derive_param_doseint: Adds a Parameter for Dose Intensity

In admiral: ADaM in R Asset Library

Adds a Parameter for Dose Intensity

Description

Adds a record for the dose intensity for each by group (e.g., subject and visit) where the source parameters are available.

Note: This is a wrapper function for the more generic derive_param_computed().

The analysis value of the new parameter is derived as Total Dose / Planned Dose * 100

Usage

derive_param_doseint(
  dataset,
  by_vars,
  set_values_to = exprs(PARAMCD = "TNDOSINT"),
  tadm_code = "TNDOSE",
  tpadm_code = "TSNDOSE",
  zero_doses = "Inf",
  filter = NULL
)

Arguments

dataset	Input dataset The variables specified by the by_vars argument are expected to be in the dataset. PARAMCD, and AVAL are expected as well. The variable specified by by_vars and PARAMCD must be a unique key of the input dataset after restricting it by the filter condition (filter parameter) and to the parameters specified by tadm_code and padm_code.
by_vars	Grouping variables Only variables specified in by_vars will be populated in the newly created records. Permitted Values: list of variables created by exprs() e.g. exprs(USUBJID, VISIT)
set_values_to	Variables to be set The specified variables are set to the specified values for the new observations. For example exprs(PARAMCD = "MAP") defines the parameter code for the new parameter. Permitted Values: List of variable-value pairs
tadm_code	Total Doses Administered parameter code The observations where PARAMCD equals the specified value are considered as the total dose administered. The AVAL associated with this PARAMCD will be the numerator of the dose intensity calculation. Permitted Values: character value
tpadm_code	Total Doses Planned parameter code The observations where PARAMCD equals the specified value are considered as the total planned dose. The AVAL associated with this PARAMCD will be the denominator of the dose intensity calculation. Permitted Values: character value
zero_doses	Flag indicating logic for handling 0 planned or administered doses for a by_vars group Default: Inf Permitted Values: Inf, 100 No record is returned if either the planned (tpadm_code) or administered (tadm_code) AVAL are NA. No record is returned is a record does not exist for both tadm_code and tpadm_code for the specified by_var. If zero_doses = Inf: If the planned dose (tpadm_code) is 0 and administered dose (tadm_code) is 0, NaN is returned. If the planned dose (tpadm_code) is 0 and the administered dose (tadm_code) is > 0, Inf is returned. If zero_doses = 100 : If the planned dose (tpadm_code) is 0 and administered dose (tadm_code) is 0, 0 is returned. If the planned dose (tpadm_code) is 0 and the administered dose (tadm_code) is > 0, 100 is returned.
filter	Filter condition The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account. Permitted Values: a condition

Value

The input dataset with the new parameter rows added. Note, a variable will only be populated in the new parameter rows if it is specified in by_vars.

See Also

BDS-Findings Functions for adding Parameters/Records: default_qtc_paramcd(), derive_expected_records(), derive_extreme_event(), derive_extreme_records(), derive_locf_records(), derive_param_bmi(), derive_param_bsa(), derive_param_computed(), derive_param_exist_flag(), derive_param_exposure(), derive_param_framingham(), derive_param_map(), derive_param_qtc(), derive_param_rr(), derive_param_wbc_abs(), derive_summary_records()

Examples

library(tibble)
library(lubridate, warn.conflicts = FALSE)

adex <- tribble(
  ~USUBJID, ~PARAMCD, ~VISIT, ~ANL01FL, ~ASTDT, ~AENDT, ~AVAL,
  "P001", "TNDOSE", "V1", "Y", ymd("2020-01-01"), ymd("2020-01-30"), 59,
  "P001", "TSNDOSE", "V1", "Y", ymd("2020-01-01"), ymd("2020-02-01"), 96,
  "P001", "TNDOSE", "V2", "Y", ymd("2020-02-01"), ymd("2020-03-15"), 88,
  "P001", "TSNDOSE", "V2", "Y", ymd("2020-02-05"), ymd("2020-03-01"), 88,
  "P002", "TNDOSE", "V1", "Y", ymd("2021-01-01"), ymd("2021-01-30"), 0,
  "P002", "TSNDOSE", "V1", "Y", ymd("2021-01-01"), ymd("2021-02-01"), 0,
  "P002", "TNDOSE", "V2", "Y", ymd("2021-02-01"), ymd("2021-03-15"), 52,
  "P002", "TSNDOSE", "V2", "Y", ymd("2021-02-05"), ymd("2021-03-01"), 0
)

derive_param_doseint(
  adex,
  by_vars = exprs(USUBJID, VISIT),
  set_values_to = exprs(PARAMCD = "TNDOSINT"),
  tadm_code = "TNDOSE",
  tpadm_code = "TSNDOSE"
)

derive_param_doseint(
  adex,
  by_vars = exprs(USUBJID, VISIT),
  set_values_to = exprs(PARAMCD = "TDOSINT2"),
  tadm_code = "TNDOSE",
  tpadm_code = "TSNDOSE",
  zero_doses = "100"
)

admiral documentation built on June 22, 2024, 9:06 a.m.