R/stan_jm.R

Defines functions stan_jm

Documented in stan_jm

# Part of the rstanarm package for estimating model parameters
# Copyright (C) 2013, 2014, 2015, 2016, 2017 Trustees of Columbia University
# Copyright (C) 2016, 2017 Sam Brilleman
# 
# 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.

#' Bayesian joint longitudinal and time-to-event models via Stan
#' 
#' \if{html}{\figure{stanlogo.png}{options: width="25px" alt="http://mc-stan.org/about/logo/"}}
#' Fits a shared parameter joint model for longitudinal and time-to-event 
#' (e.g. survival) data under a Bayesian framework using Stan.
#' 
#' @export
#' @template args-dots
#' @template args-prior_PD
#' @template args-algorithm
#' @template args-adapt_delta
#' @template args-max_treedepth
#' @template args-QR
#' @template args-sparse
#' 
#' @param formulaLong A two-sided linear formula object describing both the 
#'   fixed-effects and random-effects parts of the longitudinal submodel,
#'   similar in vein to formula specification in the \strong{lme4} package
#'   (see \code{\link[lme4]{glmer}} or the \strong{lme4} vignette for details). 
#'   Note however that the double bar (\code{||}) notation is not allowed 
#'   when specifying the random-effects parts of the formula, and neither
#'   are nested grouping factors (e.g. \code{(1 | g1/g2))} or 
#'   \code{(1 | g1:g2)}, where \code{g1}, \code{g2} are grouping factors. 
#'   For a multivariate joint model (i.e. more than one longitudinal marker) 
#'   this should be a list of such formula objects, with each element
#'   of the list providing the formula for one of the longitudinal submodels.
#' @param dataLong A data frame containing the variables specified in
#'   \code{formulaLong}. If fitting a multivariate joint model, then this can
#'   be either a single data frame which contains the data for all 
#'   longitudinal submodels, or it can be a list of data frames where each
#'   element of the list provides the data for one of the longitudinal 
#'   submodels.
#' @param formulaEvent A two-sided formula object describing the event
#'   submodel. The left hand side of the formula should be a \code{Surv()} 
#'   object. See \code{\link[survival]{Surv}}.
#' @param dataEvent A data frame containing the variables specified in
#'   \code{formulaEvent}.
#' @param time_var A character string specifying the name of the variable 
#'   in \code{dataLong} which represents time.
#' @param id_var A character string specifying the name of the variable in
#'   \code{dataLong} which distinguishes between individuals. This can be
#'   left unspecified if there is only one grouping factor (which is assumed
#'   to be the individual). If there is more than one grouping factor (i.e.
#'   clustering beyond the level of the individual) then the \code{id_var}
#'   argument must be specified.
#' @param family The family (and possibly also the link function) for the 
#'   longitudinal submodel(s). See \code{\link[lme4]{glmer}} for details. 
#'   If fitting a multivariate joint model, then this can optionally be a
#'   list of families, in which case each element of the list specifies the
#'   family for one of the longitudinal submodels.
#' @param assoc A character string or character vector specifying the joint
#'   model association structure. Possible association structures that can
#'   be used include: "etavalue" (the default); "etaslope"; "etaauc"; 
#'   "muvalue"; "muslope"; "muauc"; "shared_b"; "shared_coef"; or "null". 
#'   These are described in the \strong{Details} section below. For a multivariate 
#'   joint model, different association structures can optionally be used for 
#'   each longitudinal submodel by specifying a list of character
#'   vectors, with each element of the list specifying the desired association 
#'   structure for one of the longitudinal submodels. Specifying \code{assoc = NULL}
#'   will fit a joint model with no association structure (equivalent  
#'   to fitting separate longitudinal and time-to-event models). It is also 
#'   possible to include interaction terms between the association term 
#'   ("etavalue", "etaslope", "muvalue", "muslope") and observed data/covariates. 
#'   It is also possible, when fitting a multivariate joint model, to include 
#'   interaction terms between the association terms ("etavalue" or "muvalue") 
#'   corresponding to the different longitudinal outcomes. See the 
#'   \strong{Details} section as well as the \strong{Examples} below.
