Update deprecated syntax for future rstan compatibility (#8)

* Update deprecated syntax * update unit tests + skip examples + bump version --------- Co-authored-by: FBartos <[email protected]>
FBartos · Sep 20, 2023 · d1159af · d1159af
1 parent cfeef39
commit d1159af
Show file tree

Hide file tree

Showing 27 changed files with 1,540 additions and 1,529 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RoBTT
 Title: Robust Bayesian T-Test
-Version: 1.2.0
+Version: 1.2.1
 Maintainer: František Bartoš <[email protected]>
 Authors@R: c( 
     person("František", "Bartoš",     role = c("aut", "cre"),
@@ -30,8 +30,8 @@ RoxygenNote: 7.2.3
 NeedsCompilation: yes
 ByteCompile: true
 LinkingTo: 
-    StanHeaders (>= 2.18.1),
-    rstan (>= 2.21.2),
+    StanHeaders (>= 2.26.0),
+    rstan (>= 2.26.0),
     BH (>= 1.69.0),
     Rcpp (>= 0.12.15),
     RcppEigen (>= 0.3.3.4.0),
@@ -40,7 +40,7 @@ Depends:
     R (>= 4.0.0),
     Rcpp (>= 0.12.19)
 Imports:
-    rstan(>= 2.21.2),
+    rstan(>= 2.26.0),
     rstantools(>= 1.5.0),
     RcppParallel (>= 5.0.1),
     BayesTools (>= 0.2.15),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+## version 1.2.1
+Compatibility update for the rstan 2.26.
+
 ## version 1.2.0
 ### Changes
 - when specifying prior distribution for the nu parameter, coerce Spike(Inf) to NULL

diff --git a/R/main.R b/R/main.R
@@ -70,7 +70,7 @@
 #'
 #' @return \code{RoBTT} returns an object of \link[base]{class} \code{"RoBTT"}.
 #'
-#' @examples
+#' @examples \dontrun{
 #' # using the example data from Darwin
 #' data("fertilization", package = "RoBTT")
 #' fit <- RoBTT(
@@ -87,7 +87,8 @@
 #'
 #' # summary can provide many details about the model
 #' summary(fit)
-#'
+#' }
+#' 
 #' @references
 #' \insertAllCited{}
 #' @export RoBTT

diff --git a/R/plot.R b/R/plot.R
@@ -33,7 +33,7 @@
 #' x-label, y-label, title, x-axis range, and y-axis range
 #' respectively.
 #'
-#' @examples 
+#' @examples \dontrun{
 #' data("fertilization", package = "RoBTT")
 #' fit <- RoBTT(
 #'   x1       = fertilization$Self,
@@ -52,6 +52,7 @@
 #' 
 #' # plot prior and posterior of the conditional effect size estimate
 #' plot(fit, parameter = "delta", conditional = TRUE, prior = TRUE)
+#' }
 #' 
 #' @return \code{plot.RoBTT} returns either \code{NULL} if \code{plot_type = "base"}
 #' or an object object of class 'ggplot2' if \code{plot_type = "ggplot2"}.

diff --git a/R/summary.R b/R/summary.R
@@ -41,7 +41,7 @@ print.RoBTT <- function(x, ...){
 #' be omitted from the summary. Defaults to \code{FALSE}.
 #' @param ... additional arguments
 #'
-#' @examples
+#' @examples \dontrun{
 #' # using the example data from Darwin
 #' data("fertilization", package = "RoBTT")
 #' fit <- RoBTT(
@@ -72,7 +72,7 @@ print.RoBTT <- function(x, ...){
 #'
 #' # summary of individual models and their parameters can be further obtained by
 #' summary(fit, type = "individual")
-#'
+#' }
 #'
 #' @return \code{summary.RoBTT} returns a list of tables of class 'BayesTools_table'.
 #'

diff --git a/R/utilities.R b/R/utilities.R
@@ -82,6 +82,7 @@ assign("max_cores",       parallel::detectCores(logical = TRUE) - 1,  envir = Ro
     "1.0.3" = c("0.2.12", "999.999.999"),
     "1.1.0" = c("0.2.14", "999.999.999"),
     "1.2.0" = c("0.2.15", "999.999.999"),
+    "1.2.1" = c("0.2.15", "999.999.999"),
     stop("New RoBTT version needs to be defined in '.check_BayesTools' function!")
   )
 

diff --git a/inst/stan/beta.stan b/inst/stan/beta.stan
@@ -21,8 +21,8 @@ data {
   // range of the parameters
   vector[is_d == 1 ? 2 : 0] bounds_d;
   vector[is_r == 1 ? 2 : 0] bounds_r;
-  int bounds_type_d[is_d == 1 ? 2 : 0];
-  int bounds_type_r[is_r == 1 ? 2 : 0];
+  array[is_d == 1 ? 2 : 0] int bounds_type_d;
+  array[is_r == 1 ? 2 : 0] int bounds_type_r;
 
