updates

src/stan_files/model/priors_mvmer.stan

@@ -70,57 +70,57 @@
    target += gamma_custom_lpdf(yGamma3[1] | y_prior_dist_for_intercept[3], y_prior_mean_for_intercept[3],
              y_prior_scale_for_intercept[3], y_prior_df_for_intercept[3]);
   if (M > 3 && intercept_type[4] > 0)
-    gamma_lp(yGamma4[1], y_prior_dist_for_intercept[4], y_prior_mean_for_intercept[4],
+   target += gamma_custom_lpdf(yGamma4[1] | y_prior_dist_for_intercept[4], y_prior_mean_for_intercept[4],
              y_prior_scale_for_intercept[4], y_prior_df_for_intercept[4]);
   if (M > 4 && intercept_type[5] > 0)
-    gamma_lp(yGamma5[1], y_prior_dist_for_intercept[5], y_prior_mean_for_intercept[5],
+   target += gamma_custom_lpdf(yGamma5[1] | y_prior_dist_for_intercept[5], y_prior_mean_for_intercept[5],
              y_prior_scale_for_intercept[5], y_prior_df_for_intercept[5]);
   if (M > 5 && intercept_type[6] > 0)
-    gamma_lp(yGamma6[1], y_prior_dist_for_intercept[6], y_prior_mean_for_intercept[6],
+   target += gamma_custom_lpdf(yGamma6[1] | y_prior_dist_for_intercept[6], y_prior_mean_for_intercept[6],
              y_prior_scale_for_intercept[6], y_prior_df_for_intercept[6]);
   if (M > 6 && intercept_type[7] > 0)
-    gamma_lp(yGamma7[1], y_prior_dist_for_intercept[7], y_prior_mean_for_intercept[7],
+   target += gamma_custom_lpdf(yGamma7[1] | y_prior_dist_for_intercept[7], y_prior_mean_for_intercept[7],
              y_prior_scale_for_intercept[7], y_prior_df_for_intercept[7]);
   if (M > 7 && intercept_type[8] > 0)
-    gamma_lp(yGamma8[1], y_prior_dist_for_intercept[8], y_prior_mean_for_intercept[8],
+   target += gamma_custom_lpdf(yGamma8[1] | y_prior_dist_for_intercept[8], y_prior_mean_for_intercept[8],
              y_prior_scale_for_intercept[8], y_prior_df_for_intercept[8]);
   if (M > 8 && intercept_type[9] > 0)
-    gamma_lp(yGamma9[1], y_prior_dist_for_intercept[9], y_prior_mean_for_intercept[9],
+   target += gamma_custom_lpdf(yGamma9[1] | y_prior_dist_for_intercept[9], y_prior_mean_for_intercept[9],
              y_prior_scale_for_intercept[9], y_prior_df_for_intercept[9]);
   if (M > 9 && intercept_type[10] > 0)
-    gamma_lp(yGamma10[1], y_prior_dist_for_intercept[10], y_prior_mean_for_intercept[10],
+   target += gamma_custom_lpdf(yGamma10[1] | y_prior_dist_for_intercept[10], y_prior_mean_for_intercept[10],
              y_prior_scale_for_intercept[10], y_prior_df_for_intercept[10]);
   if (M > 10 && intercept_type[11] > 0)
-    gamma_lp(yGamma11[1], y_prior_dist_for_intercept[11], y_prior_mean_for_intercept[11],
+   target += gamma_custom_lpdf(yGamma11[1] | y_prior_dist_for_intercept[11], y_prior_mean_for_intercept[11],
              y_prior_scale_for_intercept[11], y_prior_df_for_intercept[11]);
   if (M > 11 && intercept_type[12] > 0)
-    gamma_lp(yGamma12[1], y_prior_dist_for_intercept[12], y_prior_mean_for_intercept[12],
+   target += gamma_custom_lpdf(yGamma12[1] | y_prior_dist_for_intercept[12], y_prior_mean_for_intercept[12],
              y_prior_scale_for_intercept[12], y_prior_df_for_intercept[12]);
   if (M > 12 && intercept_type[13] > 0)
-    gamma_lp(yGamma13[1], y_prior_dist_for_intercept[13], y_prior_mean_for_intercept[13],
+   target += gamma_custom_lpdf(yGamma13[1] | y_prior_dist_for_intercept[13], y_prior_mean_for_intercept[13],
              y_prior_scale_for_intercept[13], y_prior_df_for_intercept[13]);
   if (M > 13 && intercept_type[14] > 0)
-    gamma_lp(yGamma14[1], y_prior_dist_for_intercept[14], y_prior_mean_for_intercept[14],
+   target += gamma_custom_lpdf(yGamma14[1] | y_prior_dist_for_intercept[14], y_prior_mean_for_intercept[14],
              y_prior_scale_for_intercept[14], y_prior_df_for_intercept[14]);
   if (M > 14 && intercept_type[15] > 0)
