Development/Dev_Local_GP/update/update_new/extract_W_longs_manual.R

In drizopoulos/JMbayes2: Extended Joint Models for Longitudinal and Time-to-Event Data

model_data <- model_data
model_info <- model_info
initial_values <- last_iterations[[i]]
priors <- priors
control <- control


function (model_data, model_info, initial_values, priors,
          control) {
  betas <- initial_values$betas
  b <- initial_values$b
  gammas <- initial_values$gammas
  bs_gammas <- initial_values$bs_gammas
  alphas <- initial_values$alphas
  # outcome vectors and design matrices
  Time_right <- model_data$Time_right
  Time_left <- model_data$Time_left
  Time_start <- model_data$Time_start
  delta <- model_data$delta
  which_event <- model_data$which_event
  which_right <- model_data$which_right
  which_left <- model_data$which_left
  which_interval <- model_data$which_interval
  W0_H <- model_data$W0_H
  W_H <- model_data$W_H
  X_H <- model_data$X_H
  Z_H <- model_data$Z_H
  U_H <- model_data$U_H
  W0_h <- model_data$W0_h
  W_h <- model_data$W_h
  X_h <- model_data$X_h
  Z_h <- model_data$Z_h
  U_h <- model_data$U_h
  W0_H2 <- model_data$W0_H2
  W_H2 <- model_data$W_H2
  X_H2 <- model_data$X_H2
  Z_H2 <- model_data$Z_H2
  U_H2 <- model_data$U_H2
  # other information
  n <- model_data$n
  idT <- model_data$idT
  log_Pwk <- model_data$log_Pwk
  log_Pwk2 <- model_data$log_Pwk2
  FunForms_per_outcome <- model_info$FunForms_per_outcome
  Funs_FunsForms <- model_info$Funs_FunsForms
  # id_H is used to repeat the random effects of each subject GK_k times
  id_H <- rep(list(rep(unclass(idT), each = control$GK_k)), length(X_H))
  # this is the linear predictor for the longitudinal outcomes evaluated at the
  # Gauss-Kronrod quadrature points
  eta_H <- JMbayes2:::linpred_surv(X_H, betas, Z_H, b, id_H)
  # Wlong is the design matrix of all longitudinal outcomes according to the specified
  # functional forms per outcome already multiplied with the interaction terms matrix U
  Wlong_H <- create_Wlong(eta_H, FunForms_per_outcome, U_H, Funs_FunsForms)
  if (length(which_event)) {
    id_h <- rep(list(unclass(idT)), length(X_h))
    eta_h <- linpred_surv(X_h, betas, Z_h, b, id_h)
    Wlong_h <- create_Wlong(eta_h, FunForms_per_outcome, U_h,
                            Funs_FunsForms)
  } else {
    Wlong_h <- rep(list(matrix(0.0, length(Time_right), 1)), length(Wlong_H))
  }
  if (length(which_interval)) {
    id_H2 <- lapply(X_H2, function (i, n) rep(seq_len(n), each = control$GK_k), n = n)
    eta_H2 <- linpred_surv(X_H2, betas, Z_H, b, id_H2)
    Wlong_H2 <- create_Wlong(eta_H2, FunForms_per_outcome, U_H2,
                             Funs_FunsForms)
  } else {
    Wlong_H2 <- rep(list(matrix(0.0, control$GK_k * n, 1)), length(Wlong_H))
  }
  list(Wlong_H = Wlong_H, Wlong_h = Wlong_h, Wlong_H2 = Wlong_H2)
}






JMbayes2:::create_Wlong_mats(model_data, model_info, 
                             last_iterations[[i]], priors, 
                             control)