#' @param lag_assoc A non-negative scalar specifying the time lag that should be
#'   used for the association structure. That is, the hazard of the event at 
#'   time \emph{t} will be assumed to be associated with the value/slope/auc of 
#'   the longitudinal marker at time \emph{t-u}, where \emph{u} is the time lag.
#'   If fitting a multivariate joint model, then a different time lag can be used
#'   for each longitudinal marker by providing a numeric vector of lags, otherwise
#'   if a scalar is provided then the specified time lag will be used for all 
#'   longitudinal markers. Note however that only one time lag  can be specified 
#'   for linking each longitudinal marker to the 
#'   event, and that that time lag will be used for all association structure
#'   types (e.g. \code{"etavalue"}, \code{"etaslope"}, \code{"etaauc"}, 
#'   \code{"muvalue"}, etc) that are specified for that longitudinal marker in
#'   the \code{assoc} argument.
#' @param grp_assoc Character string specifying the method for combining information
#'   across lower level units clustered within an individual when forming the
#'   association structure. This is only relevant when a grouping factor is  
#'   specified in \code{formulaLong} that corresponds to clustering within 
#'   individuals. This can be specified as either \code{"sum"}, \code{mean},
#'   \code{"min"} or \code{"max"}. For example, specifying \code{grp_assoc = "sum"}
#'   indicates that the association structure should be based on a summation across 
#'   the lower level units clustered within an individual, or specifying
#'   \code{grp_assoc = "mean"}  indicates that the association structure 
#'   should be based on the mean (i.e. average) taken across the lower level 
#'   units clustered within an individual.
#'   So, for example, specifying \code{assoc = "muvalue"} 
#'   and \code{grp_assoc = "sum"} would mean that the log hazard at time 
#'   \emph{t} for individual \emph{i} would be linearly related to the sum of
#'   the expected values at time \emph{t} for each of the lower level 
#'   units (which may be for example tumor lesions) clustered within that 
#'   individual. 
#' @param basehaz A character string indicating which baseline hazard to use
#'   for the event submodel. Options are a B-splines approximation estimated 
#'   for the log baseline hazard (\code{"bs"}, the default), a Weibull 
#'   baseline hazard (\code{"weibull"}), or a piecewise
#'   constant baseline hazard (\code{"piecewise"}). (Note however that there  
#'   is currently limited post-estimation functionality available for
#'   models estimated using a piecewise constant baseline hazard).
#' @param basehaz_ops A named list specifying options related to the baseline
#'   hazard. Currently this can include: \cr
#'   \describe{
#'     \item{\code{df}}{A positive integer specifying the degrees of freedom 
#'     for the B-splines if \code{basehaz = "bs"}, or the number of
#'     intervals used for the piecewise constant baseline hazard if 
#'     \code{basehaz = "piecewise"}. The default is 6.}
#'     \item{\code{knots}}{An optional numeric vector specifying the internal knot 
#'     locations for the B-splines if \code{basehaz = "bs"}, or the 
#'     internal cut-points for defining intervals of the piecewise constant 
#'     baseline hazard if \code{basehaz = "piecewise"}. Knots cannot be
#'     specified if \code{df} is specified. If not specified, then the 
#'     default is to use \code{df - 4} knots if \code{basehaz = "bs"},
#'     or \code{df - 1} knots if \code{basehaz = "piecewise"}, which are
#'     placed at equally spaced percentiles of the distribution of
#'     observed event times.}
#'   }
#' @param epsilon The half-width of the central difference used to numerically
#'   calculate the derivate when the \code{"etaslope"} association structure 
#'   is used.   
#' @param qnodes The number of nodes to use for the Gauss-Kronrod quadrature
#'   that is used to evaluate the cumulative hazard in the likelihood function. 
#'   Options are 15 (the default), 11 or 7.
#' @param weights Experimental and should be used with caution. The 
#'   user can optionally supply a 2-column data frame containing a set of
#'   'prior weights' to be used in the estimation process. The data frame should
#'   contain two columns: the first containing the IDs for each individual, and 
