#92 Create function to derive reference dates in DM domain

DESCRIPTION

@@ -21,6 +21,8 @@ Authors@R: c(
     person("Pattern Institute", role = c("cph", "fnd")),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")),
     person("Pfizer Inc", role = c("cph", "fnd")),
+    person("Mohsin", "Uzzama", email = "[email protected]",
+    role = "aut"),
     person("Transition Technologies Science", role = c("cph", "fnd"))
     )
 Maintainer: Rammprasad Ganapathy <[email protected]>

NAMESPACE

@@ -8,6 +8,7 @@ export("%.>%")
 export(assign_ct)
 export(assign_datetime)
 export(assign_no_ct)
+export(cal_min_max_date)
 export(condition_add)
 export(create_iso8601)
 export(ct_map)
@@ -20,6 +21,7 @@ export(fmt_cmp)
 export(generate_oak_id_vars)
 export(hardcode_ct)
 export(hardcode_no_ct)
+export(oak_cal_ref_dates)
 export(oak_id_vars)
 export(problems)
 export(read_ct_spec)

R/cal_min_max_date.R

@@ -0,0 +1,130 @@
+#' Calculate minimum and maximum date and time in the data frame
+#'
+#' @description This function derives the earliest/latest ISO8601 datetime
+#'
+#' @param raw_dataset Raw source data frame
+#' @param date_variable Single character string. Name of the date variable
+#' @param time_variable Single character string. Name of the time variable
+#' @param val_type Single character string determining whether to look
+#'   for the earliest or the latest datetime combination. Permitted values:
+#'   "min", "max". Default to "min".
+#' @param date_format Format of source date variable
+#' @param time_format Format of source time variable
+#'
+#' @return Data frame with 2 columns: unique patient_number and datetime variable
+#'   column storing the earliest/latest datetime.
+#'
+#' @export
+#' @examples
+#' EX <- tibble::tribble(
+#'   ~patient_number,    ~EX_ST_DT, ~EX_ST_TM,
+#'   "001",           "25-04-2022",   "10:20",
+#'   "001",           "25-04-2022",   "10:15",
+#'   "001",           "25-04-2022",   "10:19",
+#'   "002",           "26-05-2022", "UNK:UNK",
+#'   "002",           "26-05-2022",   "05:59"
+#' )
+#'
+#' min <- cal_min_max_date(EX,
+#'   date_variable = "EX_ST_DT",
+#'   time_variable = "EX_ST_TM",
+#'   val_type = "min",
+#'   date_format = "dd-mmm-yyyy",
+#'   time_format = "H:M"
+#' )
+#'
+#' max <- cal_min_max_date(EX,
+#'   date_variable = "EX_ST_DT",
+#'   time_variable = "EX_ST_TM",
+#'   val_type = "max",
+#'   date_format = "dd-mmm-yyyy",
+#'   time_format = "H:M"
+#' )
+#'
+cal_min_max_date <- function(raw_dataset,
+                             date_variable,
+                             time_variable,
+                             val_type = "min",
+                             date_format,
+                             time_format) {
+  # Check if date parameter is missing or date variable is present in the raw data frame
+  date_not_in_data <- is.na(date_variable) ||
+    !utils::hasName(raw_dataset, date_variable)
+
+  # Check if time variable is used and present in the raw data frame
+  time_not_in_data <- !is.na(time_variable) &&
+    !utils::hasName(raw_dataset, time_variable)
+
+  # If date/time variables not present return empty data frame
+  if (date_not_in_data || time_not_in_data) {
+    # Return Empty data frame with patient_number and datetime columns
+    empty_df <- stats::setNames(
+      data.frame(matrix(ncol = 2L, nrow = 0L)),
+      c("patient_number", "datetime")
+    )
+    cli::cli_warn(paste(
+      "Date variable", date_variable, "or Time variable", time_variable,
+      "not present in source data"
+    ))
+    return(empty_df)
+  }
+
+  fin_df <- raw_dataset
+
+  # Time is not used in reference date then use only date
+  if (is.na(time_variable)) {
+    fin_df$datetime <- create_iso8601(raw_dataset[[date_variable]],
+      .format = date_format
+    )
+  } else {
+    # If both date and time variables are present use both date and time
+    raw_dataset$date_time <- paste0(
+      raw_dataset[[date_variable]],
+      raw_dataset[[time_variable]]
+    )
+    format <- paste0(date_format, time_format)
+
+    fin_df$datetime <- as.character(create_iso8601(raw_dataset$date_time,
+      .format = format,
+      .na = c(
+        "UNK", "NA", "U", "unk",
+        "u", "un", "UN"
+      )
+    ))
+  }
+
+  fin_df <- fin_df |>
+    dplyr::select(c("patient_number", "datetime")) |>
+    unique()
+
+  fin_df <- fin_df |>
+    dplyr::mutate(date_time = datetime) |>
+    tidyr::separate(
+      date_time,
+      sep = "-|T|:",
+      into = c("year", "month", "day", "hour", "minute"),
+      fill = "right",
+      extra = "drop"
+    ) |>
+    list() |>
+    stats::setNames("x") |>
+    with(replace(x, x == "UNK", NA)) |>
+    list() |>
+    stats::setNames("x") |>
+    with(replace(x, x == "", NA))
+
+  if (val_type == "min") {
+    final_df <- fin_df |>
+      dplyr::arrange(year, month, day, hour, minute)
+  } else {
+    final_df <- fin_df |>
+      dplyr::arrange(dplyr::desc(year), dplyr::desc(month), dplyr::desc(day), dplyr::desc(hour), dplyr::desc(minute))
+  }
+
+  # Keep first appearance in the data frame since it is already sorted
+  final_df <- final_df[!duplicated(final_df$patient_number), c("patient_number", "datetime")]
+
+  final_df <- final_df |> dplyr::filter(!is.na(datetime))
+
+  return(final_df)
+}

