refactor: restructure raw data creation script

Author: Yunuuuu

inst/script/DATASET.R inst/script/example.Rinst/script/DATASET.R renamed to inst/script/example.R

@@ -24,22 +24,3 @@ data <- faers(c(2004, 2017), c("q1", "q2"),
 #' Note: You must provide your meddra data (version: 26.1)
 data <- faers_standardize(data, "~/Data/MedDRA/MedDRA_26_1_English") # nolint
 saveRDS(data, "inst/extdata/standardized_data.rds")
-
-#' Immune-related adverse events examined in ICI-associated adverse events
-#' 
-#' @references
-#' - Chen Chen, Bin Wu, ChenYu Zhang, Ting Xu,Immune-related adverse events
-#' associated with immune checkpoint inhibitors: An updated comprehensive
-#' disproportionality analysis of the FDA adverse event reporting system,
-#' International Immunopharmacology
-#' @source
-#' https://ars.els-cdn.com/content/image/1-s2.0-S156757692100134X-mmc1.docx
-doc <- docxtractr::read_docx("inst/extdata/irAEs.docx")
-irAEs <- docxtractr::docx_extract_tbl(doc, tbl_number = 2L)
-irAEs <- tidyr::fill(
-    dplyr::mutate(irAEs, Toxicity.types = dplyr::na_if(Toxicity.types, "")),
-    Toxicity.types
-)
-data.table::setDT(irAEs)
-irAEs <- unique(irAEs)
-saveRDS(irAEs, "inst/extdata/irAEs.rds", compress = "bzip2")

inst/script/irAEs.R

@@ -0,0 +1,18 @@
+#' Immune-related adverse events examined in ICI-associated adverse events
+#'
+#' @references
+#' - Chen Chen, Bin Wu, ChenYu Zhang, Ting Xu,Immune-related adverse events
+#' associated with immune checkpoint inhibitors: An updated comprehensive
+#' disproportionality analysis of the FDA adverse event reporting system,
+#' International Immunopharmacology
+#' @source
+#' https://ars.els-cdn.com/content/image/1-s2.0-S156757692100134X-mmc1.docx
+doc <- docxtractr::read_docx("inst/extdata/irAEs.docx")
+irAEs <- docxtractr::docx_extract_tbl(doc, tbl_number = 2L)
+irAEs <- tidyr::fill(
+    dplyr::mutate(irAEs, Toxicity.types = dplyr::na_if(Toxicity.types, "")),
+    Toxicity.types
+)
+data.table::setDT(irAEs)
+irAEs <- unique(irAEs)
+saveRDS(irAEs, "inst/extdata/irAEs.rds", compress = "bzip2")