Merge pull request #190 from andrjohns/feature/basic_dist_update

Update basic_distributions syntax

Author: rok-cesnovar

basic_distributions/binormal.stan

@@ -1,17 +1,11 @@
 transformed data {
-    matrix[2,2] Sigma;
-    vector[2] mu;
-
-    mu[1] <- 0.0;
-    mu[2] <- 0.0;
-    Sigma[1,1] <- 1.0;
-    Sigma[2,2] <- 1.0;
-    Sigma[1,2] <- 0.10;
-    Sigma[2,1] <- 0.10;
+    matrix[2,2] Sigma = [[1, 0.1],
+                         [0.1, 1]];
+    vector[2] mu = [0, 0]';
 }
 parameters {
     vector[2] y;
 }
 model {
-      y ~ multi_normal(mu,Sigma);
+      y ~ multi_normal(mu, Sigma);
 }

basic_distributions/inv_wishart.stan

@@ -1,8 +1,7 @@
 transformed data {
-  cov_matrix[3] S;
-  S[1, 1] <- 2; S[1, 2] <- 0; S[1, 3] <- 0; 
-  S[2, 2] <- 1; S[2, 1] <- 0; S[2, 3] <- 0;
-  S[3, 3] <- .5; S[3, 1] <- 0; S[3, 2] <- 0; 
+  cov_matrix[3] S = [[2, 0, 0],
+                     [0, 1, 0],
+                     [0, 0, 0.5]];
 } 
 parameters {
   cov_matrix[3] W; 

basic_distributions/normal.stan

@@ -2,5 +2,5 @@ parameters {
   real y;
 }
 model {
-  y ~ normal(0,1);
+  y ~ normal(0, 1);
 }

basic_distributions/normal_mixture.stan

@@ -1,18 +1,13 @@
 transformed data {
-  real<lower=0,upper=1> theta;
-  real mu[2];
-  real<lower=0> sigma[2];
-  
-  mu[1] <- 0.0;    sigma[1] <- 0.5;
-  mu[2] <- 4.0;    sigma[2] <- 3.0;
-  theta <- 0.25;
+  real<lower=0,upper=1> theta = 0.25;
+  vector[2] mu = [0, 4]';
+  vector<lower=0>[2] sigma = [0.5, 3]';
 }
 parameters {
   real y;
 }
 model {
-  increment_log_prob(log_sum_exp(log(theta)
-                                   + normal_log(y,mu[1],sigma[1]),
-                                 log(1.0 - theta) 
-                                 + normal_log(y,mu[2],sigma[2])));
+  target += log_mix(theta,
+                    normal_lpdf(y | mu[1], sigma[1]),
+                    normal_lpdf(y | mu[2], sigma[2]));
 }

basic_distributions/ordered_pair.stan

@@ -1,14 +1,12 @@
 transformed data {
-    real L; 
-    real H;
-    L <- -5.0;
-    H <- 5.0;
+    real L = -5; 
+    real H = 5;
 }
 parameters {
-    real<lower=L,upper=H> a;
-    real<lower=a,upper=H> b;
+    real<lower=L, upper=H> a;
+    real<lower=a, upper=H> b;
 }
 model {
-//    a ~ uniform(L,b);
-//    b ~ uniform(a,H);
+//    a ~ uniform(L, b);
+//    b ~ uniform(a, H);
 }

basic_distributions/sorted_pair.stan

@@ -1,12 +1,10 @@
 parameters {
-    real<lower=-1,upper=1> x1;
-    real<lower=-1,upper=1> x2;
+    real<lower=-1, upper=1> x1;
+    real<lower=-1, upper=1> x2;
 }
 model {
 }
 generated quantities {
-    real a;
-    real b;
-    a <- fmax(x1,x2);
-    b <- fmin(x1,x2);
+    real a = fmax(x1, x2);
+    real b = fmin(x1, x2);
 }

basic_distributions/triangle.stan

@@ -1,6 +1,6 @@
 parameters {
-  real<lower=-1,upper=1> y;
+  real<lower=-1, upper=1> y;
 }
 model {
-  increment_log_prob(log1m(fabs(y)));
+  target += log1m(fabs(y));
 }

basic_distributions/uniform.stan

@@ -1,6 +1,6 @@
 parameters {
-    real<lower=0,upper=1> y;
+    real<lower=0, upper=1> y;
 }
 model {
-    y ~ uniform(0,1);
+    y ~ uniform(0, 1);
 }

basic_distributions/wishart.stan

@@ -1,12 +1,6 @@
 transformed data {
-  cov_matrix[2] S;
-
-  for (i in 1:2)
-    for (j in 1:2)
-      S[i,j] <- 0.0;
-
-  S[1,1] <- 2.0; 
-  S[2,2] <- 0.5;
+  cov_matrix[2] S = [[2, 0],
+                     [0, 0.5]];
 } 
 parameters {
   cov_matrix[2] W; 

basic_distributions/wishart2.stan

@@ -1,20 +1,18 @@
 transformed data {
   cov_matrix[4] S;
 
-  S[1,1] <- 2.9983662;
-  S[1,2] <- 0.2898776;
-  S[1,3] <- -2.650523;
-  S[1,4] <- 0.1055911;
-  S[2,2] <- 11.4803610;
-  S[2,3] <- 7.157993;
-  S[2,4] <- -3.1129955;
-  S[3,3] <- 11.676181;
-  S[3,4] <- -3.5866852;
-  S[4,4] <- 1.4482736;
+  S[1,1] = 2.9983662;
+  S[2,1] = 0.2898776;
+  S[3,1] = -2.650523;
+  S[4,1] = 0.1055911;
+  S[2,2] = 11.4803610;
+  S[3,2] = 7.157993;
+  S[4,2] = -3.1129955;
+  S[3,3] = 11.676181;
+  S[4,3] = -3.5866852;
+  S[4,4] = 1.4482736;
 
-  for (m in 1:4)
-    for (n in 1:(m-1))
-      S[m,n] <- S[n,m];
+  S = symmetrize_from_lower_tri(S);
 }
 parameters {
   cov_matrix[4] W;