rstan: Fix the deprecated array syntax

rstan/rstan/R/misc.R

@@ -863,7 +863,7 @@ remove_empty_pars <- function(pars, model_dims) {
   # following stan model code:
   #
   # transformed data { int n; n <- 0; }
-  # parameters { real y[n]; }
+  # parameters { array[n] real y; }
   #
   # Args:
   #   pars: a character vector of parameters names

rstan/rstan/man/rstan.Rd

@@ -93,7 +93,7 @@
 stanmodelcode <- "
 data {
   int<lower=0> N;
-  real y[N];
+  array[N] real y;
 }
 
 parameters {

rstan/rstan/man/sflist2stanfit.Rd

@@ -72,8 +72,8 @@ data {
   int<lower=1> N;
 } 
 parameters {
-  real y1[N]; 
-  real y2[N]; 
+  array[N] real y1;
+  array[N] real y2; 
 } 
 model {
   y1 ~ normal(0, 1);

rstan/rstan/man/stan.Rd

@@ -386,7 +386,7 @@ stan(file, model_name = "anon_model", model_code = "", fit = NA,
   }
 
   Stan treats a vector of length 1 in R as a scalar.  So technically
-  if, for example, \code{"real y[1];"} is defined in the data block, an array
+  if, for example, \code{"array[1] real y;"} is defined in the data block, an array
   such as \code{"y = array(1.0, dim = 1)"} in R should be used. This
   is also the case for specifying initial values since the same
   underlying approach for reading data from R in Stan is used, in which
@@ -425,7 +425,7 @@ stan(file, model_name = "anon_model", model_code = "", fit = NA,
 library(rstan)
 scode <- "
 parameters {
-  real y[2];
+  array[2] real y;
 }
 model {
   y[1] ~ normal(0, 1);
@@ -447,7 +447,7 @@ e2 <- extract(fit2, permuted = FALSE)
 
 excode <- '
   transformed data {
-    real y[20];
+    array[20] real y;
     y[1] = 0.5796;  y[2] = 0.2276;   y[3]  = -0.2959;
     y[4] = -0.3742; y[5] = 0.3885;   y[6]  = -2.1585;
     y[7] = 0.7111;  y[8] = 1.4424;   y[9]  = 2.5430;

rstan/rstan/man/stanc.Rd

@@ -121,7 +121,7 @@ Translate Stan model specification to C++ code
 stanmodelcode <- "
 data {
   int<lower=0> N;
-  real y[N];
+  array[N] real y;
 }
 
 parameters {

rstan/rstan/man/stanfit-class.Rd

@@ -200,7 +200,7 @@ summarizing results and various access methods also allow the underlying data
 showClass("stanfit")
 ecode <- '
   parameters {
-    real<lower=0> y[2];
+    array[2] real<lower=0> y;
   } 
   model {
     y ~ exponential(1);
@@ -241,7 +241,7 @@ print(y1star) # y1start should equal to y1
 # 
 excode <- '
   transformed data {
-    real y[20];
+    array[20] real y;
     y[1] <- 0.5796;  y[2]  <- 0.2276;   y[3] <- -0.2959; 
     y[4] <- -0.3742; y[5]  <- 0.3885;   y[6] <- -2.1585;
     y[7] <- 0.7111;  y[8]  <- 1.4424;   y[9] <- 2.5430; 

rstan/rstan/man/stanfit-method-extract.Rd

@@ -57,8 +57,8 @@
 \examples{\dontrun{
 ex_model_code <- '
   parameters {
-    real alpha[2,3];
-    real beta[2]; 
+    array[2, 3] real alpha;
+    array[2] real beta; 
   } 
   model {
     for (i in 1:2) for (j in 1:3) 
@@ -110,7 +110,7 @@ dimnames(fit_ss2)
 # 
 excode <- '
   transformed data {
-    real y[20];
+    array[20] real y;
     y[1] <- 0.5796;  y[2]  <- 0.2276;   y[3] <- -0.2959; 
     y[4] <- -0.3742; y[5]  <- 0.3885;   y[6] <- -2.1585;
     y[7] <- 0.7111;  y[8]  <- 1.4424;   y[9] <- 2.5430; 