#'   the second containing the corresponding weights. The data frame should only
#'   have one row for each individual; that is, weights should be constant 
#'   within individuals.
#' @param init The method for generating the initial values for the MCMC.
#'   The default is \code{"prefit"}, which uses those obtained from 
#'   fitting separate longitudinal and time-to-event models prior to 
#'   fitting the joint model. The separate longitudinal model is a 
#'   (possibly multivariate) generalised linear mixed 
#'   model estimated using variational bayes. This is achieved via the 
#'   \code{\link{stan_mvmer}} function with \code{algorithm = "meanfield"}.
#'   The separate Cox model is estimated using \code{\link[survival]{coxph}}. 
#'   This is achieved
#'   using the and time-to-event models prior  
#'   to fitting the joint model. The separate models are estimated using the
#'   \code{\link[lme4]{glmer}} and \code{\link[survival]{coxph}} functions.
#'   This should provide reasonable initial values which should aid the 
#'   MCMC sampler. Parameters that cannot be obtained from 
#'   fitting separate longitudinal and time-to-event models are initialised 
#'   using the "random" method for \code{\link[rstan]{stan}}.
#'   However it is recommended that any final analysis should ideally
#'   be performed with several MCMC chains each initiated from a different
#'   set of initial values; this can be obtained by setting
#'   \code{init = "random"}. In addition, other possibilities for specifying 
#'   \code{init} are the same as those described for \code{\link[rstan]{stan}}.  
#' @param priorLong,priorEvent,priorEvent_assoc The prior distributions for the 
#'   regression coefficients in the longitudinal submodel(s), event submodel,
#'   and the association parameter(s). Can be a call to one of the various functions 
#'   provided by \pkg{rstanarm} for specifying priors. The subset of these functions 
#'   that can be used for the prior on the coefficients can be grouped into several 
#'   "families":
#'   
#'   \tabular{ll}{
#'     \strong{Family} \tab \strong{Functions} \cr 
#'     \emph{Student t family} \tab \code{normal}, \code{student_t}, \code{cauchy} \cr 
#'     \emph{Hierarchical shrinkage family} \tab \code{hs}, \code{hs_plus} \cr 
#'     \emph{Laplace family} \tab \code{laplace}, \code{lasso} \cr
#'   }
#'   
#'   See the \link[=priors]{priors help page} for details on the families and 
#'   how to specify the arguments for all of the functions in the table above.
#'   To omit a prior ---i.e., to use a flat (improper) uniform prior---
#'   \code{prior} can be set to \code{NULL}, although this is rarely a good
#'   idea.
#'   
#'   \strong{Note:} Unless \code{QR=TRUE}, if \code{prior} is from the Student t
#'   family or Laplace family, and if the \code{autoscale} argument to the 
#'   function used to specify the prior (e.g. \code{\link{normal}}) is left at 
#'   its default and recommended value of \code{TRUE}, then the default or 
#'   user-specified prior scale(s) may be adjusted internally based on the scales
#'   of the predictors. See the \link[=priors]{priors help page} for details on
#'   the rescaling and the \code{\link{prior_summary}} function for a summary of
#'   the priors used for a particular model.
#' @param priorLong_intercept,priorEvent_intercept The prior distributions  
#'   for the intercepts in the longitudinal submodel(s) and event submodel. 
#'   Can be a call to \code{normal}, \code{student_t} or 
#'   \code{cauchy}. See the \link[=priors]{priors help page} for details on 
#'   these functions. To omit a prior on the intercept ---i.e., to use a flat
#'   (improper) uniform prior--- \code{prior_intercept} can be set to
#'   \code{NULL}.
#'   
#'   \strong{Note:} The prior distribution for the intercept is set so it
#'   applies to the value when all predictors are centered. Moreover, 
#'   note that a prior is only placed on the intercept for the event submodel
#'   when a Weibull baseline hazard has been specified. For the B-splines and
#'   piecewise constant baseline hazards there is not intercept parameter that
#'   is given a prior distribution; an intercept parameter will be shown in 
#'   the output for the fitted model, but this just corresponds to the 
#'   necessary post-estimation adjustment in the linear predictor due to the
#'   centering of the predictiors in the event submodel.
#'   
#' @param priorLong_aux The prior distribution for the "auxiliary" parameters
