diff --git a/DESCRIPTION b/DESCRIPTION index 8772c4c..728c3cc 100644 --- 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 index d9c5f04..0304fc5 100755 --- 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 index 84fdcef..0a18001 100644 --- a/inst/stan/HierPoolPrevIndividualSD.stan +++ b/inst/stan/HierPoolPrevIndividualSD.stan @@ -1,9 +1,9 @@ data { int N; //Number of data points int L; // Number of levels or grouping variables - int NumGroups[L]; //Number of groups for each level of grouping variable + array[L] int NumGroups; //Number of groups for each level of grouping variable int TotalGroups; //Total number of groups across all levels - int Result[N]; + array[N] int Result; vector[N] PoolSize; matrix[N,TotalGroups] Z; //Model matrix for group effects // Parameters for t-distributed priors for: @@ -17,11 +17,11 @@ data { real GroupSDSigma; } transformed data{ - int FlippedResult[N]; + array[N] int 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 index a45410c..5056e95 100644 --- a/inst/stan/HierPoolPrevTotalSD.stan +++ b/inst/stan/HierPoolPrevTotalSD.stan @@ -1,9 +1,9 @@ data { int N; //Number of data points int L; // Number of levels or grouping variables - int NumGroups[L]; //Number of groups for each level of grouping variable + array[L] int NumGroups; //Number of groups for each level of grouping variable int TotalGroups; //Total number of groups across all levels - int Result[N]; + array[N] int Result; vector[N] PoolSize; matrix[N,TotalGroups] Z; //Model matrix for group effects // Parameters for t-distributed priors for: @@ -17,11 +17,11 @@ data { real GroupSDSigma; } transformed data{ - int FlippedResult[N]; + array[N] int 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 index c2d460c..79f08ff 100644 --- a/inst/stan/PoolPrev.stan +++ b/inst/stan/PoolPrev.stan @@ -1,6 +1,6 @@ data { int N; - int Result[N]; + array[N] int Result; vector[N] PoolSize; real PriorAlpha; real PriorBeta; @@ -10,7 +10,7 @@ parameters { real p; } transformed parameters{ - real ps[N]; + array[N] real ps; real q; q = 1-p; for(n in 1:N){