rstan/rstan/man/stanfit-method-summary.Rd

@@ -48,7 +48,7 @@ array of MCMC draws as its input rather than a \code{stanfit} object.
 \examples{\dontrun{
 ecode <- '
   parameters {
-    real<lower=0> y[2];
+    array[2] real<lower=0> y;
   } 
   model {
     y ~ exponential(1);

rstan/rstan/man/stanfit-method-traceplot.Rd

@@ -55,7 +55,7 @@
 # 
 excode <- '
   transformed data {
-    real y[20];
+    array[20] real y;
     y[1] <- 0.5796;  y[2]  <- 0.2276;   y[3] <- -0.2959; 
     y[4] <- -0.3742; y[5]  <- 0.3885;   y[6] <- -2.1585;
     y[7] <- 0.7111;  y[8]  <- 1.4424;   y[9] <- 2.5430; 

rstan/rstan/man/stanfit2array-method.Rd

@@ -71,8 +71,8 @@
 \examples{\dontrun{
 ex_model_code <- '
   parameters {
-    real alpha[2,3];
-    real beta[2]; 
+    array[2, 3] real alpha;
+    array[2] real beta; 
   } 
   model {
     for (i in 1:2) for (j in 1:3) 

rstan/rstan/tests/testthat/test-partial_inits.R

@@ -4,7 +4,7 @@ test_that("partial_inits works", {
   stan_model_code <- "
     data {
       int<lower=0> N;
-      real y[N];
+      array[N] real y;
     }
 
     parameters {

rstan/rstan/tests/testthat/test-stan_fun.R

@@ -6,7 +6,7 @@ test_that("Running stan() in parallel works",  {
   data {
     int N;
   } parameters {
-    real y[N];
+    array[N] real y;
   }  model {
     y ~ normal(0, 1);
   }
@@ -48,11 +48,11 @@ test_that("stan() arguments works", {
   diag_fname2 <- "diag2.csv"
   model_code <- "
     parameters {
-      real y[2];
+      array[2] real y;
       real alpha;
     }
     transformed parameters {
-      real y2[2, 2];
+      array[2, 2] real y2;
       y2[1, 1] = y[1];
       y2[1, 2] = -y[1];
       y2[2, 1] = -y[2];

rstan/rstan/tests/testthat/test-stanfit.R

@@ -8,11 +8,11 @@ test_that("outputing csv and extracting work", {
       n = 0;
     }
     parameters {
-      real y[2];
-      real zeroleny[n];
+      array[2] real y;
+      array[n] real zeroleny;
     }
     transformed parameters {
-      real y2[2, 2];
+      array[2, 2] real y2;
       y2[1, 1] = y[1];
       y2[1, 2] = -y[1];
       y2[2, 1] = -y[2];
@@ -22,7 +22,7 @@ test_that("outputing csv and extracting work", {
       y ~ normal(0, 1);
     }
     generated quantities {
-      real y3[3, 2, 3];
+      array[3, 2, 3] real y3;
       y3[1,1,1] = 1;   y3[1,1,2] = 2;   y3[1,1,3] = 3;
       y3[1,2,1] = 4;   y3[1,2,2] = 5;   y3[1,2,3] = 6;
       y3[2,1,1] = 7;   y3[2,1,2] = 8;   y3[2,1,3] = 9;
@@ -182,7 +182,7 @@ test_that("grad log is correct", {
 
   code <- "
     data {
-      real y[20];
+      array[20] real y;
     }
     parameters {
       real mu;
@@ -241,7 +241,7 @@ test_that("Specifying arguments and data works", {
   code <- "
     data {
       int N;
-      real y[N];
+      array[N] real y;
     }
     parameters {
       real mu;