From 867cb215bc2363bc5853ab9e6a415937c7345704 Mon Sep 17 00:00:00 2001
From: Imad Ali <imadmali@gmail.com>
Date: Fri, 28 Oct 2016 02:58:17 -0400
Subject: [PATCH] debug beta_rng issue with print/while

---
 .DS_Store            | Bin 14340 -> 0 bytes
 .gitignore           |   1 -
 R/stan_betareg.fit.R |   2 +-
 exec/continuous.stan |  18 +++++++++++++++---
 inst/.DS_Store       | Bin 8196 -> 8196 bytes
 5 files changed, 16 insertions(+), 5 deletions(-)
 delete mode 100644 .DS_Store

diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
index a565bfa992e65e9460207e8a63901f371f1a4340..0000000000000000000000000000000000000000
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diff --git a/.gitignore b/.gitignore
index 28b4d6853..99ea06aaf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,5 +10,4 @@ vignettes/*.R
 !vignettes/*.Rmd
 vignettes/*.html
 vignettes/*_files
-
 .DS_Store
diff --git a/R/stan_betareg.fit.R b/R/stan_betareg.fit.R
index 71c1beedd..7274d752b 100644
--- a/R/stan_betareg.fit.R
+++ b/R/stan_betareg.fit.R
@@ -52,7 +52,7 @@ stan_betareg.fit <- function (x, y, z, weights = rep(1, NROW(x)), offset = rep(0
   if (Z_true == 0) {
     link_num_phi <- 0
   }
-  
+
   # useless assignments to pass R CMD check
   has_intercept <- min_prior_scale <- prior_df <- prior_df_for_intercept <-
     prior_dist <- prior_dist_for_intercept <- prior_mean <- prior_mean_for_intercept <-
diff --git a/exec/continuous.stan b/exec/continuous.stan
index 8fb3f2c6b..ecacaf0f9 100644
--- a/exec/continuous.stan
+++ b/exec/continuous.stan
@@ -386,7 +386,7 @@ model {
     if (family == 1) {
       if (link == 1) 
         target += normal_lpdf(y | eta, dispersion);
-      else if (link == 2) 
+      else if (link > 2) 
         target += normal_lpdf(y | exp(eta), dispersion);
       else 
         target += normal_lpdf(y | divide_real_by_vector(1, eta), dispersion);
@@ -446,6 +446,7 @@ generated quantities {
   }
   
   {
+    real yrep; // for the beta_rng underflow issue
     #include "make_eta.stan" // defines eta
     if (t > 0) eta = eta + csr_matrix_times_vector(N, q, w, v, u, b);
     if (has_intercept == 1) {
@@ -502,8 +503,19 @@ generated quantities {
     else if (family == 4 && link_phi > 0) {
       eta = linkinv_beta(eta, link);
       eta_z = linkinv_beta_z(eta_z, link_phi);
-      for (n in 1:N) 
-        mean_PPD = mean_PPD + beta_rng(eta[n] * eta_z[n], (1 - eta[n]) * eta_z[n]);
+      for (n in 1:N) {
+        if (link_phi == 3) { // workaround beta_rng underflow issue
+          yrep = beta_rng(eta[n] * eta_z[n], (1 - eta[n]) * eta_z[n]);
+          while (is_nan(yrep) == 1) {
+            print("warning: beta_rng() generated a value that is NaN.");
+            yrep = beta_rng(eta[n] * eta_z[n], (1 - eta[n]) * eta_z[n]);
+          }
+          mean_PPD = mean_PPD + yrep;
+        }
+        else {
+           mean_PPD = mean_PPD + beta_rng(eta[n] * eta_z[n], (1 - eta[n]) * eta_z[n]);
+        }
+      }
     }
     mean_PPD = mean_PPD / N;
   }
diff --git a/inst/.DS_Store b/inst/.DS_Store
index e03e5b7f982f65463a3b04d9dc81406674c0e071..7b4e7792b4542c8d2019fb4dfe01700c0c528b56 100644
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