revert some ltjmm changes

Author: mcdonohue

R/jm_data_block.R

@@ -1964,8 +1964,8 @@ set_jm_sampling_args <- function(object, cnms, user_dots = list(),
 # @param standata The list of data to pass to Stan
 # @param is_jm A logical
 # @return A character vector
-pars_to_monitor <- function(standata, is_jm = FALSE) {
-  c(if (standata$M > 0 && standata$intercept_type[1]) "yAlpha1", 
+pars_to_monitor <- function (standata, is_jm = FALSE, is_ltjmm = FALSE) {
+    c(if (standata$M > 0 && standata$intercept_type[1]) "yAlpha1", 
     if (standata$M > 1 && standata$intercept_type[2]) "yAlpha2", 
     if (standata$M > 2 && standata$intercept_type[3]) "yAlpha3", 
     if (standata$M > 3 && standata$intercept_type[4]) "yAlpha4",
@@ -2033,6 +2033,7 @@ pars_to_monitor <- function(standata, is_jm = FALSE) {
     if (is_jm && length(standata$basehaz_X)) "e_aux",
     if (standata$prior_dist_for_cov == 2 && standata$bK1 > 0) "bCov1",
     if (standata$prior_dist_for_cov == 2 && standata$bK2 > 0) "bCov2",
+    if (is_ltjmm) c('lt', 'sigma_lt'), 
     if (standata$prior_dist_for_cov == 1 && standata$len_theta_L) "theta_L",
     "mean_PPD")
 }