Re #26 Updates for cran submission.

.gitignore

@@ -39,3 +39,6 @@ vignettes/*.pdf
 .Renviron
 docs
 inst/doc
+
+# Reverse dependency check files
+revdep/*

NAMESPACE

@@ -9,9 +9,11 @@ export(model_random_walk_data)
 export(plot_kit_use)
 import(Rcpp)
 import(methods)
+importFrom(RcppParallel,RcppParallelLibs)
 importFrom(magrittr,"%>%")
 importFrom(rlang,":=")
 importFrom(rstan,sampling)
+importFrom(rstantools,rstan_config)
 importFrom(stats,rbinom)
 importFrom(stats,rnorm)
 useDynLib(bennu, .registration = TRUE)

NEWS.md

@@ -2,11 +2,15 @@
 
 * `kit_summary_table` created to provide a quick way of summarizing model 
 output by different strata
+
 * `model_random_walk_data` created to more closely mimic Bayesian data 
 generating process
+
 * `generate_model_data` deprecated as `model_random_walk_data` will supplant it
 as way of generating simulation data to test properties of the model
 
+* Updates to stan model to make it compliant to rstan 2.26 (#22)
+
 # bennu 0.2.1
 
 # bennu 0.2.0

R/bennu-package.R

@@ -9,6 +9,8 @@
 #' @import methods
 #' @import Rcpp
 #' @importFrom rstan sampling
+#' @importFrom rstantools rstan_config
+#' @importFrom RcppParallel RcppParallelLibs
 #'
 #' @references
 #' Stan Development Team (2020). RStan: the R interface to Stan. R package version 2.21.2. https://mc-stan.org

R/generate_model_data.R

@@ -13,7 +13,7 @@
 #' The probability of kit use in time is assumed to increase linearly in inverse
 #' logit space at a constant rate `0.1`.
 #' The probability of reporting for each month and region is iid distributed
-#' \eqn{\text{logit}^{-1}(p) \sim N(2,5)} which produces a mean reporting rate
+#' \eqn{logit^{-1}(p) \sim N(2,5)} which produces a mean reporting rate
 #' of approximately 88%
 #' @param N_t number of time-points
 #' @param region_coeffs vector of coefficients for regions determining kit orders

R/utils-table.R

@@ -44,6 +44,7 @@ kit_summary_table <- function(fit, ..., data = NULL,
 
 
   i <- sim_p <- times <- estimate <- Distributed <- Reported_Distributed <- NULL
+  sim_used <- Reported_Used <- Orders <- NULL
 
   percent_func <- scales::percent_format(accuracy = accuracy)
   comma_func <- scales::comma_format(accuracy = accuracy)

README.md

@@ -45,15 +45,18 @@ This example runs output for test data generated by the package:
 library(bennu)
 library(rstan)
 #> Loading required package: StanHeaders
-#> Loading required package: ggplot2
-#> rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
+#> 
+#> rstan version 2.26.22 (Stan version 2.26.1)
 #> For execution on a local, multicore CPU with excess RAM we recommend calling
 #> options(mc.cores = parallel::detectCores()).
 #> To avoid recompilation of unchanged Stan programs, we recommend calling
 #> rstan_options(auto_write = TRUE)
+#> For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions,
+#> change `threads_per_chain` option:
+#> rstan_options(threads_per_chain = 1)
 #> Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
 library(bayesplot)
-#> This is bayesplot version 1.8.1
+#> This is bayesplot version 1.10.0
 #> - Online documentation and vignettes at mc-stan.org/bayesplot
 #> - bayesplot theme set to bayesplot::theme_default()
 #>    * Does _not_ affect other ggplot2 plots

cran-comments.md

@@ -2,70 +2,10 @@
 
 Maintainer: 'Mike Irvine <mike.irvine@bccdc.ca>'
 
-New submission
-
-License components with restrictions and base license permitting such:
-  MIT + file LICENSE
-File 'LICENSE':
-  MIT License
-
-  Copyright (c) 2022 bennu authors
-
-  Permission is hereby granted, free of charge, to any person obtaining a copy
-  of this software and associated documentation files (the "Software"), to deal
-  in the Software without restriction, including without limitation the rights
-  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-  copies of the Software, and to permit persons to whom the Software is
-  furnished to do so, subject to the following conditions:
-
-  The above copyright notice and this permission notice shall be included in all
-  copies or substantial portions of the Software.
-
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-  SOFTWARE.
-
-Possibly misspelled words in DESCRIPTION:
-  Naloxone (2:31)
-  naloxone (13:11, 13:58, 14:63)
-
-> checking dependencies in R code ... NOTE
-Namespaces in Imports field not imported from:
-  'RcppParallel' 'rstantools'
-  All declared Imports should be used.
-
 > checking for GNU extensions in Makefiles ... NOTE
 GNU make is a SystemRequirements.
 
-> checking HTML version of manual ... NOTE
-Skipping checking math rendering: package 'V8' unavailable
-
-> checking for detritus in the temp directory ... NOTE
-Found the following files/directories:
-  'lastMiKTeXException'
-
-0 errors √ | 0 warnings √ | 5 notes x
-
--- bennu 0.1.0: CREATED
-
-Build ID:   bennu_0.1.0.tar.gz-12322482d4cc4946aeb968efd1be4ac9
-Platform:   Ubuntu Linux 20.04.1 LTS, R-release, GCC
-Submitted:  12m 48s ago
-
-
--- bennu 0.1.0: CREATED
-
-Build ID:   bennu_0.1.0.tar.gz-9b81e15504e64acb86418451ca038812
-Platform:   Fedora Linux, R-devel, clang, gfortran
-Submitted:  12m 48s ago
 
+0 errors √ | 0 warnings √ | 1 notes x
 
--- bennu 0.1.0: CREATED
 
-Build ID:   bennu_0.1.0.tar.gz-5e986dc4ddca490cbb12f3f43b9e81be
-Platform:   Debian Linux, R-devel, GCC ASAN/UBSAN
-Submitted:  12m 48s ago