Merge pull request #20 from andrjohns/array-syntax

Update deprecated syntax for future rstan compatibility

DESCRIPTION

@@ -26,7 +26,7 @@ Depends:
     bayesplot,
     R (>= 3.4.0),
     Rcpp (>= 0.12.9),
-    rstan (>= 2.18.1)
+    rstan (>= 2.26.0)
 Imports:
     coda,
     dplyr,
@@ -39,8 +39,8 @@ Imports:
     rlang,
     rstantools (>= 2.0.0)
 LinkingTo: 
-    StanHeaders (>= 2.18.0), 
-    rstan (>= 2.18.1), 
+    StanHeaders (>= 2.26.0), 
+    rstan (>= 2.26.0), 
     BH (>= 1.66.0),
     Rcpp (>= 0.12.9), 
     RcppArmadillo, 

inst/stan/rw1_model.stan

@@ -80,7 +80,7 @@ transformed data {
 }
 
 parameters {
-  real<lower=0> sigma_b[k];
+  array[k] real<lower=0> sigma_b;
   real<lower=0> sigma_y;
 }
 

inst/stan/rw1_model_naive.stan

@@ -17,7 +17,7 @@ transformed data {
 }
 
 parameters {
-  real<lower=0> sigma_b[k];
+  array[k] real<lower=0> sigma_b;
   real<lower=0> sigma_y;
   matrix[k, n] beta_raw;
 }

inst/stan/walker_glm.stan

@@ -11,8 +11,8 @@ functions {
   // univariate Kalman filter & smoother for non-gaussian model, 
   // returns the log-likelihood of the corresponding approximating Gaussian model
   // and a extra correction term
-  matrix glm_approx_loglik(vector y, int[] y_miss, vector a1, matrix P1, vector Ht, 
-  matrix Tt, matrix Rt, matrix xreg, int distribution, int[] u, 
+  matrix glm_approx_loglik(vector y, array[] int y_miss, vector a1, matrix P1, vector Ht, 
+  matrix Tt, matrix Rt, matrix xreg, int distribution, array[] int u, 
   vector y_original, vector xbeta_fixed) {
 
     int k = rows(xreg);
@@ -99,7 +99,7 @@ functions {
   // univariate Kalman filter & smoother for non-gaussian model, 
   // returns the log-likelihood of the corresponding approximating Gaussian model
   // and a extra correction term
-  matrix glm_approx_smoother(vector y, int[] y_miss, vector a1, matrix P1, vector Ht, 
+  matrix glm_approx_smoother(vector y, array[] int y_miss, vector a1, matrix P1, vector Ht, 
   matrix Tt, matrix Rt, matrix xreg) {
 
     int k = rows(xreg);
@@ -171,7 +171,7 @@ data {
   matrix[n, k_fixed] xreg_fixed;
   matrix[k, n] xreg_rw;
   vector[n] y;
-  int<lower=0> y_miss[n];
+  array[n] int<lower=0> y_miss;
 
   real beta_fixed_mean;
   real<lower=0> beta_fixed_sd;
@@ -190,7 +190,7 @@ data {
 
   vector[n] Ht;
   vector[n] y_original;
-  int<lower=0> u[n];
+  array[n] int<lower=0> u;
   int distribution;
   int<lower=0> N;
   matrix[k_rw1, n] gamma_rw1;
@@ -199,7 +199,7 @@ data {
 
 transformed data {
   // indexing for non-missing observations for log_lik
-  int obs_idx[n_lfo - sum(y_miss[1:n_lfo])];
+  array[n_lfo - sum(y_miss[1:n_lfo])] int obs_idx;
   vector[m] a1;
   matrix[m, m] P1 = rep_matrix(0.0, m, m);
   matrix[m, m] Tt = diag_matrix(rep_vector(1.0, m));
@@ -233,8 +233,8 @@ transformed data {
 
 parameters {
   vector[k_fixed] beta_fixed;
-  real<lower=0> sigma_rw1[k_rw1];
-  real<lower=0> sigma_rw2[k_rw2];
+  array[k_rw1] real<lower=0> sigma_rw1;
+  array[k_rw2] real<lower=0> sigma_rw2;
 }
 
 transformed parameters {
@@ -290,8 +290,8 @@ generated quantities{
     vector[n] y_rep_j;
     matrix[k, n] beta_j;
     matrix[k_rw2, n] nu_j;
-    real beta_array[k, n, N];
-    real nu_array[k_rw2, n, N];
+    array[k, n, N] real beta_array;
+    array[k_rw2, n, N] real nu_array;
     vector[N] w = rep_vector(0.0, N); //importance sampling weights
 
     // This is the simplest but not the most efficient way to sample multiple realizations

inst/stan/walker_lm.stan

@@ -3,7 +3,7 @@ functions {
   // note that these functions are not fully optimised yet
 
   // univariate Kalman filter for RW1+RW2 model, returns the log-likelihood
-  vector gaussian_filter(vector y, int[] y_miss, vector a1, matrix P1, real Ht, 
+  vector gaussian_filter(vector y, array[] int y_miss, vector a1, matrix P1, real Ht, 
   matrix Tt, matrix Rt, matrix xreg, vector gamma2_y) {
 
     int k = rows(xreg);
@@ -40,7 +40,7 @@ functions {
 
   }
 
-  matrix gaussian_smoother(vector y, int[] y_miss, vector a1, matrix P1, real Ht, 
+  matrix gaussian_smoother(vector y, array[] int y_miss, vector a1, matrix P1, real Ht, 
   matrix Tt, matrix Rt, matrix xreg,vector gamma2_y) {
 
     int k = rows(xreg);
@@ -111,7 +111,7 @@ data {
   matrix[n, k_fixed] xreg_fixed;
   matrix[k, n] xreg_rw;
   vector[n] y;
-  int<lower=0> y_miss[n];
+  array[n] int<lower=0> y_miss;
   real<lower=0> sigma_y_shape;
   real<lower=0> sigma_y_rate;
 
@@ -136,7 +136,7 @@ data {
 
 transformed data {
   // indexing for non-missing observations for log_lik
-  int obs_idx[n_lfo - sum(y_miss[1:n_lfo])];
+  array[n_lfo - sum(y_miss[1:n_lfo])] int obs_idx;
   vector[m] a1;
   matrix[m, m] P1 = rep_matrix(0.0, m, m);
   matrix[m, m] Tt = diag_matrix(rep_vector(1.0, m));
@@ -170,8 +170,8 @@ transformed data {
 
 parameters {
   vector[k_fixed] beta_fixed;
-  real<lower=0> sigma_rw1[k_rw1];
-  real<lower=0> sigma_rw2[k_rw2];
+  array[k_rw1] real<lower=0> sigma_rw1;
+  array[k_rw2] real<lower=0> sigma_rw2;
   real<lower=0> sigma_y;
 }