#'   in the longitudinal submodels (if applicable). 
#'   The "auxiliary" parameter refers to a different parameter 
#'   depending on the \code{family}. For Gaussian models \code{priorLong_aux} 
#'   controls \code{"sigma"}, the error 
#'   standard deviation. For negative binomial models \code{priorLong_aux} controls 
#'   \code{"reciprocal_dispersion"}, which is similar to the 
#'   \code{"size"} parameter of \code{\link[stats]{rnbinom}}:
#'   smaller values of \code{"reciprocal_dispersion"} correspond to 
#'   greater dispersion. For gamma models \code{priorLong_aux} sets the prior on 
#'   to the \code{"shape"} parameter (see e.g., 
#'   \code{\link[stats]{rgamma}}), and for inverse-Gaussian models it is the 
#'   so-called \code{"lambda"} parameter (which is essentially the reciprocal of
#'   a scale parameter). Binomial and Poisson models do not have auxiliary 
#'   parameters. 
#'   
#'   \code{priorLong_aux} can be a call to \code{exponential} to 
#'   use an exponential distribution, or \code{normal}, \code{student_t} or 
#'   \code{cauchy}, which results in a half-normal, half-t, or half-Cauchy 
#'   prior. See \code{\link{priors}} for details on these functions. To omit a 
#'   prior ---i.e., to use a flat (improper) uniform prior--- set 
#'   \code{priorLong_aux} to \code{NULL}.
#'   
#'   If fitting a multivariate joint model, you have the option to
#'   specify a list of prior distributions, however the elements of the list
#'   that correspond to any longitudinal submodel which does not have an 
#'   auxiliary parameter will be ignored. 
#' @param priorEvent_aux The prior distribution for the "auxiliary" parameters
#'   in the event submodel. The "auxiliary" parameters refers to different  
#'   parameters depending on the baseline hazard. For \code{basehaz = "weibull"}
#'   the auxiliary parameter is the Weibull shape parameter. For 
#'   \code{basehaz = "bs"} the auxiliary parameters are the coefficients for the
#'   B-spline approximation to the log baseline hazard.
#'   For \code{basehaz = "piecewise"} the auxiliary parameters are the piecewise
#'   estimates of the log baseline hazard.
#' @param prior_covariance Cannot be \code{NULL}; see \code{\link{priors}} for
#'   more information about the prior distributions on covariance matrices.
#'   Note however that the default prior for covariance matrices in 
#'   \code{stan_jm} is slightly different to that in \code{\link{stan_glmer}} 
#'   (the details of which are described on the \code{\link{priors}} page).
#'   
#' @details The \code{stan_jm} function can be used to fit a joint model (also 
#'   known as a shared parameter model) for longitudinal and time-to-event data 
#'   under a Bayesian framework. The underlying
#'   estimation is carried out using the Bayesian C++ package Stan 
#'   (\url{http://mc-stan.org/}). \cr
#'   \cr 
#'   The joint model may be univariate (with only one longitudinal submodel) or
#'   multivariate (with more than one longitudinal submodel). 
#'   For the longitudinal submodel a (possibly multivariate) generalised linear 
#'   mixed model is assumed with any of the \code{\link[stats]{family}} choices 
#'   allowed by \code{\link[lme4]{glmer}}. If a multivariate joint model is specified 
#'   (by providing a list of formulas in the \code{formulaLong} argument), then
#'   the multivariate longitudinal submodel consists of a multivariate generalized  
#'   linear model (GLM) with group-specific terms that are assumed to be correlated
#'   across the different GLM submodels. That is, within
#'   a grouping factor (for example, patient ID) the group-specific terms are
#'   assumed to be correlated across the different GLM submodels. It is 
#'   possible to specify a different outcome type (for example a different
#'   family and/or link function) for each of the GLM submodels, by providing
#'   a list of \code{\link[stats]{family}} objects in the \code{family} 
#'   argument. Multi-level 
#'   clustered data are allowed, and that additional clustering can occur at a 
#'   level higher than the individual-level (e.g. patients clustered within 
#'   clinics), or at a level lower than the individual-level (e.g. tumor lesions
#'   clustered within patients). If the clustering occurs at a level lower than
#'   the individual, then the user needs to indicate how the lower level 
#'   clusters should be handled when forming the association structure between
