Get rid of warnings and notes from rcmdcheck

.Rbuildignore

@@ -3,3 +3,6 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.github$
+^LICENSE\.md$
+inst/TextAnalysis

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

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)

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"))

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), 

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

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")]]

TextAnalysis/top10_analysis.R → inst/TextAnalysis/top10_analysis.R

@@ -214,9 +214,9 @@ proportion_database <- rbind(
 )
 proportion_database[nrow(proportion_database), "ID"] <- "Sum"
 
-write.csv(frequency_database, file=here::here("TextAnalysis", "top10_frequency.csv"), row.names=FALSE)
-write.csv(presence_database, file=here::here("TextAnalysis", "top10_presence.csv"), row.names=FALSE)
-write.csv(proportion_database, file=here::here("TextAnalysis", "top10_proportion.csv"), row.names=FALSE)
+write.csv(frequency_database, file=here::here("inst", "TextAnalysis", "top10_frequency.csv"), row.names=FALSE)
+write.csv(presence_database, file=here::here("inst", "TextAnalysis", "top10_presence.csv"), row.names=FALSE)
+write.csv(proportion_database, file=here::here("inst","TextAnalysis", "top10_proportion.csv"), row.names=FALSE)
 
 # Upload xlsx to Google Drive
 authorize_GoogleDrive <- FALSE
@@ -227,9 +227,9 @@ if (authorize_GoogleDrive) {
 }
 
 # Plot results ------------------------------------------------------------
-frequency_database <- read.csv(file=here::here("TextAnalysis", "top10_frequency.csv"))
-presence_database<-read.csv(file=here::here("TextAnalysis", "top10_presence.csv"))
-proportion_database<-read.csv(file=here::here("TextAnalysis", "top10_proportion.csv"))
+frequency_database <- read.csv(file=here::here("inst", "TextAnalysis", "top10_frequency.csv"))
+presence_database<-read.csv(file=here::here("inst", "TextAnalysis", "top10_presence.csv"))
+proportion_database<-read.csv(file=here::here("inst", "TextAnalysis", "top10_proportion.csv"))
 
 colnames(presence_database) <- col_name
 data_reshape <- reshape2::melt(
@@ -244,7 +244,7 @@ sum_by_group <- aggregate(value ~ keyword+keyword_id+group+Source, data = data_m
 sum_by_group <- sum_by_group[order(sum_by_group$keyword_id),]
 group <- unique(sum_by_group$group)
 
-jpeg(filename = here::here("TextAnalysis", "top10_barplot_sum.jpg"), width=200, height=150, units="mm", res=1200)
+jpeg(filename = here::here("inst", "TextAnalysis", "top10_barplot_sum.jpg"), width=200, height=150, units="mm", res=1200)
 ggplot(sum_by_group, aes(fill=Source, y=value, x=keyword_id)) + 
   geom_bar(position="dodge", stat="identity") +
   facet_wrap(~group, scales = "free_x") +
@@ -260,7 +260,7 @@ mean_by_group <- aggregate(value ~ keyword+keyword_id+group+Source, data = data_
 mean_by_group <- mean_by_group[order(mean_by_group$keyword_id),]
 group <- unique(mean_by_group$group)
 
-jpeg(filename = here::here("TextAnalysis", "top10_barplot_mean.jpg"), width=200, height=150, units="mm", res=1200)
+jpeg(filename = here::here("inst", "TextAnalysis", "top10_barplot_mean.jpg"), width=200, height=150, units="mm", res=1200)
 ggplot(mean_by_group, aes(fill=Source, y=value*100, x=keyword_id)) + 
   geom_bar(position="dodge", stat="identity") +
   facet_wrap(~group, scales = "free_x") +

TextAnalysis/top20_analysis.R → inst/TextAnalysis/top20_analysis.R

@@ -223,9 +223,9 @@ for (org in seq_along(subfolder_info)){
   )
   proportion_database[nrow(proportion_database), "ID"] <- "Sum"
 
-  write.csv(frequency_database, file=here::here("TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
-  write.csv(presence_database, file=here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
-  write.csv(proportion_database, file=here::here("TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  write.csv(frequency_database, file=here::here("inst", "TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  write.csv(presence_database, file=here::here("inst", "TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  write.csv(proportion_database, file=here::here("inst", "TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
   # Upload xlsx to Google Drive
   if (authorize_GoogleDrive) {
     # Google Drive folder id
@@ -234,9 +234,9 @@ for (org in seq_along(subfolder_info)){
   }
 
   # Plot results ------------------------------------------------------------
-  frequency_database <- read.csv(file=here::here("TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")))
-  presence_database<-read.csv(file=here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")))
-  proportion_database<-read.csv(file=here::here("TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")))
+  frequency_database <- read.csv(file=here::here("inst", "TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")))
+  presence_database<-read.csv(file=here::here("inst", "TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")))
+  proportion_database<-read.csv(file=here::here("inst", "TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")))
 
   word_frequency <- as.matrix(frequency_database[frequency_database$ID == "Sum", 4:ncol(frequency_database)])
   word_presence <- as.matrix(presence_database[presence_database$ID == "Sum", 4:ncol(presence_database)])
@@ -266,7 +266,7 @@ for (org in seq_along(subfolder_info)){
   )
 
   # barplot
-  jpeg(filename = here::here("TextAnalysis", paste0("top20_barplot_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
+  jpeg(filename = here::here("inst", "TextAnalysis", paste0("top20_barplot_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
   par(mar = c(6, 4, 1, 1), mfrow = c(3, 1))
   frequency_barplot <- barplot(height = word_frequency, xaxt = "n", ylab = "Frequency")
   text(frequency_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.8)
@@ -280,14 +280,14 @@ for (org in seq_along(subfolder_info)){
 
   dev.off()
 
-  jpeg(filename = here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
+  jpeg(filename = here::here("inst", "TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
   par(mar = c(6, 4, 1, 1), mfrow = c(1, 1))
   presence_barplot <- barplot(height = word_presence, xaxt = "n", ylab = "Frequency") # range: 26-83, median:68
   text(presence_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.7)
   dev.off()
 
   # wordcloud figure
-  jpeg(filename = here::here("TextAnalysis", paste0("top20_wordcloud_", names(subfolder_info)[org], ".jpg")), width = 200, height = 200, units = "mm", res = 1200)
+  jpeg(filename = here::here("inst", "TextAnalysis", paste0("top20_wordcloud_", names(subfolder_info)[org], ".jpg")), width = 200, height = 200, units = "mm", res = 1200)
   par(mar = c(1, 1, 1, 1), mfrow = c(1, 1))
   wordcloud(
     words = xlabels, freq = word_presence, rot.per = 0.35,

_pkgdown.yml → pkgdown/_pkgdown.yml

@@ -33,6 +33,7 @@ reference:
   - read_in
   - shiny_dd
   - validate_Rd
+  - make_hex
 
 
 navbar: