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Adds a Parameter for the Last Disease Assessment

Source: R/derive_param_lasta.R
derive_param_lasta.Rd

Adds a parameter for the last disease assessment (optionally) up to first progressive disease

Usage

derive_param_lasta(
  dataset,
  filter_source,
  order = vars(ADT),
  source_pd = NULL,
  source_datasets = NULL,
  subject_keys = vars(STUDYID, USUBJID),
  set_values_to
)

Arguments

dataset

Input dataframe from which the Last Disease Assessment will be be derived from and added to.

The column PARAMCD and the columns specified in subject_keys and order are expected.

After applying filter_source and/or source_pd the columns specified by subject_keys and order must be a unique key of the dataframe

Permitted Values: a data.frame() object

filter_source

Filter to be applied to dataset to derive the Last Disease Assessment

order

Sort order, after which the last record shall be taken by the subject_keys to determine Last Disease Assessment. Created using vars().

Permitted Values: list of variables or desc(<variable>) function calls created by vars(), e.g., vars(ADT, desc(AVAL))

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.

subject_keys

Columns to uniquely identify a subject

A list of symbols created using vars().

set_values_to

Columns to set

A named list returned by vars() defining the columns to be set for the new parameter, e.g. vars(PARAMCD = "LSTAC", PARAM = "Last Disease Assessment Censored at First PD by Investigator") is expected. The values must be symbols, character strings, numeric values, or NA.

Value

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

Details

Calculates the last disease assessment by accessing the last record defined in subject_keys after it has been arranged using the order argument.

Creates a new parameter record (keeping all columns passed) from the last source record (i.e. the last record defined in subject_keys after it has been arranged using the order argument). One new record for each subject in the filtered input dataset is added to the input dataset.

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

See also

ADRS Functions for adding Parameters: derive_param_bor(), derive_param_clinbenefit(), derive_param_confirmed_bor(), derive_param_confirmed_resp(), derive_param_response()

Author

Stephen Gormley

Examples


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

adsl <- tribble(
  ~USUBJID, ~TRTSDT,                      ~EOSDT,
  "01",     ymd("2020-12-06"), ymd("2022-03-06"),
  "02",     ymd("2021-01-16"), ymd("2022-02-03"),
  "03",     ymd("2021-01-09"), ymd("2021-02-24"),
  "04",     ymd("2021-04-21"), ymd("2021-09-15")
) %>%
  mutate(STUDYID = "a_study_id")

adrs <- tribble(
  ~USUBJID, ~PARAMCD, ~AVAL, ~AVALC, ~ASEQ, ~ADT, ~ANL01FL,
  "01", "RSP", NA, "Y", 1, ymd("2021-04-08"), NA,
  "02", "RSP", NA, "N", 1, ymd("2021-05-07"), NA,
  "03", "RSP", NA, "N", 1, NA, NA,
  "04", "RSP", NA, "N", 1, NA, NA,
  "01", "PD", NA, "N", 1, NA, NA,
  "02", "PD", NA, "Y", 1, ymd("2021-05-07"), NA,
  "03", "PD", NA, "N", 1, NA, NA,
  "04", "PD", NA, "N", 1, NA, NA,
  "01", "OVR", 3, "SD", 1, ymd("2021-03-07"), "Y",
  "01", "OVR", 2, "PR", 1, ymd("2021-04-08"), "Y",
  "02", "OVR", 3, "SD", 1, ymd("2021-03-07"), "Y",
  "02", "OVR", NA, NA, 1, ymd("2021-04-07"), NA,
  "02", "OVR", 6, "PD", 1, ymd("2021-05-07"), "Y",
  "03", "OVR", 3, "SD", 1, ymd("2021-01-30"), NA,
  "03", "OVR", 3, "SD", 2, ymd("2021-01-30"), "Y",
  "04", "OVR", NA, "NE", 1, ymd("2021-05-21"), "Y",
  "04", "OVR", 5, "NON-PD", 1, ymd("2021-06-30"), "Y",
  "04", "OVR", NA, "NE", 1, ymd("2021-07-24"), "Y",
  "04", "OVR", NA, "ND", 1, ymd("2021-09-30"), "Y"
) %>%
  mutate(STUDYID = "a_study_id")

pd <- date_source(
  dataset_name = "adrs",
  date         = ADT,
  filter       = PARAMCD == "PD" & AVALC == "Y"
)

derive_param_lasta(
  adrs,
  filter_source = PARAMCD == "OVR" & ANL01FL == "Y",
  source_pd = pd,
  source_datasets = list(adrs = adrs),
  set_values_to = vars(
    PARAMCD = "LSTAC",
    PARAM = "Last Disease Assessment Censored at First PD by Investigator",
    PARCAT1 = "Tumor Response",
    PARCAT2 = "Investigator",
    PARCAT3 = "Recist 1.1",
    ANL01FL = "Y"
  )
) %>%
  filter(PARAMCD == "LSTAC")
#> # A tibble: 4 x 12
#>   USUBJID PARAMCD  AVAL AVALC  ASEQ ADT        ANL01FL STUDYID PARAM PARCAT1
#>   <chr>   <chr>   <dbl> <chr> <dbl> <date>     <chr>   <chr>   <chr> <chr>  
#> 1 01      LSTAC       2 PR        1 2021-04-08 Y       a_stud… Last… Tumor …
#> 2 02      LSTAC       6 PD        1 2021-05-07 Y       a_stud… Last… Tumor …
#> 3 03      LSTAC       3 SD        2 2021-01-30 Y       a_stud… Last… Tumor …
#> 4 04      LSTAC      NA ND        1 2021-09-30 Y       a_stud… Last… Tumor …
#> # … with 2 more variables: PARCAT2 <chr>, PARCAT3 <chr>