CRAN release 0.2.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bennu
 Title: Bayesian Estimation of Naloxone Kit Number Under-Reporting
-Version: 0.1.0
+Version: 0.2.1.9000
 Authors@R: c(
     person(given = "Mike",
            family = "Irvine",
@@ -12,7 +12,7 @@ Authors@R: c(
 Description: Bayesian model and associated tools for generating estimates of 
     total naloxone kit numbers distributed and used from naloxone kit orders 
     data. Provides functions for generating simulated data of naloxone kit use
-    and functions for generating samples from the posterior
+    and functions for generating samples from the posterior.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

LICENSE

@@ -1,21 +1,2 @@
-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.
+YEAR: 2023
+COPYRIGHT HOLDER: Michael Irvine

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022 bennu authors
+Copyright (c) 2023 Michael Irvine
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NEWS.md

@@ -1,3 +1,9 @@
+# bennu (development version)
+
+# bennu 0.2.1
+
+# bennu 0.2.0
+
 # bennu 0.1.0
 
 * `est_naloxone` can accept `psi_vector` of variable length and additionally

R/est_naloxone.R

@@ -28,6 +28,7 @@
 #' @param adapt_delta (double, between 0 and 1, defaults to 0.8)
 #' @param ... other parameters to pass to [rstan::sampling]
 #' @family inference
+#' @return An S4 stanfit class object containing the fitted model
 #' @export
 est_naloxone_vec <- function(N_region, N_t, N_distributed, regions,
                              times, Orders2D, Reported_Distributed,
@@ -126,6 +127,7 @@ est_naloxone_vec <- function(N_region, N_t, N_distributed, regions,
 #'   \item{region_name}{Optional label for region}
 #' }
 #' @examples
+#' \dontrun{
 #' library(rstan)
 #' library(bayesplot)
 #'
@@ -138,8 +140,10 @@ est_naloxone_vec <- function(N_region, N_t, N_distributed, regions,
 #'   pars = c("sigma", "mu0"),
 #'   off_diag_args = list(size = 1, alpha = 0.5)
 #' )
+#' }
 #' @inheritParams est_naloxone_vec
 #' @family inference
+#' @return An S4 stanfit class object containing the fitted model
 #' @export
 est_naloxone <- function(d,
                          psi_vec = c(0.7, 0.2, 0.1),

R/generate_model_data.R

@@ -18,6 +18,17 @@
 #' @param c_region logit probability of kit use per region
 #' @param reporting_freq The frequency that distribution data is provided.
 #'  If `NULL` distribution frequency matches orders frequency
+#' @return A tibble
+#' \describe{
+#'   \item{Orders}{Kit orders per time and region}
+#'   \item{regions}{Numeric index indicating region of orders and distributions}
+#'   \item{Reported_Used}{Number of kits reported as used}
+#'   \item{Reported_Distributed}{Number of kits reported as distributed}
+#'   \item{p_use}{Probability that a kit was used}
+#'   \item{p_reported}{Probability that a distributed kit was reported}
+#'   \item{times}{Index for time}
+#'   \item{region_name}{String index for the region}
+#' }
 #' @export
 #' @importFrom stats rbinom rnorm
 #' @family data generation