setup_S_model {INLAjoint}

Setup survival part for outcome m

Description

Setup survival part for outcome m (internal function) input:

Usage

setup_S_model(
  formula,
  formLong,
  dataSurv,
  LSurvdat,
  timeVar,
  assoc,
  id,
  m,
  K,
  M,
  NFT,
  corLong,
  dataOnly,
  SurvInfo,
  strata
)

Arguments

formula

with inla.surv() object as an outcome

formLong

formula from the longitudinal part, if any

dataSurv

dataset(s) for the survival part

LSurvdat

dataset for the longitudinal part converted to survival format (internal, used to get covariates if missing in the survival dataset when sharing linear predictors including covariates from longitudinal into survival)

timeVar

names of the variables that are time-dependent (only linear for now)

assoc

association parameters between K longitudinal outcomes and M survival outcomes (list of K vectors of size M)

id

name of the variable that gives the individual id

m

identifies the outcome among 1:M time-to-event outcomes

K

number of longitudinal outcomes

M

number of survival outcomes

NFT

maximum number of functions of time (fixed value)

corLong

boolean that indicates if random effects across longitudinal markers are correlated, when multiple longitudinal markers are included in the model

dataOnly

boolean for internal use, indicates if only preparing data (i.e., not fitting the model)

SurvInfo

information about survival submodels for internal use

strata

covariate for stratified proportional hazards model output:

Value

YS_data includes the values of the survival outcome and covariates associated to this survival part, with the association parameters but the provided id are temporary and they will be updated after the cox expansion to make them unique and allow for time dependency

YSformF formula for this survival outcome (not including association parameters)