters of the random effect covariance matrix |
| .sim_re | Simulates random effects vector from a tramME object |
| .th2vc | Convert from theta vector to vc matrix |
| .tramME2ctm | Create a corresponding ctm model for a tramME model |
| .vc2th | Convert from vc matrix to theta vector |
| AaregME | Mixed-effects version of 'Aareg' |
| 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.tramME | Duplicate a tramME object |
| duplicate.tramTMB | Create a duplicate of the tramTMB object |
| fe_terms | Create fixed effects data and initial parameters |
| 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 | ME version of tram::Lm |
| logLik.tramME | Get the log-likelihood of the model |
| lpterms | Generic method for extracting terms of the linear predictor |
| lpterms.tramME | Get inidvidual terms of the linear predictor and their confidence intervals |
| model.frame.tramME | Extract model frame from a tramME model |
| model.matrix.tramME | Model matrix for tramME mdoels |
| 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 |
| parboot.tramME | Do parametric bootsrap using a tarmME model |
| plot.trafo.tramME | Plotting method for 'trafo.tramME' objects |
| plot.tramME | Plotting method for tramME objects |
| PolrME | Mixed-effects version of '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 |
| residuals.LmME | Residuals of a LmME model |
| residuals.tramME | Residuals of a tramME model |
| re_terms | Create random effects data and initial paramaters |
| sigma.LmME | Extract the SD of the error term of an LmME model. |
| simulate.tramME | Simulate from a tramME model |
| summary.tramME | Summary method for tramME model |
| SurvregME | Mixed-effects version of 'Survreg' |
| trafo | Generic method for extracting baseline transformations |
| trafo.tramME | Get the baseline transformation function and its confidence interval |
| tramME_model | Create an object that defines a tramME_model |
| tramTMB | Create a tramTMB object |
| tramTMB_inputs | Create inputs of the tramTMB model |
| 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. |