[DEV] Add sum of log_lik in output generated quantities

suzuki-shm · Jul 2, 2019 · 78797bd · 78797bd
1 parent fe13b54
commit 78797bd
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Showing 21 changed files with 41 additions and 1 deletion.
diff --git a/sphere/sphere_utils.py b/sphere/sphere_utils.py
@@ -180,6 +180,7 @@ def get_pars(model_name, has_log_lik=False):
     elif model_name == "invmievonmises":
         pars = ["alpha", "O", "kappa", "ori", "nu", "lambda",
                 "PTR",  "wPTR", "mwPTR"]
+    pars.append("log_lik_sum")
 
     if has_log_lik:
         pars.append("log_lik")

diff --git a/stan/cardioid.stan b/stan/cardioid.stan
@@ -76,6 +76,7 @@ generated quantities {
     vector<lower=0.0, upper=1.0>[K] CV[S] ;
     vector<lower=0.0>[K] CSD[S] ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // See (Jones&Pewsey, 2005) about this transformation
@@ -94,4 +95,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * cardioid_mixture_lpdf(RADIAN[i] | K, alpha, ori, rho[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/dvonmises.stan b/stan/dvonmises.stan
@@ -84,6 +84,7 @@ generated quantities {
     vector<lower=0.0, upper=1.0>[K] CV[S] ;
     vector<lower=0.0>[K] CSD[S] ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -102,4 +103,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * dvon_mises_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], L) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/explinearcardioid.stan b/stan/explinearcardioid.stan
@@ -72,6 +72,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         PTR[s] = exp(2.0 * pi() * rho[s]) ;
@@ -81,4 +82,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * explinearcardioid_mixture_lpdf(RADIAN[i]| K, alpha, ori, rho[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/invmiaecardioid.stan b/stan/invmiaecardioid.stan
@@ -131,6 +131,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // See (Jones&Pewsey, 2005) about this transformation
@@ -143,4 +144,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * invmiaecardioid_mixture_lpdf(RADIAN[i] | K, alpha, ori, rho[SUBJECT[i]], nu[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/invmiaejonespewsey.stan b/stan/invmiaejonespewsey.stan
@@ -158,6 +158,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -168,4 +169,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * invmiaejonespewsey_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], psi[SUBJECT[i]], nu[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/invmiaevonmises.stan b/stan/invmiaevonmises.stan
@@ -122,6 +122,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -132,5 +133,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * invmiaevon_mises_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], nu[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
-
diff --git a/stan/invmiaewrappedcauchy.stan b/stan/invmiaewrappedcauchy.stan
@@ -131,6 +131,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // See (Jones&Pewsey, 2005) about this transformation
@@ -143,4 +144,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * invmiaewrappedcauchy_mixture_lpdf(RADIAN[i] | K, alpha, ori, rho[SUBJECT[i]], nu[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/invmievonmises.stan b/stan/invmievonmises.stan
@@ -119,6 +119,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -129,4 +130,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * invmievon_mises_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], nu[SUBJECT[i]], lambda[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/invsejonespewsey.stan b/stan/invsejonespewsey.stan
@@ -185,6 +185,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -195,4 +196,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * invsejonespewsey_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], psi[SUBJECT[i]], lambda[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/invsevonmises.stan b/stan/invsevonmises.stan
@@ -157,6 +157,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -167,4 +168,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * invsevon_mises_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], lambda[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/jonespewsey.stan b/stan/jonespewsey.stan
@@ -100,6 +100,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -110,4 +111,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * jonespewsey_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], psi[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/linearcardioid.stan b/stan/linearcardioid.stan
@@ -75,6 +75,7 @@ generated quantities {
     vector<lower=0.0, upper=1.0>[K] CV[S] ;
     vector<lower=0.0>[K] CSD[S] ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         PTR[s] = (1 + pi() * rho[s])  ./ (1 - pi() * rho[s]) ;
@@ -87,4 +88,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * linearcardioid_mixture_lpdf(RADIAN[i]| K, alpha, ori, rho[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/miaecardioid.stan b/stan/miaecardioid.stan
@@ -110,6 +110,7 @@ generated quantities {
     vector<lower=0.0, upper=1.0>[K] CV[S] ;
     vector<lower=0.0>[K] CSD[S] ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // See (Jones&Pewsey, 2005) about this transformation
@@ -128,4 +129,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * miaecardioid_mixture_lpdf(RADIAN[i] | K, alpha, ori, rho[SUBJECT[i]], nu[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/miaejonespewsey.stan b/stan/miaejonespewsey.stan
@@ -107,6 +107,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -117,4 +118,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * miaejonespewsey_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], psi[SUBJECT[i]], nu[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/miaevonmises.stan b/stan/miaevonmises.stan
@@ -105,6 +105,7 @@ generated quantities {
     vector<lower=0.0, upper=1.0>[K] CV[S] ;
     vector<lower=0.0>[K] CSD[S] ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -123,4 +124,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * miaevon_mises_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], nu[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/miaewrappedcauchy.stan b/stan/miaewrappedcauchy.stan
@@ -110,6 +110,7 @@ generated quantities {
     vector<lower=0.0, upper=1.0>[K] CV[S] ;
     vector<lower=0.0>[K] CSD[S] ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // See (Jones&Pewsey, 2005) about this transformation
@@ -128,4 +129,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * miaewrappedcauchy_mixture_lpdf(RADIAN[i] | K, alpha, ori, rho[SUBJECT[i]], nu[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/sejonespewsey.stan b/stan/sejonespewsey.stan
@@ -118,6 +118,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -128,4 +129,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * sejonespewsey_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], psi[SUBJECT[i]], lambda[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/sevonmises.stan b/stan/sevonmises.stan
@@ -92,6 +92,7 @@ generated quantities {
     vector<lower=1.0>[K] wPTR[S] ;
     vector<lower=1.0>[S] mwPTR ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -102,4 +103,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * sevon_mises_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]], lambda[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/vonmises.stan b/stan/vonmises.stan
@@ -67,6 +67,7 @@ generated quantities {
     vector<lower=0.0, upper=1.0>[K] CV[S] ;
     vector<lower=0.0>[K] CSD[S] ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // Fold change of max p.d.f. to min p.d.f.
@@ -85,4 +86,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * von_mises_mixture_lpdf(RADIAN[i] | K, alpha, ori, kappa[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }
diff --git a/stan/wrappedcauchy.stan b/stan/wrappedcauchy.stan
@@ -76,6 +76,7 @@ generated quantities {
     vector<lower=0.0, upper=1.0>[K] CV[S] ;
     vector<lower=0.0>[K] CSD[S] ;
     vector[I] log_lik ;
+    real log_lik_sum ;
 
     for(s in 1:S){
         // See (Jones&Pewsey, 2005) about this transformation
@@ -94,4 +95,5 @@ generated quantities {
     for(i in 1:I){
         log_lik[i] = DEPTH[i] * wrappedcauchy_mixture_lpdf(RADIAN[i] | K, alpha, ori, rho[SUBJECT[i]]) ;
     }
+    log_lik_sum = sum(log_lik) ;
 }