From 9b63afa35f0f3cd4383e0b11a3355a7561da4c5f Mon Sep 17 00:00:00 2001
From: Bai Li <bai.li@noaa.gov>
Date: Thu, 19 Oct 2023 16:53:14 -0400
Subject: [PATCH] update documentation

---
 DESCRIPTION     |  9 ++++++---
 NAMESPACE       |  5 +++++
 R/add_object.R  |  2 ++
 R/make_hex.R    |  4 ++++
 R/shiny_dd.r    |  1 +
 R/validate_Rd.R |  2 +-
 man/Catch.Rd    |  2 +-
 man/make_hex.Rd | 14 ++++++++++++++
 8 files changed, 34 insertions(+), 5 deletions(-)
 create mode 100644 man/make_hex.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index b002ddb..62a0d0c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,14 +5,17 @@ Authors@R:
     person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))
 Description: What the package does (one paragraph).
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+License: GPL (>= 3) | file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Imports: 
     mvbutils,
-    tools
+    tools,
+    hexSticker,
+    jsonlite,
+    jsonvalidate,
+    shiny
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
index bd3aacd..c2d5178 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,3 +9,8 @@ export(read_in)
 export(shiny_dd)
 export(validate_Rd)
 import(tools)
+importFrom(hexSticker,sticker)
+importFrom(jsonlite,fromJSON)
+importFrom(jsonlite,toJSON)
+importFrom(jsonvalidate,json_validate)
+importFrom(shiny,runApp)
diff --git a/R/add_object.R b/R/add_object.R
index c96ad09..d5f24e5 100644
--- a/R/add_object.R
+++ b/R/add_object.R
@@ -3,6 +3,8 @@
 #' @param input_list A list of fields corresponding to entries. Must include
 #'  \code{name,description,Examples, Units, Rationale, Alternatives, Range of possible values}
 #' @return An R list in the JSON format which includes the new term.
+#' @importFrom jsonlite fromJSON toJSON
+#' @importFrom jsonvalidate json_validate
 #' @export
 add_object <- function(input_list) {
   json_obj <- jsonlite::fromJSON(system.file("extdata","top20.json", package = "stockassessmentdictionary"))
diff --git a/R/make_hex.R b/R/make_hex.R
index 1c0b046..151eb95 100644
--- a/R/make_hex.R
+++ b/R/make_hex.R
@@ -1,3 +1,7 @@
+#' Create a hexagonal sticker for the 'fishdictionary' package.
+#'
+#' @importFrom hexSticker sticker
+#' @return The function does not return any value but creates a hexagonal sticker image.
 make_hex <- function(){
   hexSticker::sticker(paste0("./static/pictures/", c("nounbook.png","nounfish.png")), 
                       package="fishdictionary", p_size=20, s_x=c(1,1), s_y=c(.4,.9), 
diff --git a/R/shiny_dd.r b/R/shiny_dd.r
index bfecbce..705e538 100644
--- a/R/shiny_dd.r
+++ b/R/shiny_dd.r
@@ -1,6 +1,7 @@
 #' Run the data dictionary app
 #'
 #' Run the data dictionary app
+#' @importFrom shiny runApp
 #' @export
 #' @param browse Logical. Use browser for running Shiny app.
 #' @examples
diff --git a/R/validate_Rd.R b/R/validate_Rd.R
index f771ea5..ee815ae 100644
--- a/R/validate_Rd.R
+++ b/R/validate_Rd.R
@@ -13,7 +13,7 @@ validate_Rd <- function(Rd_file) {
   if (is.null(Rd_file)) stop("Please provide the path to the R documentation (Rd) file.")
 
   Rd <- tools::parse_Rd(Rd_file)
-  tags <- tools:::RdTags(Rd)
+  tags <- lapply(Rd, attr, "Rd_tag")
 
   # Validate name
   name <- Rd[[which(tags == "\\name")]]
diff --git a/man/Catch.Rd b/man/Catch.Rd
index c093698..8d8942c 100644
--- a/man/Catch.Rd
+++ b/man/Catch.Rd
@@ -10,7 +10,7 @@
 \item{Rationale}{Landings and catch are sometimes thought to be
 interchangeable but they are not given that catch can also include
 bycatch or unwanted catch.}
-\item{Alternatives}{total mortality}
+\item{Alternatives}{total mortality, harvest, total removals}
 \item{Range of possible values}{0--Inf}
 \item{Units}{mt, numbers}
 }
diff --git a/man/make_hex.Rd b/man/make_hex.Rd
new file mode 100644
index 0000000..2ce2ee1
--- /dev/null
+++ b/man/make_hex.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/make_hex.R
+\name{make_hex}
+\alias{make_hex}
+\title{Create a hexagonal sticker for the 'fishdictionary' package.}
+\usage{
+make_hex()
+}
+\value{
+The function does not return any value but creates a hexagonal sticker image.
+}
+\description{
+Create a hexagonal sticker for the 'fishdictionary' package.
+}