Table 2.

Additional functions with descriptions that can be applied to objects of class mjoint^a

Function(s)	Returns
logLik, AIC, BIC	the log-likelihood, Akaike information criterion and Bayesian information criterion statistics, respectively
coef, fixef	the fixed effects parameter estimates
ranef	the BLUPs (and optional standard errors)
printa, summaryc	short and long model summary outputs, respectively
fitted, resid	the fitted values and raw residuals from the multivariate LMM sub-model, respectively
plot b	the MCEM algorithm convergence trace plots
sigma	the residual standard errors from the LMM sub-model
vcov	the variance-covariance matrix of the main parameters of the fitted model (except the baseline hazard)
getVarCov	the random effects variance-covariance matrix
confint	the confidence intervals based on asymptotic normality
update	specific parts of a fitted model can be updated, e.g. by adding or removing terms from a sub-model, and then re-fitted
sampleData	sample data (with or without replacement) from a joint model

^aprint() also applies to objects of class summary.mjoint and bootSE inheriting from the summary() and bootSE() functions, respectively

^bplot() also accepts objects of class ranef.mjoint inheriting from the ranef() function, which displays a caterpillar plot (with 95% prediction intervals) for each random effect

^csummary() can also take the optional argument of an object of class bootSE inheriting from the function bootSE(), which overrides the approximate SEs and CIs with those from a bootstrap estimation routine