R/globals.R

@@ -1,4 +1,6 @@
 utils::globalVariables(c(
   "USUBJID", "VISIT", "dom_dt", "dom_tm", "ref_dt",
-  "ref_tm"
+  "ref_tm", "datetime", "date_time", "year", "month",
+  "day", "hour", "minute", "dataset_name", "date_var",
+  "dformat", "tformat", "sdtm_var_name", "patient_number"
 ))

R/oak_cal_ref_dates.R

@@ -0,0 +1,120 @@
+#' Calculate Reference dates in ISO8601 character format.
+#'
+#' Populate RFSTDTC variable in demographic domain in ISO8601 character format.
+#'
+#' @description Derive RFSTDTC, RFENDTC, RFXENDTC, RFXSTDTC based on the input dates and time.
+#'
+#'
+#' @param ds_in Data frame. DM domain.
+#' @param der_var Character string. The reference date to be derived.
+#' @param min_max Minimum or Maximum date to be calculated based on the input.
+#'        Default set to Minimum. Values should be min or max.
+#' @param ref_date_config_df Data frame which has the details of the variables to
+#'        be used for the calculation of reference dates.
+#'        Should have columns listed below:
+#'          dataset_name : Name of the raw dataset.
+#'          date_var : Date variable name from the raw dataset.
+#'          time_var : Time variable name from the raw dataset.
+#'          dformat : Format of the date collected in raw data.
+#'          tformat: Format of the time collected in raw data.
+#'          sdtm_var_name : Reference variable name.
+#' @param raw_source List contains all the raw datasets.
+#' @return DM data frame with the reference dates populated.
+#' @export
+#' @examples
+#' dm <- tibble::tribble(
+#'   ~patient_number,   ~USUBJID, ~SUBJID, ~SEX,
+#'   "001",           "XXXX-001",   "001",  "F",
+#'   "002",           "XXXX-002",   "002",  "M",
+#'   "003",           "XXXX-003",   "003",  "M"
+#' )
+#'
+#' ref_date_config_df <- tibble::tribble(
+#'   ~dataset_name,   ~date_var,   ~time_var,      ~dformat, ~tformat, ~sdtm_var_name,
+#'   "EX1",         "EX_ST_DT1", "EX_ST_TM1",  "dd-mm-yyyy",    "H:M",      "RFSTDTC",
+#'   "EX2",         "EX_ST_DT2",          NA, "dd-mmm-yyyy",       NA,      "RFSTDTC",
+#'   "EX1",         "EX_EN_DT1", "EX_EN_TM1",  "dd-mm-yyyy",    "H:M",      "RFENDTC",
+#'   "EX2",         "EX_ST_DT2",          NA, "dd-mmm-yyyy",       NA,      "RFENDTC"
+#' )
+#'
+#' EX1 <- tibble::tribble(
+#'   ~patient_number, ~EX_ST_DT1,   ~EX_EN_DT1, ~EX_ST_TM1, ~EX_EN_TM1,
+#'   "001",         "15-05-2023", "15-05-2023",    "10:20",    "11:00",
+#'   "001",         "15-05-2023", "15-05-2023",     "9:15",    "10:00",
+#'   "001",         "15-05-2023", "15-05-2023",     "8:19",    "09:00",
+#'   "002",         "02-10-2023", "02-10-2023",  "UNK:UNK",         NA,
+#'   "002",         "03-11-2023", "03-11-2023",    "11:19",         NA
+#' )
+#'
+#' EX2 <- tibble::tribble(
+#'   ~patient_number,     ~EX_ST_DT2,
+#'   "001",            "11-JUN-2023",
+#'   "002",            "24-OCT-2023",
+#'   "002",            "25-JUL-2023",
+#'   "002",            "30-OCT-2023",