#'   the longitudinal and event submodels (see the \code{grp_assoc} argument
#'   described above). \cr
#'   \cr
#'   For the event submodel a parametric
#'   proportional hazards model is assumed. The baseline hazard can be estimated 
#'   using either a cubic B-splines approximation (\code{basehaz = "bs"}, the
#'   default), a Weibull distribution (\code{basehaz = "weibull"}), or a
#'   piecewise constant baseline hazard (\code{basehaz = "piecewise"}).
#'   If the B-spline or piecewise constant baseline hazards are used, 
#'   then the degrees of freedom or the internal knot locations can be 
#'   (optionally) specified. If
#'   the degrees of freedom are specified (through the \code{df} argument) then
#'   the knot locations are automatically generated based on the 
#'   distribution of the observed event times (not including censoring times). 
#'   Otherwise internal knot locations can be specified 
#'   directly through the \code{knots} argument. If neither \code{df} or
#'   \code{knots} is specified, then the default is to set \code{df} equal to 6.
#'   It is not possible to specify both \code{df} and \code{knots}. \cr
#'   \cr
#'   Time-varying covariates are allowed in both the 
#'   longitudinal and event submodels. These should be specified in the data 
#'   in the same way as they normally would when fitting a separate 
#'   longitudinal model using \code{\link[lme4]{lmer}} or a separate 
#'   time-to-event model using \code{\link[survival]{coxph}}. These time-varying
#'   covariates should be exogenous in nature, otherwise they would perhaps 
#'   be better specified as an additional outcome (i.e. by including them as an 
#'   additional longitudinal outcome in the joint model). \cr
#'   \cr
#'   Bayesian estimation of the joint model is performed via MCMC. The Bayesian  
#'   model includes independent priors on the 
#'   regression coefficients for both the longitudinal and event submodels, 
#'   including the association parameter(s) (in much the same way as the
#'   regression parameters in \code{\link{stan_glm}}) and
#'   priors on the terms of a decomposition of the covariance matrices of the
#'   group-specific parameters. 
#'   See \code{\link{priors}} for more information about the priors distributions
#'   that are available. \cr
#'   \cr
#'   Gauss-Kronrod quadrature is used to numerically evaluate the integral  
#'   over the cumulative hazard in the likelihood function for the event submodel.
#'   The accuracy of the numerical approximation can be controlled using the
#'   number of quadrature nodes, specified through the \code{qnodes} 
#'   argument. Using a higher number of quadrature nodes will result in a more 
#'   accurate approximation.
#'   
#'   \subsection{Association structures}{
#'   The association structure for the joint model can be based on any of the 
#'   following parameterisations: 
#'     \itemize{
#'       \item current value of the linear predictor in the 
#'         longitudinal submodel (\code{"etavalue"}) 
#'       \item first derivative (slope) of the linear predictor in the 
#'         longitudinal submodel (\code{"etaslope"}) 
#'       \item the area under the curve of the linear predictor in the 
#'         longitudinal submodel (\code{"etaauc"}) 
#'       \item current expected value of the longitudinal submodel 
#'         (\code{"muvalue"})
#'       \item the area under the curve of the expected value from the 
#'         longitudinal submodel (\code{"muauc"})
#'       \item shared individual-level random effects (\code{"shared_b"}) 
#'       \item shared individual-level random effects which also incorporate 
#'         the corresponding fixed effect as well as any corresponding 
#'         random effects for clustering levels higher than the individual)
#'         (\code{"shared_coef"})
#'       \item interactions between association terms and observed data/covariates
#'         (\code{"etavalue_data"}, \code{"etaslope_data"}, \code{"muvalue_data"}, 
#'         \code{"muslope_data"}). These are described further below.
#'       \item interactions between association terms corresponding to different 
#'         longitudinal outcomes in a multivariate joint model 
#'         (\code{"etavalue_etavalue(#)"}, \code{"etavalue_muvalue(#)"},
#'         \code{"muvalue_etavalue(#)"}, \code{"muvalue_muvalue(#)"}). These
#'         are described further below.      
#'       \item no association structure (equivalent to fitting separate 
