use data.table in CRAN and add more examples

DESCRIPTION

@@ -3,15 +3,15 @@ Title: R interface for FDA Adverse Event Reporting System
 Version: 0.0.0.9000
 Authors@R: 
  person("Yun", "Peng", , "yunyunpp96@outlook.com", role = c("aut", "cre"))
-Description: R interface for FDA Adverse Event Reporting System (FAERS).
+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.
 License: MIT + file LICENSE
 Depends: 
  R (>= 3.5.0)
 Imports: 
  brio,
  cli,
  curl,
- data.table (>= 1.14.9),
+ data.table,
  httr2,
  MCMCpack,
  methods,
@@ -22,7 +22,7 @@ Imports:
  xml2
 Suggests: 
  testthat (>= 3.0.0)
-Remotes: Rdatatable/data.table
+biocViews: Software, DataImport
 Encoding: UTF-8
 ByteCompile: true
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -3,6 +3,7 @@
 export(faers)
 export(faers_available)
 export(faers_before_period)
+export(faers_combine)
 export(faers_data)
 export(faers_dedup)
 export(faers_deleted_cases)

R/combine.R

@@ -4,6 +4,13 @@
 #' [FAERSxml] object
 #' @param x A list of [FAERSxml] or [FAERSascii] objects.
 #' @return A [FAERSxml] or [FAERSascii] object.
+#' @examples 
+#' \dontrun{
+#' data1 <- faers(2012, "q1")
+#' data2 <- faers(2013, "q4")
+#' faers_combine(list(data1, data2))
+#' }
+#' @export 
 faers_combine <- function(x) {
  assert_(x, is.list, "a list")
  l <- length(x)

R/dedup.R

@@ -2,6 +2,11 @@
 #' @param object A [FAERSascii] object.
 #' @param ... Other arguments passed to specific methods.
 #' @return A [FAERSascii] object.
+#' @examples 
+#' \dontrun{
+#' data <- faers(c(2012, 2013), c("q1", "q3"))
+#' faers_dedup(data)
+#' }
 #' @export
 #' @name faers_dedup
 methods::setGeneric("faers_dedup", function(object, ...) {

R/faers.R

@@ -4,6 +4,10 @@
 #' @param handle_opts Extra handle options passed to each request
 #' [new_handle][curl::new_handle].
 #' @return A [FAERSxml] or [FAERSascii] object.
+#' @examples 
+#' \dontrun{
+#' data <- faers(c(2012, 2013), c("q1", "q3"))
+#' }
 #' @export
 faers <- function(years, quarters, format = NULL, dir = getwd(), compress_dir = dir, handle_opts = list()) {
  format <- match.arg(format, faers_file_format)

R/merge.R

@@ -11,6 +11,12 @@
 #' Only the initial instance, of the "caseid" column will be preserved.
 #'
 #' @return A [data.table][data.table::data.table] object.
+#' @examples 
+#' \dontrun{
+#' data <- faers(c(2012, 2013), c("q1", "q3"))
+#' faers_merge(data, "indi")
+#' faers_merge(data, c("demo", "indi"))
+#' }
 #' @export
 #' @name faers_merge
 methods::setGeneric("faers_merge", function(object, ...) {

R/methods-utils.R

@@ -24,6 +24,14 @@
 #' - `faers_filter`: apply a function to extract wanted `primaryid`, then use
 #' `faers_keep` to filter.
 #' @export
+#' @examples 
+#' \dontrun{
+#' data <- faers(2012, "q1")
+#' faers_get(data, "indi")
+#' data[["indi"]]
+#' faers_get(data, "demo")
+#' data[["demo"]]
+#' }
 #' @rdname FAERS-methods
 methods::setGeneric("faers_get", function(object, ...) {
  methods::makeStandardGeneric("faers_get")

R/phv_.R

@@ -249,7 +249,7 @@ phv_bcpnn_mcmc <- function(a, b, c, d, alpha = 0.05, n_mcmc = 1e5L) {
  out <- data.table::as.data.table(do.call("rbind", out))
  data.table::setnames(out, c("ci_low", "ci_high"))
  out[, ic := ic]
- data.table::setcolorder(out, "ic", before = 1L)
+ data.table::setcolorder(out, c("ic", "ci_low", "ci_high"))
  out[]
 }
 

R/standardize.R

@@ -274,8 +274,9 @@ athena_standardize_drug <- function(terms, path = NULL, force = FALSE) {
  )))
  )]
  out <- data$concept[match(..__mapped_concept_ids__.., concept_id)] # nolint
+ old_nms <- data.table::copy(names(out))
  out[, athena_drug_names := terms] # nolint
- data.table::setcolorder(out, "athena_drug_names", before = 1L)
+ data.table::setcolorder(out, c("athena_drug_names", old_nms))
 }
 
 utils::globalVariables(c(

R/unify.R

@@ -15,8 +15,9 @@ unify_ascii <- function(data, field, year, quarter) {
  drug = unify_ascii_drug(data, year, quarter),
  outc = unify_ascii_outc(data, year, quarter)
  )
+ old_nms <- data.table::copy(names(data))
  data[, c("year", "quarter") := list(year, quarter)]
- data.table::setcolorder(data, c("year", "quarter"), before = 1L)
+ data.table::setcolorder(data, c("year", "quarter", old_nms))
  data[!is.na(primaryid)]
 }
 

R/utils.R

@@ -16,6 +16,8 @@ is_from_laers <- function(years, quarters) {
 #' @param inclusive A bool, whether to include the period specifid.
 #' @return An atomic logical with the same length of the max length of `years`
 #' and `quarters`.
+#' @examples 
+#' faers_before_period(c(2011, 2012), c("q1", "q3"), 2011, "q2")
 #' @export
 faers_before_period <- function(years, quarters, y, q, inclusive = TRUE) {
  periods <- recycle_scalar(years = years, quarters = quarters)