update for rstan tools

noaa-nwfsc · Sep 11, 2023 · c9a53a4 · c9a53a4
1 parent ba10aa7
commit c9a53a4
Show file tree

Hide file tree

Showing 10 changed files with 1,746 additions and 1,215 deletions.
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.1.0
-Date: 2022-02-09 16:29:23 UTC
-SHA: b21d92a5ae04e0190728231bf84d3529c758df21
+Version: 1.2.0
+Date: 2023-09-11 22:08:20 UTC
+SHA: ba10aa7dd9c9ea57675350652ba4e2bf4df1b7cf
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: zoid
 Title: Bayesian Zero-and-One Inflated Dirichlet Regression Modelling 
-Version: 1.1.0
+Version: 1.2.0
 Authors@R: 
     c(person(given = "Eric J.",
            family = "Ward",
@@ -37,16 +37,16 @@ License: GPL (>=3)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Biarch: true
 URL: https://nwfsc-cb.github.io/zoid/
 BugReports: https://github.com/nwfsc-cb/zoid/issues
 Depends: 
     R (>= 3.4.0)
 Imports: 
-    methods,
-    gtools,
     compositions,
+    gtools,
+    methods,
     Rcpp (>= 0.12.0),
     RcppParallel (>= 5.0.1),
     rstan (>= 2.26.0),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# zoid 1.2.0
+
+* Updated Stan code to reflect changes needed to be compatible with Stan 2.26 (arrays)
+
 # zoid 1.1.0
 
 * Changed treatment of zeros in Stan model. Package consistent with Jensen et al. (in review)

diff --git a/R/fit_prior.R b/R/fit_prior.R
@@ -30,7 +30,7 @@ fit_prior <- function(n_bins, n_draws = 10000, target = 1 / n_bins, iterations =
       n_draws = n_draws,
       method = "BFGS"
     ), silent = TRUE)
-    if (class(o) != "try-error") {
+    if(!identical(class(o), "try-error")) {
       if (o$value < best) {
         best <- o$value
         best_value <- list(

diff --git a/src/Makevars b/src/Makevars
@@ -3,8 +3,8 @@
 STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")
 
 STANC_FLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "cat(ifelse(utils::packageVersion('rstan') >= 2.26, '-DUSE_STANC3',''))")
-PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(STANC_FLAGS)
+PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(STANC_FLAGS) -D_HAS_AUTO_PTR_ETC=0
 PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()")
 PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")
 
-CXX_STD = CXX14
+CXX_STD = CXX17
diff --git a/src/RcppExports.o b/src/RcppExports.o
diff --git a/src/stanExports_dirichregmod.h b/src/stanExports_dirichregmod.h
diff --git a/src/stanExports_dirichregmod.o b/src/stanExports_dirichregmod.o
diff --git a/src/zoid.so b/src/zoid.so