derive_param_doseint: Adds a Parameter for Dose Intensity
In epijim/admiral: ADaM in R Asset Library

Description Usage Arguments Details Value Author(s) Examples

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

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

`dataset`	Input dataset The variables specified by the `by_vars` parameter, `PARAMCD`, and `AVAL` are expected. 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 Permitted Values: list of variables
`set_values_to`	Variables to be set The specified variables are set to the specified values for the new observations. For example `vars(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

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

The input dataset with the new parameter rows added

Alice Ehmann

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

adex <- tibble::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=vars(USUBJID, VISIT),
  set_values_to = vars(PARAMCD = "TNDOSINT"),
  tadm_code = "TNDOSE",
  tpadm_code = "TSNDOSE")

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