#'         longitudinal and event models) (\code{"null"} or \code{NULL}) 
#'     }
#'   More than one association structure can be specified, however,
#'   not all possible combinations are allowed.   
#'   Note that for the lagged association structures baseline values (time = 0) 
#'   are used for the instances 
#'   where the time lag results in a time prior to baseline. When using the 
#'   \code{"etaauc"} or \code{"muauc"} association structures, the area under
#'   the curve is evaluated using Gauss-Kronrod quadrature with 15 quadrature 
#'   nodes. By default, \code{"shared_b"} and \code{"shared_coef"} contribute 
#'   all random effects to the association structure; however, a subset of the 
#'   random effects can be chosen by specifying their indices between parentheses 
#'   as a suffix, for example, \code{"shared_b(1)"} or \code{"shared_b(1:3)"} or 
#'   \code{"shared_b(1,2,4)"}, and so on. \cr
#'   \cr 
#'   In addition, several association terms (\code{"etavalue"}, \code{"etaslope"},
#'   \code{"muvalue"}, \code{"muslope"}) can be interacted with observed 
#'   data/covariates. To do this, use the association term's main handle plus a
#'   suffix of \code{"_data"} then followed by the model matrix formula in 
#'   parentheses. For example if we had a variable in our dataset for gender 
#'   named \code{sex} then we might want to obtain different estimates for the 
#'   association between the current slope of the marker and the risk of the 
#'   event for each gender. To do this we would specify 
#'   \code{assoc = c("etaslope", "etaslope_data(~ sex)")}. \cr
#'   \cr
#'   It is also possible, when fitting  a multivariate joint model, to include 
#'   interaction terms between the association terms themselves (this only
#'   applies for interacting \code{"etavalue"} or \code{"muvalue"}). For example, 
#'   if we had a joint model with two longitudinal markers, we could specify 
#'   \code{assoc = list(c("etavalue", "etavalue_etavalue(2)"), "etavalue")}.
#'   The first element of list says we want to use the value of the linear
#'   predictor for the first marker, as well as it's interaction with the
#'   value of the linear predictor for the second marker. The second element of 
#'   the list says we want to also include the expected value of the second marker 
#'   (i.e. as a "main effect"). Therefore, the linear predictor for the event 
#'   submodel would include the "main effects" for each marker as well as their
#'   interaction. \cr
#'   \cr
#'   There are additional examples in the \strong{Examples} section below.
#'   }
#' 
#' @return A \link[=stanreg-objects]{stanjm} object is returned.
#' 
#' @seealso \code{\link{stanreg-objects}}, \code{\link{stanmvreg-methods}}, 
#'   \code{\link{print.stanmvreg}}, \code{\link{summary.stanmvreg}},
#'   \code{\link{posterior_traj}}, \code{\link{posterior_survfit}}, 
#'   \code{\link{posterior_predict}}, \code{\link{posterior_interval}},
#'   \code{\link{pp_check}}, \code{\link{ps_check}}, \code{\link{stan_mvmer}}.
#' 
#' @examples
#' \donttest{
#' #####
#' # Univariate joint model, with association structure based on the 
#' # current value of the linear predictor
#' f1 <- stan_jm(formulaLong = logBili ~ year + (1 | id), 
#'               dataLong = pbcLong,
#'               formulaEvent = Surv(futimeYears, death) ~ sex + trt, 
#'               dataEvent = pbcSurv,
#'               time_var = "year",
#'               # this next line is only to keep the example small in size!
#'               chains = 1, cores = 1, seed = 12345, iter = 1000)
#' print(f1) 
#' summary(f1) 
#'         
#' #####
#' # Univariate joint model, with association structure based on the 
#' # current value and slope of the linear predictor
#' f2 <- stan_jm(formulaLong = logBili ~ year + (year | id), 
#'               dataLong = pbcLong,
#'               formulaEvent = Surv(futimeYears, death) ~ sex + trt, 
#'               dataEvent = pbcSurv,
#'               assoc = c("etavalue", "etaslope"),
#'               time_var = "year",
#'               chains = 1, cores = 1, seed = 12345, iter = 1000)
#' print(f2)  
#' 
#' #####
#' # Univariate joint model, with association structure based on the 
#' # lagged value of the linear predictor, where the lag is 2 time 
#' # units (i.e. 2 years in this example)
#' f3 <- stan_jm(formulaLong = logBili ~ year + (1 | id), 
#'               dataLong = pbcLong,
