Merge branch 'master' of https://github.com/stan-dev/example-models

Author: mitzimorris

.github/workflows/compile.yml

@@ -0,0 +1,41 @@
+name: Compile models
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+        architecture: 'x64'
+    
+    - uses: actions/checkout@v2
+      with:
+       repository: 'stan-dev/performance-tests-cmdstan'
+       submodules: recursive
+    
+    - uses: actions/checkout@v2
+      with:
+        path: 'example-models-new'
+        fetch-depth: 0
+    
+    - name: Write modified models
+      run: |
+        cd example-models-new
+        echo "example-models-new/basic_distributions/binormal.stan" > ../test-models.txt
+        git diff --name-only origin/master $GITHUB_SHA --diff-filter=AM | grep ".stan$" |  sed -e 's/^/example-models-new\//' >> ../test-models.txt
+
+    - name: Compile all new or modified models
+      run: |
+        cd cmdstan
+        make build
+        cd ..
+        ./runPerformanceTests.py --runs=0 --tests-file test-models.txt  

ARM/Ch.21/finite_populations.stan

@@ -50,7 +50,7 @@ model {
               + bernoulli_lpmf(y[i] |  p_eff[i]);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 |  omega)   // z[i] == 1
-                            + bernoulli_lpmf(0 | p_eff[i]),
+                            + bernoulli_lpmf(y[i] | p_eff[i]),
                             bernoulli_lpmf(0 | omega));  // z[i] == 0
 }
 

ARM/Ch.21/r_sqr.data.R

@@ -34,7 +34,7 @@ model {
               + bernoulli_lpmf(y[i] | p);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 | omega)   // z[i] == 1
-                            + bernoulli_lpmf(0 | p),
+                            + bernoulli_lpmf(y[i] | p),
                             bernoulli_lpmf(0 | omega)); // z[i] == 0
 }
 

ARM/Ch.21/r_sqr.stan

@@ -54,7 +54,7 @@ model {
               + bernoulli_logit_lpmf(y[i] | logit_p[i]);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 | omega)   // z[i] == 1
-                            + bernoulli_logit_lpmf(0 | logit_p[i]),
+                            + bernoulli_logit_lpmf(y[i] | logit_p[i]),
                             bernoulli_lpmf(0 | omega)); // z[i] == 0
 }
 

BPA/Ch.06/Mb.stan

@@ -59,7 +59,7 @@ model {
               + bernoulli_logit_lpmf(y[i] | logit_p[i]);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 | omega)   // z[i] == 1
-                            + bernoulli_logit_lpmf(0 | logit_p[i]),
+                            + bernoulli_logit_lpmf(y[i] | logit_p[i]),
                             bernoulli_lpmf(0 | omega)); // z[i] == 0
 }
 

BPA/Ch.06/Mt.stan

@@ -51,7 +51,7 @@ model {
               + bernoulli_logit_lpmf(y[i] | logit_p[i]);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 | omega)   // z[i] == 1
-                            + bernoulli_logit_lpmf(0 | logit_p[i]),
+                            + bernoulli_logit_lpmf(y[i] | logit_p[i]),
                             bernoulli_lpmf(0 | omega)); // z[i] == 0
   }
 }