+#'   "002",           "UNK-OCT-2023"
+#' )
+#'
+#' raw_source <- list(EX1 = EX1, EX2 = EX2)
+#'
+#' dm_df <- oak_cal_ref_dates(dm,
+#'   der_var = "RFSTDTC",
+#'   min_max = "min",
+#'   ref_date_config_df = ref_date_config_df,
+#'   raw_source
+#' )
+#'
+oak_cal_ref_dates <- function(ds_in = dm,
+                              der_var,
+                              min_max = "min",
+                              ref_date_config_df,
+                              raw_source) {
+  # Check if ref_date_config_df is a data frame and has all required variables
+  admiraldev::assert_data_frame(ref_date_config_df, required_vars = exprs(
+    dataset_name, date_var,
+    time_var, dformat,
+    tformat, sdtm_var_name
+  ))
+
+  admiraldev::assert_list_of(raw_source, "data.frame")
+
+  ds_out <- data.frame()
+  for (i in seq_along(ref_date_config_df$dataset_name)) {
+    raw_dataset_name <- ref_date_config_df$dataset_name[i]
+    date_variable <- ref_date_config_df$date_var[i]
+    date_format <- ref_date_config_df$dformat[i]
+    time_var <- ref_date_config_df$time_var[i]
+    time_format <- ref_date_config_df$tformat[i]
+    sdtm_var <- ref_date_config_df$sdtm_var_name[i]
+    raw_dataset <- raw_source[[raw_dataset_name]]
+
+    if (der_var == sdtm_var && !is.null(raw_dataset)) {
+      ds_out1 <- cal_min_max_date(
+        raw_dataset = raw_dataset,
+        date_variable = date_variable,
+        time_variable = time_var,
+        date_format = date_format,
+        time_format = time_format,
+        val_type = min_max
+      )
+      ds_out <- rbind(ds_out, ds_out1)
+    } else if (der_var == sdtm_var && is.null(raw_dataset)) {
+      warning(paste0(
+        raw_dataset_name,
+        " is not present in the source data list but referenced in ref_date_config_df"
+      ))
+    }
+  }
+
+  if (min_max == "min") {
+    df_final <- ds_out |> dplyr::arrange(patient_number, datetime)
+  } else {
+    df_final <- ds_out |> dplyr::arrange(dplyr::desc(datetime))
+  }
+
+  df_final <- df_final[!duplicated(df_final$patient_number), c("patient_number", "datetime")]
+  colnames(df_final)[colnames(df_final) == "datetime"] <- der_var
+
+  dm <- dplyr::left_join(ds_in, y = df_final, by = "patient_number")
+  return(dm)
+}

_pkgdown.yml

@@ -49,11 +49,19 @@ reference:
   - dtc_formats
   - problems
 
+- title: Calculation of reference dates in DM
+  contents:
+  - oak_cal_ref_dates
+
 - title: Explicit dot pipe operator
   desc: A simple alternative to `%>% {...}`
   contents:
   - "%.>%"
 
+- title: Calculation of minimum/maximum ISO8601 dates
+  contents:
+  - cal_min_max_date
+
 authors:
   Ramiro Magno:
     href: https://www.pattern.institute/team/rmagno/
@@ -63,3 +71,5 @@ authors:
     href: https://www.linkedin.com/in/edgar-manukyan-20987927
   Shiyu Chen:
     href: https://www.linkedin.com/in/shiyu-chen-55a55410a/
+  Mohsin Uzzama:
+    href: https://www.linkedin.com/in/mohsin-uzzama-34066741/