#'               formulaEvent = Surv(futimeYears, death) ~ sex + trt, 
#'               dataEvent = pbcSurv,
#'               time_var = "year",
#'               assoc = "etavalue", lag_assoc = 2,
#'               chains = 1, cores = 1, seed = 12345, iter = 1000)
#' print(f3) 
#' 
#' #####
#' # Univariate joint model, where the association structure includes 
#' # interactions with observed data. Here we specify that we want to use 
#' # an association structure based on the current value of the linear 
#' # predictor from the longitudinal submodel (i.e. "etavalue"), but we 
#' # also want to interact this with the treatment covariate (trt) from
#' # pbcLong data frame, so that we can estimate a different association 
#' # parameter (i.e. estimated effect of log serum bilirubin on the log 
#' # hazard of death) for each treatment group
#' f4 <- stan_jm(formulaLong = logBili ~ year + (1 | id), 
#'               dataLong = pbcLong,
#'               formulaEvent = Surv(futimeYears, death) ~ sex + trt, 
#'               dataEvent = pbcSurv,
#'               time_var = "year",
#'               assoc = c("etavalue", "etavalue_data(~ trt)"),
#'               chains = 1, cores = 1, seed = 12345, iter = 1000)
#' print(f4)
#' 
#' ######
#' # Multivariate joint model, with association structure based 
#' # on the current value and slope of the linear predictor in the 
#' # first longitudinal submodel and the area under the marker 
#' # trajectory for the second longitudinal submodel
#' mv1 <- stan_jm(
#'         formulaLong = list(
#'           logBili ~ year + (1 | id), 
#'           albumin ~ sex + year + (year | id)),
#'         dataLong = pbcLong,
#'         formulaEvent = Surv(futimeYears, death) ~ sex + trt, 
#'         dataEvent = pbcSurv,
#'         assoc = list(c("etavalue", "etaslope"), "etaauc"), 
#'         time_var = "year",
#'         chains = 1, cores = 1, seed = 12345, iter = 100)
#' print(mv1)
#' 
#' #####
#' # Multivariate joint model, where the association structure is formed by 
#' # including the expected value of each longitudinal marker (logBili and 
#' # albumin) in the linear predictor of the event submodel, as well as their 
#' # interaction effect (i.e. the interaction between the two "etavalue" terms). 
#' # Note that whether such an association structure based on a marker by 
#' # marker interaction term makes sense will depend on the context of your 
#' # application -- here we just show it for demostration purposes).
#' mv2 <- stan_jm(
#'         formulaLong = list(
#'           logBili ~ year + (1 | id), 
#'           albumin ~ sex + year + (year | id)),
#'         dataLong = pbcLong,
#'         formulaEvent = Surv(futimeYears, death) ~ sex + trt, 
#'         dataEvent = pbcSurv,
#'         assoc = list(c("etavalue", "etavalue_etavalue(2)"), "etavalue"),
#'         time_var = "year", 
#'         chains = 1, cores = 1, seed = 12345, iter = 100)
#'         
#' #####
#' # Multivariate joint model, with one bernoulli marker and one
#' # Gaussian marker. We will artificially create the bernoulli
#' # marker by dichotomising log serum bilirubin
#' pbcLong$ybern <- as.integer(pbcLong$logBili >= mean(pbcLong$logBili))
#' mv3 <- stan_jm(
#'         formulaLong = list(
#'           ybern ~ year + (1 | id), 
#'           albumin ~ sex + year + (year | id)),
#'         dataLong = pbcLong,
#'         formulaEvent = Surv(futimeYears, death) ~ sex + trt, 
#'         dataEvent = pbcSurv,
#'         family = list(binomial, gaussian),
#'         time_var = "year", 
#'         chains = 1, cores = 1, seed = 12345, iter = 1000)
#' }
#' 
stan_jm <- function(formulaLong, dataLong, formulaEvent, dataEvent, time_var, 
                    id_var, family = gaussian, assoc = "etavalue", 
                    lag_assoc = 0, grp_assoc, epsilon = 1E-5,
                    basehaz = c("bs", "weibull", "piecewise"), basehaz_ops, 
                    qnodes = 15, init = "prefit", weights,	
                    priorLong = normal(), priorLong_intercept = normal(), 
                    priorLong_aux = cauchy(0, 5), priorEvent = normal(), 
                    priorEvent_intercept = normal(), priorEvent_aux = cauchy(),
                    priorEvent_assoc = normal(), prior_covariance = lkj(), 
                    prior_PD = FALSE, algorithm = c("sampling", "meanfield", "fullrank"), 
                    adapt_delta = NULL, max_treedepth = 10L, QR = FALSE, 
                    sparse = FALSE, ...) {
  