-    gamma_lp(yGamma15[1], y_prior_dist_for_intercept[15], y_prior_mean_for_intercept[15],
+   target += gamma_custom_lpdf(yGamma15[1] | y_prior_dist_for_intercept[15], y_prior_mean_for_intercept[15],
              y_prior_scale_for_intercept[15], y_prior_df_for_intercept[15]);
   if (M > 15 && intercept_type[16] > 0)
-    gamma_lp(yGamma16[1], y_prior_dist_for_intercept[16], y_prior_mean_for_intercept[16],
+   target += gamma_custom_lpdf(yGamma16[1] | y_prior_dist_for_intercept[16], y_prior_mean_for_intercept[16],
              y_prior_scale_for_intercept[16], y_prior_df_for_intercept[16]);
   if (M > 16 && intercept_type[17] > 0)
-    gamma_lp(yGamma17[1], y_prior_dist_for_intercept[17], y_prior_mean_for_intercept[17],
+   target += gamma_custom_lpdf(yGamma17[1] | y_prior_dist_for_intercept[17], y_prior_mean_for_intercept[17],
              y_prior_scale_for_intercept[17], y_prior_df_for_intercept[17]);
   if (M > 17 && intercept_type[18] > 0)
-    gamma_lp(yGamma18[1], y_prior_dist_for_intercept[18], y_prior_mean_for_intercept[18],
+   target += gamma_custom_lpdf(yGamma18[1] | y_prior_dist_for_intercept[18], y_prior_mean_for_intercept[18],
              y_prior_scale_for_intercept[18], y_prior_df_for_intercept[18]);
   if (M > 18 && intercept_type[19] > 0)
-    gamma_lp(yGamma19[1], y_prior_dist_for_intercept[19], y_prior_mean_for_intercept[19],
+   target += gamma_custom_lpdf(yGamma19[1] | y_prior_dist_for_intercept[19], y_prior_mean_for_intercept[19],
              y_prior_scale_for_intercept[19], y_prior_df_for_intercept[19]);
   if (M > 19 && intercept_type[20] > 0)
-    gamma_lp(yGamma20[1], y_prior_dist_for_intercept[20], y_prior_mean_for_intercept[20],
+   target += gamma_custom_lpdf(yGamma20[1] | y_prior_dist_for_intercept[20], y_prior_mean_for_intercept[20],
              y_prior_scale_for_intercept[20], y_prior_df_for_intercept[20]);
-  
+
   // Log priors, population level params
   if (yK[1] > 0)
     target += beta_custom_lpdf(z_yBeta1 | y_prior_dist[1], y_prior_scale1, y_prior_df1,
@@ -135,74 +135,74 @@
             y_global_prior_df[3], yLocal3, yGlobal3, yMix3, yOol3,
             y_slab_df[3], y_caux3);
   if (M > 3 && yK[4] > 0)
-    beta_lp(z_yBeta4, y_prior_dist[4], y_prior_scale4, y_prior_df4,
+    target += beta_custom_lpdf(z_yBeta4 | y_prior_dist[4], y_prior_scale4, y_prior_df4,
             y_global_prior_df[4], yLocal4, yGlobal4, yMix4, yOol4,
             y_slab_df[4], y_caux4);
   if (M > 4 && yK[5] > 0)
-    beta_lp(z_yBeta5, y_prior_dist[5], y_prior_scale5, y_prior_df5,
+    target += beta_custom_lpdf(z_yBeta5 | y_prior_dist[5], y_prior_scale5, y_prior_df5,
             y_global_prior_df[5], yLocal5, yGlobal5, yMix5, yOol5,
             y_slab_df[5], y_caux5);
   if (M > 5 && yK[6] > 0)
-    beta_lp(z_yBeta6, y_prior_dist[6], y_prior_scale6, y_prior_df6,
+    target += beta_custom_lpdf(z_yBeta6 | y_prior_dist[6], y_prior_scale6, y_prior_df6,
             y_global_prior_df[6], yLocal6, yGlobal6, yMix6, yOol6,
             y_slab_df[6], y_caux6);
   if (M > 6 && yK[7] > 0)
-    beta_lp(z_yBeta7, y_prior_dist[7], y_prior_scale7, y_prior_df7,
+    target += beta_custom_lpdf(z_yBeta7 | y_prior_dist[7], y_prior_scale7, y_prior_df7,
             y_global_prior_df[7], yLocal7, yGlobal7, yMix7, yOol7,
             y_slab_df[7], y_caux7);
   if (M > 7 && yK[8] > 0)
-    beta_lp(z_yBeta8, y_prior_dist[8], y_prior_scale8, y_prior_df8,
+    target += beta_custom_lpdf(z_yBeta8 | y_prior_dist[8], y_prior_scale8, y_prior_df8,
             y_global_prior_df[8], yLocal8, yGlobal8, yMix8, yOol8,
             y_slab_df[8], y_caux8);
   if (M > 8 && yK[9] > 0)
-    beta_lp(z_yBeta9, y_prior_dist[9], y_prior_scale9, y_prior_df9,