   // prior distribution specification of the parameteres
   vector[is_d == 0 ? 1 : 0] fixed_d;
@@ -35,8 +35,8 @@ data {
 parameters{
   real<lower = 0, upper = 1> mu;
   real<lower = 0> sigma2;
-  real<lower = coefs_lb(bounds_type_d, bounds_d), upper = coefs_ub(bounds_type_d, bounds_d)> delta[is_d];
-  real<lower = coefs_lb(bounds_type_r, bounds_r), upper = coefs_ub(bounds_type_r, bounds_r)> rho[is_r];
+  array[is_d] real<lower = coefs_lb(bounds_type_d, bounds_d), upper = coefs_ub(bounds_type_d, bounds_d)> delta;
+  array[is_r] real<lower = coefs_lb(bounds_type_r, bounds_r), upper = coefs_ub(bounds_type_r, bounds_r)> rho;
 }
 transformed parameters {
   real pooled_sigma;

diff --git a/inst/stan/gamma.stan b/inst/stan/gamma.stan
@@ -21,8 +21,8 @@ data {
   // range of the parameters
   vector[is_d == 1 ? 2 : 0] bounds_d;
   vector[is_r == 1 ? 2 : 0] bounds_r;
-  int bounds_type_d[is_d == 1 ? 2 : 0];
-  int bounds_type_r[is_r == 1 ? 2 : 0];
+  array[is_d == 1 ? 2 : 0] int bounds_type_d;
+  array[is_r == 1 ? 2 : 0] int bounds_type_r;
 
   // prior distribution specification of the parameteres
   vector[is_d == 0 ? 1 : 0] fixed_d;
@@ -35,8 +35,8 @@ data {
 parameters{
   real<lower = 0> mu;
   real<lower = 0> sigma2;
-  real<lower = coefs_lb(bounds_type_d, bounds_d), upper = coefs_ub(bounds_type_d, bounds_d)> delta[is_d];
-  real<lower = coefs_lb(bounds_type_r, bounds_r), upper = coefs_ub(bounds_type_r, bounds_r)> rho[is_r];
+  array[is_d] real<lower = coefs_lb(bounds_type_d, bounds_d), upper = coefs_ub(bounds_type_d, bounds_d)> delta;
+  array[is_r] real<lower = coefs_lb(bounds_type_r, bounds_r), upper = coefs_ub(bounds_type_r, bounds_r)> rho;
 }
 transformed parameters {
   real pooled_sigma;

diff --git a/inst/stan/include/common_functions.stan b/inst/stan/include/common_functions.stan
@@ -14,7 +14,7 @@ functions {
   }
 
   // function for setting parameter bounds
-  real coefs_lb(int[] type_in, vector bound_in) {
+  real coefs_lb(array[] int type_in, vector bound_in) {
     int type;
     real bound;
     real lb;
@@ -30,7 +30,7 @@ functions {
       lb = bound;
     return lb;
   }
-  real coefs_ub(int[] type_in, vector bound_in) {
+  real coefs_ub(array[] int type_in, vector bound_in) {
     int type;
     real bound;
     real lb;
@@ -56,7 +56,7 @@ functions {
   // type 6 = inverse-gamma
   // type 7 = uniform
   // type 8 = beta
-  real set_prior(real parameter, int prior_type, vector prior_parameters, int[] bounds_type, vector bounds){
+  real set_prior(real parameter, int prior_type, vector prior_parameters, array[] int bounds_type, vector bounds){
     real ll;
 
     if(prior_type == 1){

diff --git a/inst/stan/lognormal.stan b/inst/stan/lognormal.stan
@@ -21,8 +21,8 @@ data {
   // range of the parameters
   vector[is_d == 1 ? 2 : 0] bounds_d;
   vector[is_r == 1 ? 2 : 0] bounds_r;
-  int bounds_type_d[is_d == 1 ? 2 : 0];
-  int bounds_type_r[is_r == 1 ? 2 : 0];
+  array[is_d == 1 ? 2 : 0] int bounds_type_d;
+  array[is_r == 1 ? 2 : 0] int bounds_type_r;
 