  #-----------------------------
  # Pre-processing of arguments
  #-----------------------------  
  
  # Set seed if specified
  dots <- list(...)
  if ("seed" %in% names(dots))
    set.seed(dots$seed)
  
  algorithm <- match.arg(algorithm)
  basehaz   <- match.arg(basehaz)
  
  if (missing(basehaz_ops)) basehaz_ops <- NULL
  if (missing(weights))     weights     <- NULL
  if (missing(id_var))      id_var      <- NULL
  if (missing(time_var))    time_var    <- NULL
  if (missing(grp_assoc))   grp_assoc   <- NULL

  if (!is.null(weights)) 
    stop("'weights' are not yet implemented.")
  if (QR)               
    stop("'QR' decomposition is not yet implemented.")
  if (sparse)
    stop("'sparse' option is not yet implemented.")
  
  if (is.null(time_var))
    stop("'time_var' must be specified.")

  # Formula
  formulaLong <- validate_arg(formulaLong, "formula"); M <- length(formulaLong)
	if (M > 3L)
	  stop("'stan_jm' is currently limited to a maximum of 3 longitudinal outcomes.")
  
  # Data
  dataLong <- validate_arg(dataLong, "data.frame", validate_length = M)  
  dataEvent <- as.data.frame(dataEvent)

  # Family
  ok_family_classes <- c("function", "family", "character")
  ok_families <- c("binomial", "gaussian", "Gamma", 
                   "inverse.gaussian", "poisson", "neg_binomial_2")
  family <- validate_arg(family, ok_family_classes, validate_length = M)
  family <- lapply(family, validate_famlink, ok_families)
  
  # Assoc
  ok_assoc_classes <- c("NULL", "character")
  assoc <- validate_arg(assoc, ok_assoc_classes, validate_length = M)

  # Is priorLong* already a list?
  priorLong <- broadcast_prior(priorLong, M)
  priorLong_intercept <- broadcast_prior(priorLong_intercept, M)
  priorLong_aux <- broadcast_prior(priorLong_aux, M)
 
  #-----------
  # Fit model
  #-----------
  
  stanfit <- stan_jm.fit(formulaLong = formulaLong, dataLong = dataLong, 
                         formulaEvent = formulaEvent, dataEvent = dataEvent, 
                         time_var = time_var, id_var = id_var, family = family,
                         assoc = assoc, lag_assoc = lag_assoc, grp_assoc = grp_assoc, 
                         epsilon = epsilon, basehaz = basehaz, basehaz_ops = basehaz_ops, 
                         qnodes = qnodes, init = init, weights = weights, 
                         priorLong = priorLong, 
                         priorLong_intercept = priorLong_intercept, 
                         priorLong_aux = priorLong_aux, 
                         priorEvent = priorEvent, 
                         priorEvent_intercept = priorEvent_intercept, 
                         priorEvent_aux = priorEvent_aux, 
                         priorEvent_assoc = priorEvent_assoc, 
                         prior_covariance = prior_covariance, prior_PD = prior_PD, 
                         algorithm = algorithm, adapt_delta = adapt_delta, 
                         max_treedepth = max_treedepth, QR = QR, sparse = sparse, ...)
  if (algorithm != "optimizing" && !is(stanfit, "stanfit")) return(stanfit)
  y_mod <- attr(stanfit, "y_mod")
  e_mod <- attr(stanfit, "e_mod")
  a_mod <- attr(stanfit, "a_mod")
  cnms  <- attr(stanfit, "cnms")
  flevels <- attr(stanfit, "flevels")
  assoc <- attr(stanfit, "assoc")
  id_var <- attr(stanfit, "id_var")
  basehaz    <- attr(stanfit, "basehaz")
  grp_stuff  <- attr(stanfit, "grp_stuff")
  prior_info <- attr(stanfit, "prior_info")
  stanfit <- drop_attributes(stanfit, "y_mod", "e_mod", "a_mod", "cnms", 
                             "flevels", "assoc", "id_var", "basehaz", 
                             "grp_stuff", "prior_info")
  
  terms <- c(fetch(y_mod, "terms"), list(terms(e_mod$mod)))
  n_yobs <- fetch_(y_mod, "x", "N")
  n_grps <- sapply(flevels, n_distinct)
  n_subjects <- e_mod$Npat

  fit <- nlist(stanfit, formula = c(formulaLong, formulaEvent), family,
               id_var, time_var, weights, qnodes, basehaz, assoc,
               M, cnms, flevels, n_grps, n_subjects, n_yobs, epsilon,
               algorithm, terms, glmod = y_mod, survmod = e_mod, 
               assocmod = a_mod, grp_stuff, dataLong, dataEvent,
               prior.info = prior_info, stan_function = "stan_jm", 
               call = match.call(expand.dots = TRUE))
  
  out <- stanmvreg(fit)
  return(out)
}

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rstanarm documentation built on Feb. 11, 2020, 5:06 p.m.