derive_var_last_dose_amt: Derive Last Dose Amount
In epijim/admiral: ADaM in R Asset Library

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/derive_var_last_dose_amt.R

Add a variable for dose amount from the last dose to the input dataset.

derive_var_last_dose_amt(
  dataset,
  dataset_ex,
  filter_ex = NULL,
  by_vars = vars(STUDYID, USUBJID),
  dose_id = vars(),
  dose_date,
  analysis_date,
  single_dose_condition = (EXDOSFRQ == "ONCE"),
  new_var,
  dose_var = EXDOSE,
  traceability_vars = NULL
)

`dataset`	Input dataset. The variables specified by the `by_vars` and `analysis_date` parameters are expected.
`dataset_ex`	Input EX dataset. The variables specified by the `by_vars`, `dose_date`, `new_vars` parameters, and source variables from `traceability_vars` parameter are expected.
`filter_ex`	Filtering condition applied to EX dataset. For example, it can be used to filter for valid dose. Defaults to NULL.
`by_vars`	Variables to join by (created by `dplyr::vars`).
`dose_id`	Variables to identify unique dose (created by `dplyr::vars`). Defaults to empty `vars()`.
`dose_date`	The EX dose date variable.
`analysis_date`	The analysis date variable.
`single_dose_condition`	The condition for checking if `dataset_ex` is single dose. An error is issued if the condition is not true. Defaults to `(EXDOSFRQ == "ONCE")`.
`new_var`	The new variable added to `dataset`.
`dose_var`	The EX source dose amount variable. Defaults to `EXDOSE`.
`traceability_vars`	A named list returned by `vars()` listing the traceability variables, e.g. `vars(LDOSEDOM = "EX", LDOSESEQ = EXSEQ)`. The left-hand side (names of the list elements) gives the names of the traceability variables in the returned dataset. The right-hand side (values of the list elements) gives the values of the traceability variables in the returned dataset. These can be either strings or symbols referring to existing variables.

The last dose amount is derived as the dose amount where the maximum dose_date is lower to or equal to the analysis_date per by_vars for each observation in dataset.

Input dataset with additional column new_var.

Annie Yang

derive_vars_last_dose()

library(dplyr, warn.conflicts = FALSE)
library(admiral.test)
data(ae)
data(ex_single)

ae %>%
  head(100) %>%
  derive_var_last_dose_amt(
    head(ex_single, 100),
    filter_ex = (EXDOSE > 0 | (EXDOSE == 0 & grepl("PLACEBO", EXTRT))) &
      nchar(EXENDTC) >= 10,
    dose_date = EXENDTC,
    analysis_date = AESTDTC,
    single_dose_condition = (EXSTDTC == EXENDTC),
    new_var = LDOSE,
    dose_var = EXDOSE
  ) %>%
  select(STUDYID, USUBJID, AESEQ, AESTDTC, LDOSE)

# or with traceability variables
ae %>%
  head(100) %>%
  derive_var_last_dose_amt(
    head(ex_single, 100),
    filter_ex = (EXDOSE > 0 | (EXDOSE == 0 & grepl("PLACEBO", EXTRT))) &
      nchar(EXENDTC) >= 10,
    dose_date = EXENDTC,
    analysis_date = AESTDTC,
    single_dose_condition = (EXSTDTC == EXENDTC),
    new_var = LDOSE,
    dose_var = EXDOSE,
    traceability_vars = dplyr::vars(LDOSEDOM = "EX", LDOSESEQ = EXSEQ, LDOSEVAR = "EXDOSE")
  ) %>%
  select(STUDYID, USUBJID, AESEQ, AESTDTC, LDOSEDOM, LDOSESEQ, LDOSEVAR, LDOSE)