R: Adds a Parameter for Best Overall Response (without...

derive_param_bor {admiralonco}

R Documentation

Adds a Parameter for Best Overall Response (without confirmation)

Description

The derive_param_bor() function has been superseded in favor of derive_extreme_event().

Adds a parameter for best overall response, without confirmation, optionally up to first progressive disease

Usage

derive_param_bor(
  dataset,
  dataset_adsl,
  filter_source,
  source_pd = NULL,
  source_datasets = NULL,
  reference_date,
  ref_start_window,
  missing_as_ne = FALSE,
  aval_fun,
  set_values_to,
  subject_keys = get_admiral_option("subject_keys")
)

Arguments

`dataset`	The input dataframe from which the Best Overall Response will be derived from and added to. The columns `PARAMCD`, `ADT`, and `AVALC`and the columns specified in `subject_keys` and `reference_date` are expected. After applying `filter_source` and/or `source_pd` the column `ADT` and the columns specified by `subject_keys` must be a unique key of the dataframe. Permitted Values: a `data.frame()` object
`dataset_adsl`	ADSL input dataset. The columns specified in the subject_keys argument are expected. For each subject in the passed `dataset` a new row is added to the input `dataset`. Columns in `dataset_adsl` that also appear in `dataset` will be populated with the appropriate subject-specific value for these new rows. Permitted Values: a `data.frame()` object
`filter_source`	Filter to be applied to `dataset` to derive the Best Overall Response
`source_pd`	Date of first progressive disease (PD) If the parameter is specified, the observations of the input `dataset` for deriving the new parameter are restricted to observations up to the specified date. Observations at the specified date are included. For subjects without first PD date all observations are take into account. Permitted Values: a `date_source` object (see `date_source()` for details)
`source_datasets`	Source dataframe to be used to calculate the first PD date A named list of dataframes is expected (although for BOR) only one dataframe is needed. It links the `dataset_name` from `source_pd` with an existing dataframe. For example if `source_pd = pd_date` with pd_date <- date_source( dataset_name = "adrs", date = ADT, filter = PARAMCD == PD ) and the actual response dataframe in the script is `myadrs`, `source_datasets = list(adrs = myadrs)` should be specified.
`reference_date`	Reference date The reference date is used along with `ref_start_window` to determine those records that occur before and after `ADT` (see Details section for further information). Usually it is treatment start date (`TRTSDT`) or randomization date (`RANDDT`). Permitted Values: a numeric date column
`ref_start_window`	Stable disease time window The ref_start_window is used along with `reference_date` to determine those records that occur before and after `ADT` (i.e. for a record determine whether `ADT` >= `reference_date` + `ref_start_window`), see Details section for further information. Permitted Values: a non-negative numeric scalar
`missing_as_ne`	Consider no assessments as `"NE"`? If the argument is set to `TRUE`, the response is set to `"NE"` for subjects in `dataset_adsl` without an assessment in the `dataset` after the filter has been applied. Otherwise, the response is set to `"MISSING"` for these subjects. Permitted Values: a logical scalar
`aval_fun`	Deprecated, please use `set_values_to` instead. Function to map character analysis value (`AVALC`) to numeric analysis value (`AVAL`) The (first) argument of the function must expect a character vector and the function must return a numeric vector.
`set_values_to`	New columns to set A named list returned by `exprs()` defining the columns to be set for the new parameter, e.g. `exprs(PARAMCD = "BOR", PARAM = "Best Overall Response")` is expected. The values must be symbols, character strings, numeric values, or `NA`.
`subject_keys`	Columns to uniquely identify a subject Permitted Values: A list of symbols created using `exprs()`.

Details

Calculates the best overall response (BOR) parameter, as detailed below.

Records after PD can be removed using the source_pd and source_datasets arguments.

Note:

All CR, PR and PD response records are considered for Best Overall Response.
All SD or NON-CR/NON-PD records where ADT >= reference_date + ref_start_window are also considered for Best Overall Response.
Subjects with ONLY an SD or NON-CR/NON-PD records where ADT < reference_date + ref_start_window are assigned a Best Overall Response of NE.
The Best Response, from the records in steps 1 to 3, is then selected in the following order of preference: CR, PR, SD, NON-CR/NON-PD, PD, NE, MISSING
The AVAL column is added and set using the aval_fun(AVALC) function
The columns specified by the set_values_to parameter and records are added to the dataframe passed into the dataset argument

Note: Any responses of SD or NON-CR/NON-PD that occur before reference_date + ref_start_window are ignored in the calculation of BOR. All other responses are included in the calculation of BOR, irrespective of the number of days from the reference date.

