Merge pull request #14 from andrjohns/array-syntax

Update deprecated syntax for future rstan compatibility
AngusMcLure · Nov 16, 2023 · d39a365 · d39a365
2 parents 85828d9 + 1a83427
commit d39a365
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Showing 5 changed files with 15 additions and 18 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -36,7 +36,7 @@ Imports:
     progress,
     Rcpp (>= 0.12.0),
     RcppParallel (>= 5.0.1),
-    rstan (>= 2.18.1),
+    rstan (>= 2.26.0),
     rstantools (>= 2.3.1.1),
     stats,
     stringr
@@ -45,8 +45,8 @@ LinkingTo:
     Rcpp (>= 0.12.0),
     RcppEigen (>= 0.3.3.3.0),
     RcppParallel (>= 5.0.1),
-    rstan (>= 2.18.1),
-    StanHeaders (>= 2.18.0)
+    rstan (>= 2.26.0),
+    StanHeaders (>= 2.26.0)
 SystemRequirements: GNU make
 RoxygenNote: 7.2.3
 Language: en-AU

diff --git a/configure b/configure
@@ -3,6 +3,3 @@
 # Generated by rstantools.  Do not edit by hand.
 
 "${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"
-
-# Add configuration needed for big object files
-echo "PKG_CXXFLAGS += -Wa,-mbig-obj" >> ./src/Makevars
diff --git a/inst/stan/HierPoolPrevIndividualSD.stan b/inst/stan/HierPoolPrevIndividualSD.stan
@@ -1,9 +1,9 @@
 data {
   int<lower=1> N; //Number of data points
   int<lower=1> L; // Number of levels or grouping variables
-  int<lower=1> NumGroups[L]; //Number of groups for each level of grouping variable
+  array[L] int<lower=1> NumGroups; //Number of groups for each level of grouping variable
   int<lower=L> TotalGroups; //Total number of groups across all levels
-  int<lower=0, upper=1> Result[N];
+  array[N] int<lower=0, upper=1> Result;
   vector<lower=0>[N] PoolSize;
   matrix<lower = 0, upper = 1>[N,TotalGroups] Z; //Model matrix for group effects
   // Parameters for t-distributed priors for:
@@ -17,11 +17,11 @@ data {
   real<lower=0> GroupSDSigma;
 }
 transformed data{
-  int<lower=0, upper=1> FlippedResult[N];
+  array[N] int<lower=0, upper=1> FlippedResult;
   //Get a sparse version of the model matrix for group effects (Z)
   vector[L*N] Zw;
-  int Zv[L*N];
-  int Zu[N+1];
+  array[L*N] int Zv;
+  array[N+1] int Zu;
   Zw = csr_extract_w(Z);
   Zv = csr_extract_v(Z);
   Zu = csr_extract_u(Z);

diff --git a/inst/stan/HierPoolPrevTotalSD.stan b/inst/stan/HierPoolPrevTotalSD.stan
@@ -1,9 +1,9 @@
 data {
   int<lower=1> N; //Number of data points
   int<lower=1> L; // Number of levels or grouping variables
-  int<lower=1> NumGroups[L]; //Number of groups for each level of grouping variable
+  array[L] int<lower=1> NumGroups; //Number of groups for each level of grouping variable
   int<lower=L> TotalGroups; //Total number of groups across all levels
-  int<lower=0, upper=1> Result[N];
+  array[N] int<lower=0, upper=1> Result;
   vector<lower=0>[N] PoolSize;
   matrix<lower = 0, upper = 1>[N,TotalGroups] Z; //Model matrix for group effects
   // Parameters for t-distributed priors for:
@@ -17,11 +17,11 @@ data {
   real<lower=0> GroupSDSigma;
 }
 transformed data{
-  int<lower=0, upper=1> FlippedResult[N];
+  array[N] int<lower=0, upper=1> FlippedResult;
   //Get a sparse version of the model matrix for group effects (Z)
   vector[L*N] Zw;
-  int Zv[L*N];
-  int Zu[N+1];
+  array[L*N] int Zv;
+  array[N+1] int Zu;
   Zw = csr_extract_w(Z);
   Zv = csr_extract_v(Z);
   Zu = csr_extract_u(Z);

diff --git a/inst/stan/PoolPrev.stan b/inst/stan/PoolPrev.stan
@@ -1,6 +1,6 @@
 data {
   int<lower=1> N;
-  int<lower=0, upper=1> Result[N];
+  array[N] int<lower=0, upper=1> Result;
   vector<lower=0>[N] PoolSize;
   real<lower=0> PriorAlpha;
   real<lower=0> PriorBeta;
@@ -10,7 +10,7 @@ parameters {
   real<lower=0, upper=1> p;
 }
 transformed parameters{
-  real<lower=0, upper=1> ps[N];
+  array[N] real<lower=0, upper=1> ps;
   real q;
   q = 1-p;
   for(n in 1:N){