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# Part of the rstanarm package for estimating model parameters
# Copyright (C) 2015, 2016, 2017 Trustees of Columbia University
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#' Fitted model objects
#'
#' The \pkg{rstanarm} model-fitting functions return an object of class
#' \code{'stanreg'}, which is a list containing at a minimum the components listed
#' below. Each \code{stanreg} object will also have additional classes (e.g. 'aov',
#' 'betareg', 'glm', 'polr', etc.) and several additional components depending
#' on the model and estimation algorithm. \cr
#' \cr
#' Some additional details apply to models estimated using the \code{\link{stan_mvmer}}
#' or \code{\link{stan_jm}} modelling functions. The \code{\link{stan_mvmer}} modelling
#' function returns an object of class \code{'stanmvreg'}, which inherits the
#' \code{'stanreg'} class, but has a number of additional elements described in the
#' subsection below. The \code{\link{stan_jm}} modelling function returns an object of class
#' \code{'stanjm'}, which inherits both the \code{'stanmvreg'} and \code{'stanreg'}
#' classes, but has a number of additional elements described in the subsection below.
#' Both the \code{'stanjm'} and \code{'stanmvreg'} classes have several of their own
#' methods for situations in which the default \code{'stanreg'} methods are not
#' suitable; see the \strong{See Also} section below.
#'
#' @name stanreg-objects
#'
#' @section Elements for \code{stanreg} objects:
#' \describe{
#' \item{\code{coefficients}}{
#' Point estimates, as described in \code{\link{print.stanreg}}.
#' }
#' \item{\code{ses}}{
#' Standard errors based on \code{\link[stats]{mad}}, as described in
#' \code{\link{print.stanreg}}.
#' }
#' \item{\code{residuals}}{
#' Residuals of type \code{'response'}.
#' }
#' \item{\code{fitted.values}}{
#' Fitted mean values. For GLMs the linear predictors are transformed by the
#' inverse link function.
#' }
#' \item{\code{linear.predictors}}{
#' Linear fit on the link scale. For linear models this is the same as
#' \code{fitted.values}.
#' }
#' \item{\code{covmat}}{
#' Variance-covariance matrix for the coefficients based on draws from the
#' posterior distribution, the variational approximation, or the asymptotic
#' sampling distribution, depending on the estimation algorithm.
#' }
#' \item{\code{model,x,y}}{
#' If requested, the the model frame, model matrix and response variable used,
#' respectively.
#' }
#' \item{\code{family}}{
#' The \code{\link[stats]{family}} object used.
#' }
#' \item{\code{call}}{
#' The matched call.
#' }
#' \item{\code{formula}}{
#' The model \code{\link[stats]{formula}}.
#' }
#' \item{\code{data,offset,weights}}{
#' The \code{data}, \code{offset}, and \code{weights} arguments.
#' }
#' \item{\code{algorithm}}{
#' The estimation method used.
#' }
#' \item{\code{prior.info}}{
#' A list with information about the prior distributions used.
#' }
#' \item{\code{stanfit,stan_summary}}{
#' The object of \code{\link[rstan]{stanfit-class}} returned by RStan and a
#' matrix of various summary statistics from the stanfit object.
#' }
#' \item{\code{rstan_version}}{
#' The version of the \pkg{rstan} package that was used to fit the model.
#' }
#' }
#'
#' @section Elements for \code{stanmvreg} objects:
#' \describe{
#' The \code{stanmvreg} objects contain the majority of the elements described
#' above for \code{stanreg} objects, but in most cases these will be a list with each
#' elements of the list correponding to one of the submodels (for example,
#' the \code{family} element of a \code{stanmvreg} object will be a list with each
#' element of the list containing the \code{\link[stats]{family}} object for one
#' submodel). In addition, \code{stanmvreg} objects contain the following additional
#' elements:
#' \item{\code{cnms}}{
#' The names of the grouping factors and group specific parameters, collapsed
#' across the longitudinal or glmer submodels.
#' }
#' \item{\code{flevels}}{
#' The unique factor levels for each grouping factor, collapsed across the
#' longitudinal or glmer submodels.
#' }
#' \item{\code{n_markers}}{
#' The number of longitudinal or glmer submodels.
#' }
#' \item{\code{n_yobs}}{
#' The number of observations for each longitudinal or glmer submodel.
#' }
#' \item{\code{n_grps}}{
#' The number of levels for each grouping factor (for models estimated using
#' \code{\link{stan_jm}}, this will be equal to \code{n_subjects} if the
#' individual is the only grouping factor).
#' }
#' \item{\code{runtime}}{
#' The time taken to fit the model (in minutes).
#' }
#' }
#'
#' @section Additional elements for \code{stanjm} objects:
#' \describe{
#' The \code{stanjm} objects contain the elements described above for
#' \code{stanmvreg} objects, but also contain the following additional
#' elements:
#' \item{\code{id_var,time_var}}{
#' The names of the variables distinguishing between individuals, and
#' representing time in the longitudinal submodel.
#' }
#' \item{\code{n_subjects}}{
#' The number of individuals.
#' }
#' \item{\code{n_events}}{
#' The number of non-censored events.
#' }
#' \item{\code{eventtime,status}}{
#' The event (or censoring) time and status indicator for each individual.
#' }
#' \item{\code{basehaz}}{
#' A list containing information about the baseline hazard.
#' }
#' \item{\code{assoc}}{
#' An array containing information about the association structure.
#' }
#' \item{\code{epsilon}}{
#' The width of the one-sided difference used to numerically evaluate the
#' slope of the longitudinal trajectory; only relevant if a slope-based
#' association structure was specified (e.g. etaslope, muslope, etc).
#' }
#' \item{\code{qnodes}}{
#' The number of Gauss-Kronrod quadrature nodes used to evaluate the
#' cumulative hazard in the joint likelihood function.
#' }
#' }
#'
#' @note The \code{\link{stan_biglm}} function is an exception. It returns a
#' \link[rstan:stanfit-class]{stanfit} object rather than a stanreg object.
#'
#' @seealso \code{\link{stanreg-methods}}, \code{\link{stanmvreg-methods}}
#'
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