Also Note: All columns from the input dataset are kept. For subjects with no records in the input dataset (after the filter is applied) all columns are kept from ADSL which are also in the input dataset. Columns which are not to be populated for the new parameter or populated differently (e.g. RSSTRESC, VISIT, PARCATy, ANLzzFL, ...) should be overwritten using the set_values_to parameter.

Value

The dataframe passed in the dataset argument with additional columns and/or rows as set in the set_values_to argument.

Author(s)

Stephen Gormley

Examples


library(magrittr)
library(dplyr)
library(tibble)
library(lubridate)
library(admiral)

# Create ADSL dataset
adsl <- tribble(
  ~USUBJID, ~TRTSDTC,
  "1",      "2020-01-01",
  "2",      "2019-12-12",
  "3",      "2019-11-11",
  "4",      "2019-12-30",
  "5",      "2020-01-01",
  "6",      "2020-02-02",
  "7",      "2020-02-02",
  "8",      "2020-04-01"
) %>%
  mutate(
    TRTSDT = ymd(TRTSDTC),
    STUDYID = "XX1234"
  )

# Create ADRS dataset
ovr_obs <- tribble(
  ~USUBJID, ~ADTC, ~AVALC, ~ANL01FL,
  "1", "2020-01-01", "PR", "Y",
  "1", "2020-02-01", "CR", "Y",
  "1", "2020-02-16", "NE", "Y",
  "1", "2020-03-01", "CR", "Y",
  "1", "2020-04-01", "SD", "Y",
  "2", "2020-01-01", "SD", "Y",
  "2", "2020-02-01", "PR", "Y",
  "2", "2020-03-01", "SD", "Y",
  "2", "2020-03-13", "CR", "Y",
  "3", "2019-11-12", "CR", "Y",
  "3", "2019-12-02", "CR", "Y",
  "3", "2020-01-01", "SD", "Y",
  "4", "2020-01-01", "PR", "Y",
  "4", "2020-03-01", "SD", "N",
  "4", "2020-04-01", "SD", "Y",
  "4", "2020-05-01", "PR", "Y",
  "4", "2020-05-15", "NON-CR/NON-PD", "Y",
  "5", "2020-01-01", "PR", "Y",
  "5", "2020-01-10", "SD", "Y",
  "5", "2020-01-20", "PR", "Y",
  "5", "2020-05-15", "NON-CR/NON-PD", "Y",
  "6", "2020-02-06", "PR", "Y",
  "6", "2020-02-16", "CR", "Y",
  "6", "2020-03-30", "PR", "Y",
  "6", "2020-04-12", "PD", "Y",
  "6", "2020-05-01", "CR", "Y",
  "6", "2020-06-01", "CR", "Y",
  "7", "2020-02-06", "PR", "Y",
  "7", "2020-02-16", "CR", "Y",
  "7", "2020-04-01", "NE", "N"
) %>%
  mutate(PARAMCD = "OVR")

pd_obs <-
  bind_rows(tribble(
    ~USUBJID, ~ADTC,        ~AVALC,
    "2",      "2020-03-01", "Y",
    "4",      "2020-02-01", "Y"
  ) %>%
    mutate(PARAMCD = "PD"))

adrs <- bind_rows(ovr_obs, pd_obs) %>%
  mutate(
    ADT = ymd(ADTC),
    STUDYID = "XX1234"
  ) %>%
  select(-ADTC) %>%
  derive_vars_merged(
    dataset_add = adsl,
    by_vars     = exprs(STUDYID, USUBJID),
    new_vars    = exprs(TRTSDT)
  )

pd_date <- date_source(
  dataset_name = "adrs",
  date         = ADT,
  filter       = PARAMCD == "PD"
)

aval_fun_pass <- function(arg) {
  case_when(
    arg == "CR" ~ 11,
    arg == "PR" ~ 22,
    arg == "SD" ~ 33,
    arg == "NON-CR/NON-PD" ~ 44,
    arg == "PD" ~ 55,
    arg == "NE" ~ 66,
    arg == "MISSING" ~ 77,
    TRUE ~ NA_real_
  )
}

# Derive best overall response parameter
derive_param_bor(
  adrs,
  dataset_adsl = adsl,
  filter_source = PARAMCD == "OVR" & ANL01FL == "Y",
  source_pd = pd_date,
  source_datasets = list(adrs = adrs),
  aval_fun = aval_fun_pass,
  reference_date = TRTSDT,
  ref_start_window = 28,
  set_values_to = exprs(
    PARAMCD = "BOR",
    PARAM = "Best Overall Response"
  )
) %>%
  filter(PARAMCD == "BOR")

[Package admiralonco version 1.0.0 Index]