Initial mockup of assign_datetime()

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(print,iso8601)
 export(assign_ct)
+export(assign_datetime)
 export(assign_no_ct)
 export(clear_cache)
 export(create_iso8601)

R/assign_datetime.R

@@ -0,0 +1,100 @@
+#' Derive an ISO8601 date-time variable
+#'
+#' [assign_datetime()] maps one or more variables with date/time components in a
+#' raw dataset to a target SDTM variable following the ISO8601 format.
+#'
+#' @param raw_dat The raw dataset (dataframe); must include the
+#'   variables passed in `id_vars` and `raw_var`.
+#' @param raw_var The raw variable(s): a character vector indicating the name(s)
+#'   of the raw variable(s) in `raw_dat` with date or time components to be
+#'   parsed into a ISO8601 format variable in `tgt_var`.
+#' @param raw_fmt A date/time parsing format. Either a character vector or a
+#'   list of character vectors. If a character vector is passed then each
+#'   element is taken as parsing format for each variable indicated in
+#'   `raw_var`. If a list is provided, then each element must be a character
+#'   vector of formats. The first vector of formats is used for parsing the
+#'   first variable in `raw_var`, and so on.
+#' @param tgt_var The target SDTM variable: a single string indicating the name
+#'   of variable to be derived.
+#' @param raw_unk A character vector of string literals to be regarded as
+#'   missing values during parsing.
+#' @param tgt_dat Target dataset: a data frame to be merged against `raw_dat` by
+#'   the variables indicated in `id_vars`. This parameter is optional, see
+#'   section Value for how the output changes depending on this argument value.
+#' @param id_vars Key variables to be used in the join between the raw dataset
+#'   (`raw_dat`) and the target data set (`raw_dat`).
+#' @param .warn Whether to warn about parsing failures.
+#'
+#' @returns The returned data set depends on the value of `tgt_dat`:
+#' - If no target dataset is supplied, meaning that `tgt_dat` defaults to
+#' `NULL`, then the returned data set is `raw_dat`, selected for the variables
+#' indicated in `id_vars`, and a new extra column: the derived variable, as
+#' indicated in `tgt_var`.
+#' - If the target dataset is provided, then it is merged with the raw data set
+#' `raw_dat` by the variables indicated in `id_vars`, with a new column: the
+#' derived variable, as indicated in `tgt_var`.
+#'
+#' @examples
+#' md1 <-
+#'   tibble::tribble(
+#'     ~oak_id, ~raw_source, ~patient_number, ~MDBDR, ~MDEDR, ~MDETM,
+#'     1L, "MD1", 375, NA, NA, NA,
+#'     2L, "MD1", 375, "15-Sep-20", NA, NA,
+#'     3L, "MD1", 376, "17-Feb-21", "17-Feb-21", NA,
+#'     4L, "MD1", 377, "4-Oct-20", NA, NA,
+#'     5L, "MD1", 377, "20-Jan-20", "20-Jan-20", "10:00:00",
+#'     6L, "MD1", 377, "UN-UNK-2019", "UN-UNK-2019", NA,
+#'     7L, "MD1", 377, "20-UNK-2019", "20-UNK-2019", NA,
+#'     8L, "MD1", 378, "UN-UNK-2020", "UN-UNK-2020", NA,
+#'     9L, "MD1", 378, "26-Jan-20", "26-Jan-20", "07:00:00",
+#'     10L, "MD1",	378, "28-Jan-20", "1-Feb-20", NA,
+#'     11L, "MD1",	378, "12-Feb-20", "18-Feb-20", NA,
+#'     12L, "MD1",	379, "10-UNK-2020", "20-UNK-2020", NA,
+#'     13L, "MD1",	379, NA, NA, NA,
+#'     14L, "MD1",	379, NA, "17-Feb-20", NA
+#'   )
+#'
+#' cm <-
+#'   assign_datetime(
+#'     raw_dat = md1,
+#'     raw_var = "MDBDR",
+#'     raw_fmt = "d-m-y",
+#'     raw_unk = c("UN", "UNK"),
+#'     tgt_var = "CMSTDTC"
+#'   )
+#'
+#' cm
+#' problems(cm$CMSTDTC)
+#'
+#' @export
+assign_datetime <-
+  function(raw_dat,
+           raw_var,
+           raw_fmt,
+           tgt_var,
+           raw_unk = c("UN", "UNK"),
+           tgt_dat = NULL,
+           id_vars = oak_id_vars(),
+           .warn = TRUE) {
+
+    tgt_val <-
+      create_iso8601(!!!raw_dat[raw_var], .format = raw_fmt, .na = raw_unk)
+
+    der_dat <-
+      raw_dat |>
+      dplyr::select(c(id_vars, raw_var)) |>
+      dplyr::mutate("{tgt_var}" := tgt_val) |>
+      dplyr::select(-rlang::sym(raw_var))
+
+    der_dat <-
+      if (!is.null(tgt_dat)) {
+        der_dat |>
+          dplyr::right_join(y = tgt_dat, by = id_vars) |>
+          dplyr::relocate(tgt_var, .after = dplyr::last_col())
+      } else {
+        der_dat
+      }
+
+    der_dat
+
+  }