first revision following BioConductor submission reviewing advice

.github/workflows/pr-commands.yaml

@@ -64,7 +64,7 @@ jobs:
  shell: Rscript {0}
 
  - name: Style
- run: styler::style_pkg()
+ run: styler::style_pkg(style = styler::tidyverse_style, indent_by = 4)
  shell: Rscript {0}
 
  - name: commit

DESCRIPTION

@@ -3,10 +3,11 @@ Title: R interface for FDA Adverse Event Reporting System
 Version: 0.99.3
 Authors@R: 
  person("Yun", "Peng", , "yunyunp96@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2801-3332"))
-Description: FAERS is a database for the spontaneous reporting of adverse events and medication errors involving human drugs and therapeutic biological products. faers is the bridge between FAERS and R.
+BugReports: https://github.com/Yunuuuu/faers
+Description: The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.
 License: MIT + file LICENSE
 Depends: 
- R (>= 3.5.0)
+ R (>= 4.4.0)
 Imports: 
  brio,
  cli,
@@ -23,6 +24,7 @@ Imports:
  vroom,
  xml2
 Suggests: 
+ BiocStyle,
  countrycode,
  knitr,
  rmarkdown,

NEWS.md

@@ -0,0 +1,3 @@
+# faers 0.99.0
+
+* Initial Bioconductor submission.

R/athena.R

@@ -36,7 +36,7 @@ athena <- function(use = NULL, list = FALSE, force = FALSE, url = NULL) {
 }
 
 #' @inheritDotParams athena -use -list
-#' @noRd 
+#' @noRd
 athena_standardize_drug <- function(terms, ...) {
  data <- athena(use = c("concept", "concept_synonym"), ..., list = FALSE)
  data$concept <- data$concept[domain_id == "Drug"] # nolint

R/available.R

@@ -10,7 +10,7 @@
 #' @return A logical indicates FAERS can have data for the `years` and
 #' `quarters` required?
 #' @examples
-#'  faers_available(c(2011, 2023), c("q1", "q2"))
+#' faers_available(c(2011, 2023), c("q1", "q2"))
 #' @export
 faers_available <- function(years, quarters, force = FALSE, internal = FALSE) {
  assert_inclusive(quarters, faers_file_quarters)

R/counts.R

@@ -15,6 +15,10 @@
 #' data <- faers_dedup(data)
 #' faers_counts(data)
 #' }
+#' std_data <- readRDS(system.file("extdata", "standardized_data.rds",
+#' package = "faers"
+#' ))
+#' faers_counts(std_data)
 #' @export
 #' @name faers_counts
 methods::setGeneric("faers_counts", function(.object, ...) {
@@ -31,8 +35,8 @@ methods::setGeneric("faers_counts", function(.object, ...) {
 #' combination for all columns will define the interested events.
 #' @param .fn A function or formula defined the preprocessing function before
 #' creating contingency table, with the `.field` data as the input and return a
-#' [data.table][data.table::data.table]. 
-#' 
+#' [data.table][data.table::data.table].
+#'
 #' Note: When using the `set*` or `:=` function from `data.table` with the
 #' "demo", "drug", "ther", "rpsr", and "outc" data, exercise caution as these
 #' functions directly modify the internal data. In such cases, it is advisable

R/dedup.R

@@ -310,7 +310,8 @@ dedup_faers_ascii <- function(data, deleted_cases = NULL) {
 
 utils::globalVariables(c(
  "drug_seq", "drugname", "indi_meddra_code", "start_dt",
- "indi_drug_seq", "dsg_drug_seq", "primaryid", "caseversion", "fda_dt", "i_f_code", "event_dt", "year", "caseid", "age_in_years_round",
+ "indi_drug_seq", "dsg_drug_seq", "primaryid", "caseversion", "fda_dt",
+ "i_f_code", "event_dt", "year", "caseid", "age_in_years_round",
  "meddra_code",
  paste0(c("", "i."), rep(
  c(

R/import-standalone-cli.R

@@ -85,7 +85,7 @@ is_installed <- local({
  out <- requireNamespace(pkg, quietly = TRUE) &&
  utils::packageVersion(pkg) >= version
  }
- cache[[id]] <<- out
+ cache[[id]] <- out
  }
  out
  }

R/period.R

@@ -38,4 +38,3 @@ is_before_period <- function(years, quarters, y, q, inclusive = TRUE) {
 is_from_laers <- function(years, quarters) {
  is_before_period(years, quarters, 2012L, "q3")
 }
-

R/rxnorm.R

@@ -86,7 +86,8 @@ rxnorm_getApproximateMatch <- function(terms, max_entries = NULL, option = NULL,
 # rxnorm_findRxcuiByString(I("Lipitor+10+mg+Tab"), search = 1L)
 rxnorm_findRxcuiByString <- function(names, allsrc = NULL, srclist = NULL, search = NULL, pool_size = 5L, retry = 0L) {
  reqs <- lapply(names, function(term) {
- rxnorm_api(.path = "rxcui",
+ rxnorm_api(
+ .path = "rxcui",
  name = term,
  allsrc = allsrc,
  srclist = srclist, search = search
@@ -194,7 +195,7 @@ rxnorm_perform <- function(req) {
 ###########################################################
 #' All values in dots should be named. If rxnorm_api_name is `NULL`, `path` must
 #' contain format strings used by sprintf.
-#' @noRd 
+#' @noRd
 rxnorm_api <- function(.path, ..., .format = "xml") {
  req <- httr2::req_url_path_append(
  req = httr2::req_url_path(req = httr2::request(rxnorm_host), "REST"),

R/unify.R

@@ -1,13 +1,13 @@
 #' @section Unification:
-#' For all fields data: 
+#' For all fields data:
 #' - All names have been converted to lowercase.
 #' - Rename "isr" into "primaryid" for periods before 2012q3.
-#' 
+#'
 #' Field specific operations:
 #' - `demo`:
 #' - Rename "gndr_cod" into "sex" for periods before 2014q2.
 #' - Rename "case" and "i_f_cod" into "caseid" and "i_f_code" for legacy aers,
-#' before 2012q3. 
+#' before 2012q3.
 #' - "age_in_years" was added, measured in years.
 #' - "country_code" was added (encoded according to the `iso2c` standards), it
 #' will be convenient to translate it into other code with