monitor PS for std.lv

ecmerkle · May 10, 2024 · 0da0d05 · 0da0d05
1 parent 7734f3e
commit 0da0d05
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/R/bsam.R b/R/bsam.R
@@ -6,10 +6,11 @@ bsam <- function(..., ngibbs = 50L) {
   dotdotdot <- list(...)
 
   if (!("mcmcextra" %in% names(dotdotdot))) {
-    mcmcextra <- list(dosam = TRUE, data = list(ngibbs = ngibbs, fullpsi_c = 0))
+    mcmcextra <- list(dosam = TRUE, data = list(ngibbs = ngibbs, fullpsi_c = 0), monitor = "PS")
   } else {
     mcmcextra <- dotdotdot$mcmcextra
     mcmcextra$dosam <- TRUE
+    mcmcextra$monitor <- c(mcmcextra$monitor, "PS")
     mcmcextra$data <- c(mcmcextra$data, list(ngibbs = ngibbs, fullpsi_c = 0L))
   }
 

diff --git a/inst/stan/stanmarg_bsam.stan b/inst/stan/stanmarg_bsam.stan
@@ -1418,6 +1418,12 @@ generated quantities { // these matrices are saved in the output but do not figu
     gamma0[mm] = rep_vector(0, maxdim);
     Omega_inv[mm] = diag_matrix(gamma0[mm]);
 
+    if (Ndum[mm] > 0) {
+      for (j in 1:Ndum[mm]) {
+	Theta_sd_dum[g, dum_ov_idx[mm, j], dum_ov_idx[mm, j]] = pow(.0001, .5);
+      }
+    }
+
     for (r in 1:m) {
       real askel = Alpha_skeleton[g, r, 1];
       if (is_inf(askel)) {
@@ -1466,11 +1472,6 @@ generated quantities { // these matrices are saved in the output but do not figu
 
       // sample lvs
       Psi0_inv = inverse_spd( quad_form_sym(Psi[g], IBinv') );
-      if (Ndum[mm] > 0) {
-	for (j in 1:Ndum[mm]) {
-	  Theta_sd_dum[g, dum_ov_idx[mm, j], dum_ov_idx[mm, j]] = pow(.0001, .5);
-	}
-      }
       Lamt_Thet_inv = Lambda[g]' * inverse_spd( quad_form_sym(Theta_r[g], Theta_sd_dum[g]) ); // mxp
 
       D = inverse_spd( Lamt_Thet_inv * Lambda[g] + Psi0_inv );