Methods for stanmvreg objects

S3 methods for stanmvreg objects. There are also several methods (listed in See Also, below) with their own individual help pages. The main difference between these methods and the stanreg methods is that the methods described here generally include an additional argument m which allows the user to specify which submodel they wish to return the result for. If the argument m is set to NULL then the result will generally be a named list with each element of the list containing the result for one of the submodels.

# S3 method for stanmvreg
coef(object, m = NULL, ...)

# S3 method for stanmvreg
fitted(object, m = NULL, ...)

# S3 method for stanmvreg
residuals(object, m = NULL, ...)

# S3 method for stanmvreg
se(object, m = NULL, ...)

# S3 method for stanmvreg
formula(x, fixed.only = FALSE, random.only = FALSE, m = NULL, ...)

# S3 method for stanmvreg
update(object, formula., ..., evaluate = TRUE)

# S3 method for stanjm
update(object, formulaLong., formulaEvent., ..., evaluate = TRUE)

# S3 method for stanmvreg
fixef(object, m = NULL, remove_stub = TRUE, ...)

# S3 method for stanmvreg
ngrps(object, ...)

# S3 method for stanmvreg
ranef(object, m = NULL, ...)

# S3 method for stanmvreg
sigma(object, m = NULL, ...)

Arguments

object, x	A fitted model object returned by one of the multivariate rstanarm modelling functions. See stanreg-objects.
m	Integer specifying the number or name of the submodel
...	Ignored, except by the update method. See update.
fixed.only	A logical specifying whether to only retain the fixed effect part of the longitudinal submodel formulas
random.only	A logical specifying whether to only retain the random effect part of the longitudinal submodel formulas
formula.	An updated formula for the model. For a multivariate model formula. should be a list of formulas, as described for the formula argument in stan_mvmer.
evaluate	See update.
formulaLong., formulaEvent.	An updated formula for the longitudinal or event submodel, when object was estimated using stan_jm. For a multivariate joint model formulaLong. should be a list of formulas, as described for the formulaLong argument in stan_jm.
remove_stub	Logical specifying whether to remove the string identifying the submodel (e.g. y1|, y2|, Long1|, Long2|, Event|) from each of the parameter names.

Details

Most of these methods are similar to the methods defined for objects of class 'lm', 'glm', 'glmer', etc. However there are a few exceptions:

coef

Medians are used for point estimates. See the Point estimates section in print.stanmvreg for more details. coef returns a list equal to the length of the number of submodels. The first elements of the list are the coefficients from each of the fitted longitudinal submodels and are the same layout as those returned by coef method of the lme4 package, that is, the sum of the random and fixed effects coefficients for each explanatory variable for each level of each grouping factor. The final element of the returned list is a vector of fixed effect coefficients from the event submodel.

se

The se function returns standard errors based on mad. See the Uncertainty estimates section in print.stanmvreg for more details.

confint

Not supplied, since the posterior_interval function should be used instead to compute Bayesian uncertainty intervals.

residuals

Residuals are always of type "response" (not "deviance" residuals or any other type).

See also

• The print, summary, and prior_summary methods for stanmvreg objects for information on the fitted model.

• The plot method to plot estimates and diagnostics.

• The pp_check method for graphical posterior predictive checking of the longitudinal or glmer submodels.

• The ps_check method for graphical posterior predictive checking of the event submodel.

• The posterior_traj for predictions for the longitudinal submodel (for models estimated using stan_jm), as well as it's associated plot method.

• The posterior_survfit for predictions for the event submodel, including so-called "dynamic" predictions (for models estimated using stan_jm), as well as it's associated plot method.

• The posterior_predict for predictions for the glmer submodel (for models estimated using stan_mvmer).

• The posterior_interval for uncertainty intervals for model parameters.

• The loo, and log_lik methods for leave-one-out model comparison, and computing the log-likelihood of (possibly new) data.

• The as.matrix, as.data.frame, and as.array methods to access posterior draws.

Other S3 methods for stanmvreg objects, which have separate documentation, including print.stanmvreg, and summary.stanmvreg.

Also posterior_interval for an alternative to confint, and posterior_predict, posterior_traj and posterior_survfit for predictions based on the fitted joint model.