rstantools

DESCRIPTION

@@ -12,16 +12,23 @@ Description: This package fits models to bycatch data, and can expand to fleet-w
 License: GPL-3
 Encoding: UTF-8
 Depends:
-    R (>= 4.0.0), Rcpp (>= 1.0.5), methods
+    R (>= 3.4.0)
 Imports:
-    rstan (>= 2.21.2),
-    rstantools (>= 2.1.1),
     ggplot2,
     loo (>= 2.4.1),
     dplyr (>= 1.0.2),
-    rlang (>= 0.4.1)
-LinkingTo: StanHeaders (>= 2.21.0.7), rstan (>= 2.21.2), BH (>= 1.75.0.0),
-        Rcpp (>= 1.0.5), RcppEigen (>= 0.3.3.9.1)
+    rlang (>= 0.4.1),
+    methods,
+    Rcpp (>= 0.12.0),
+    RcppParallel (>= 5.0.1),
+    rstan (>= 2.18.1),
+    rstantools (>= 2.3.0)
+LinkingTo: BH (>= 1.66.0),
+    Rcpp (>= 0.12.0),
+    RcppEigen (>= 0.3.3.3.0),
+    RcppParallel (>= 5.0.1),
+    rstan (>= 2.18.1),
+    StanHeaders (>= 2.18.0)
 Suggests:
     testthat,
     parallel,

NAMESPACE

@@ -9,7 +9,6 @@ export(plot_fitted)
 import(Rcpp)
 import(ggplot2)
 import(methods)
-import(rstantools)
 importFrom(rstan,extract)
 importFrom(rstan,sampling)
 importFrom(rstan,vb)

R/bycatch-package.R

@@ -8,10 +8,9 @@
 #' @useDynLib bycatch, .registration = TRUE
 #' @import methods
 #' @import Rcpp
-#' @import rstantools
 #' @importFrom rstan sampling
 #'
 #' @references
-#' Stan Development Team (2018). RStan: the R interface to Stan. R package version 2.18.2. http://mc-stan.org
+#' Stan Development Team (2023). RStan: the R interface to Stan. R package version 2.21.8. https://mc-stan.org
 #'
 NULL

R/stanmodels.R

@@ -1,43 +1,25 @@
-# Part of the bayesdfa package for estimating model parameters
-# Copyright (C) 2015, 2016, 2017 Trustees of Columbia University
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+# Generated by rstantools.  Do not edit by hand.
 
-# This file is only intended to be used during the installation process
-# nocov start
-MODELS_HOME <- "src"
-if (!file.exists(MODELS_HOME)) MODELS_HOME <- sub("R$", "src", getwd())
+# names of stan models
+stanmodels <- c("bycatch")
 
-stan_files <- dir(file.path(MODELS_HOME, "stan_files"),
-  pattern = "stan$", full.names = TRUE
-)
-stanmodels <- lapply(stan_files, function(f) {
-  model_cppname <- sub("\\.stan$", "", basename(f))
-  stanfit <- rstan::stanc(f,
-    allow_undefined = TRUE,
-    obfuscate_model_name = FALSE
-  )
-  stanfit$model_cpp <- list(
-    model_cppname = stanfit$model_name,
-    model_cppcode = stanfit$cppcode
-  )
-  return(do.call(methods::new, args = c(stanfit[-(1:3)],
-    Class = "stanmodel",
-    mk_cppmodule = function(x) get(paste0("model_", model_cppname))
-  )))
+# load each stan module
+Rcpp::loadModule("stan_fit4bycatch_mod", what = TRUE)
+
+# instantiate each stanmodel object
+stanmodels <- sapply(stanmodels, function(model_name) {
+  # create C++ code for stan model
+  stan_file <- if(dir.exists("stan")) "stan" else file.path("inst", "stan")
+  stan_file <- file.path(stan_file, paste0(model_name, ".stan"))
+  stanfit <- rstan::stanc_builder(stan_file,
+                                  allow_undefined = TRUE,
+                                  obfuscate_model_name = FALSE)
+  stanfit$model_cpp <- list(model_cppname = stanfit$model_name,
+                            model_cppcode = stanfit$cppcode)
+  # create stanmodel object
+  methods::new(Class = "stanmodel",
+               model_name = stanfit$model_name,
+               model_code = stanfit$model_code,
+               model_cpp = stanfit$model_cpp,
+               mk_cppmodule = function(x) get(paste0("rstantools_model_", model_name)))
 })
-names(stanmodels) <- sub("\\.stan$", "", basename(stan_files))
-rm(MODELS_HOME)
-# nocov end

bycatch.Rproj

@@ -14,6 +14,7 @@ LaTeX: pdfLaTeX
 
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
 
 BuildType: Package
 PackageUseDevtools: Yes