   // prior distribution specification of the parameteres
   vector[is_d == 0 ? 1 : 0] fixed_d;
@@ -35,8 +35,8 @@ data {
 parameters{
   real<lower = 0> mu;
   real<lower = 0> sigma2;
-  real<lower = coefs_lb(bounds_type_d, bounds_d), upper = coefs_ub(bounds_type_d, bounds_d)> delta[is_d];
-  real<lower = coefs_lb(bounds_type_r, bounds_r), upper = coefs_ub(bounds_type_r, bounds_r)> rho[is_r];
+  array[is_d] real<lower = coefs_lb(bounds_type_d, bounds_d), upper = coefs_ub(bounds_type_d, bounds_d)> delta;
+  array[is_r] real<lower = coefs_lb(bounds_type_r, bounds_r), upper = coefs_ub(bounds_type_r, bounds_r)> rho;
 }
 transformed parameters {
   real pooled_sigma;

diff --git a/inst/stan/normal.stan b/inst/stan/normal.stan
@@ -21,8 +21,8 @@ data {
   // range of the parameters
   vector[is_d == 1 ? 2 : 0] bounds_d;
   vector[is_r == 1 ? 2 : 0] bounds_r;
-  int bounds_type_d[is_d == 1 ? 2 : 0];
-  int bounds_type_r[is_r == 1 ? 2 : 0];
+  array[is_d == 1 ? 2 : 0] int bounds_type_d;
+  array[is_r == 1 ? 2 : 0] int bounds_type_r;
 
   // prior distribution specification of the parameteres
   vector[is_d == 0 ? 1 : 0] fixed_d;
@@ -35,8 +35,8 @@ data {
 parameters{
   real mu;
   real<lower = 0> sigma2;
-  real<lower = coefs_lb(bounds_type_d, bounds_d), upper = coefs_ub(bounds_type_d, bounds_d)> delta[is_d];
-  real<lower = coefs_lb(bounds_type_r, bounds_r), upper = coefs_ub(bounds_type_r, bounds_r)> rho[is_r];
+  array[is_d] real<lower = coefs_lb(bounds_type_d, bounds_d), upper = coefs_ub(bounds_type_d, bounds_d)> delta;
+  array[is_r] real<lower = coefs_lb(bounds_type_r, bounds_r), upper = coefs_ub(bounds_type_r, bounds_r)> rho;
 }
 transformed parameters {
   real pooled_sigma;

diff --git a/inst/stan/t.stan b/inst/stan/t.stan
@@ -23,14 +23,14 @@ data {
   vector[is_d  == 1 ? 2 : 0] bounds_d;
   vector[is_r  == 1 ? 2 : 0] bounds_r;
   vector[is_nu == 1 ? 2 : 0] bounds_nu;
-  int bounds_type_d[is_d   == 1 ? 2 : 0];
-  int bounds_type_r[is_r   == 1 ? 2 : 0];
-  int bounds_type_nu[is_nu == 1 ? 2 : 0];
+  array[is_d   == 1 ? 2 : 0] int bounds_type_d;
+  array[is_r   == 1 ? 2 : 0] int bounds_type_r;
+  array[is_nu == 1 ? 2 : 0] int bounds_type_nu;
 
   // prior distribution specification of the parameteres
-  real fixed_d[is_d   == 0 ? 1 : 0];
-  real fixed_r[is_r   == 0 ? 1 : 0];
-  real fixed_nu[is_nu == 0 ? 1 : 0];
+  array[is_d   == 0 ? 1 : 0] real fixed_d;
+  array[is_r   == 0 ? 1 : 0] real fixed_r;
+  array[is_nu == 0 ? 1 : 0] real fixed_nu;
   vector[is_d  == 1 ? 3 : 0] prior_parameters_d;
   vector[is_r  == 1 ? 3 : 0] prior_parameters_r;
   vector[is_nu == 1 ? 3 : 0] prior_parameters_nu;
@@ -41,15 +41,15 @@ data {
 parameters{
   real mu;
   real<lower = 0> sigma2;
-  real<lower = coefs_lb(bounds_type_d,  bounds_d),  upper = coefs_ub(bounds_type_d,  bounds_d)>  delta[is_d];
-  real<lower = coefs_lb(bounds_type_r,  bounds_r),  upper = coefs_ub(bounds_type_r,  bounds_r)>  rho[is_r];
-  real<lower = coefs_lb(bounds_type_nu, bounds_nu), upper = coefs_ub(bounds_type_nu, bounds_nu)> nu_p[is_nu];
+  array[is_d] real<lower = coefs_lb(bounds_type_d,  bounds_d),  upper = coefs_ub(bounds_type_d,  bounds_d)>  delta;
+  array[is_r] real<lower = coefs_lb(bounds_type_r,  bounds_r),  upper = coefs_ub(bounds_type_r,  bounds_r)>  rho;
+  array[is_nu] real<lower = coefs_lb(bounds_type_nu, bounds_nu), upper = coefs_ub(bounds_type_nu, bounds_nu)> nu_p;
 }
 transformed parameters {
   real pooled_sigma;
-  real sigma_i[2];
-  real scale_i[2];
-  real mu_i[2];
+  array[2] real sigma_i;
+  array[2] real scale_i;
+  array[2] real mu_i;
   real nu;
 
 

diff --git a/man/RoBTT.Rd b/man/RoBTT.Rd
diff --git a/man/plot.RoBTT.Rd b/man/plot.RoBTT.Rd
diff --git a/man/summary.RoBTT.Rd b/man/summary.RoBTT.Rd