+    target += beta_custom_lpdf(z_yBeta9 | y_prior_dist[9], y_prior_scale9, y_prior_df9,
             y_global_prior_df[9], yLocal9, yGlobal9, yMix9, yOol9,
             y_slab_df[9], y_caux9);
   if (M > 9 && yK[10] > 0)
-    beta_lp(z_yBeta10, y_prior_dist[10], y_prior_scale10, y_prior_df10,
+    target += beta_custom_lpdf(z_yBeta10 | y_prior_dist[10], y_prior_scale10, y_prior_df10,
             y_global_prior_df[10], yLocal10, yGlobal10, yMix10, yOol10,
             y_slab_df[10], y_caux10);
   if (M > 10 && yK[11] > 0)
-    beta_lp(z_yBeta11, y_prior_dist[11], y_prior_scale11, y_prior_df11,
+    target += beta_custom_lpdf(z_yBeta11 | y_prior_dist[11], y_prior_scale11, y_prior_df11,
             y_global_prior_df[11], yLocal11, yGlobal11, yMix11, yOol11,
             y_slab_df[11], y_caux11);
   if (M > 11 && yK[12] > 0)
-    beta_lp(z_yBeta12, y_prior_dist[12], y_prior_scale12, y_prior_df12,
+    target += beta_custom_lpdf(z_yBeta12 | y_prior_dist[12], y_prior_scale12, y_prior_df12,
             y_global_prior_df[12], yLocal12, yGlobal12, yMix12, yOol12,
             y_slab_df[12], y_caux12);
   if (M > 12 && yK[13] > 0)
-    beta_lp(z_yBeta13, y_prior_dist[13], y_prior_scale13, y_prior_df13,
+    target += beta_custom_lpdf(z_yBeta13 | y_prior_dist[13], y_prior_scale13, y_prior_df13,
             y_global_prior_df[13], yLocal13, yGlobal13, yMix13, yOol13,
             y_slab_df[13], y_caux13);
   if (M > 13 && yK[14] > 0)
-    beta_lp(z_yBeta14, y_prior_dist[14], y_prior_scale14, y_prior_df14,
+    target += beta_custom_lpdf(z_yBeta14 | y_prior_dist[14], y_prior_scale14, y_prior_df14,
             y_global_prior_df[14], yLocal14, yGlobal14, yMix14, yOol14,
             y_slab_df[14], y_caux14);
   if (M > 14 && yK[15] > 0)
-    beta_lp(z_yBeta15, y_prior_dist[15], y_prior_scale15, y_prior_df15,
+    target += beta_custom_lpdf(z_yBeta15 | y_prior_dist[15], y_prior_scale15, y_prior_df15,
             y_global_prior_df[15], yLocal15, yGlobal15, yMix15, yOol15,
             y_slab_df[15], y_caux15);
   if (M > 15 && yK[16] > 0)
-    beta_lp(z_yBeta16, y_prior_dist[16], y_prior_scale16, y_prior_df16,
+    target += beta_custom_lpdf(z_yBeta16 | y_prior_dist[16], y_prior_scale16, y_prior_df16,
             y_global_prior_df[16], yLocal16, yGlobal16, yMix16, yOol16,
             y_slab_df[16], y_caux16);
   if (M > 16 && yK[17] > 0)
-    beta_lp(z_yBeta17, y_prior_dist[17], y_prior_scale17, y_prior_df17,
+    target += beta_custom_lpdf(z_yBeta17 | y_prior_dist[17], y_prior_scale17, y_prior_df17,
             y_global_prior_df[17], yLocal17, yGlobal17, yMix17, yOol17,
             y_slab_df[17], y_caux17);
   if (M > 17 && yK[18] > 0)
-    beta_lp(z_yBeta18, y_prior_dist[18], y_prior_scale18, y_prior_df18,
+    target += beta_custom_lpdf(z_yBeta18 | y_prior_dist[18], y_prior_scale18, y_prior_df18,
             y_global_prior_df[18], yLocal18, yGlobal18, yMix18, yOol18,
             y_slab_df[18], y_caux18);
   if (M > 18 && yK[19] > 0)
-    beta_lp(z_yBeta19, y_prior_dist[19], y_prior_scale19, y_prior_df19,
+    target += beta_custom_lpdf(z_yBeta19 | y_prior_dist[19], y_prior_scale19, y_prior_df19,
             y_global_prior_df[19], yLocal19, yGlobal19, yMix19, yOol19,
             y_slab_df[19], y_caux19);
   if (M > 19 && yK[20] > 0)
-    beta_lp(z_yBeta20, y_prior_dist[20], y_prior_scale20, y_prior_df20,
+    target += beta_custom_lpdf(z_yBeta20 | y_prior_dist[20], y_prior_scale20, y_prior_df20,
             y_global_prior_df[20], yLocal20, yGlobal20, yMix20, yOol20,
             y_slab_df[20], y_caux20);
-            
+
   // Log priors, group level terms
   if (prior_dist_for_cov == 1) { // decov
     target += decov_lpdf(z_b | z_T, rho, zeta, tau, b_prior_regularization,