derive_var_last_dose_grp: Derive Last Dose with User-Defined Groupings
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_grp.R

Add a variable for user-defined dose grouping of the last dose to the input dataset.

derive_var_last_dose_grp(
  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,
  grp_brks,
  grp_lbls,
  include_lowest = TRUE,
  right = TRUE,
  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 output variable defined by the user.
`grp_brks`	User supplied breaks to apply to groups. Refer to `breaks` parameter in `cut()` for details.
`grp_lbls`	User supplied labels to apply to groups. Refer to `labels` parameter in `cut()` for details.
`include_lowest`	logical, indicating if a value equal to the lowest (or highest, for right = FALSE) ‘breaks’ value should be included. Refer to `include.lowest` parameter in `cut()` for details.
`right`	Logical, indicating if the intervals should be closed on the right (and open on the left) or vice versa. Refer to `right` parameter in `cut()` for details.
`dose_var`	The 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.

Last dose is the dose with maximum dose_date that is lower to or equal to the analysis_date per by_vars for each observation in dataset. The last dose group is then derived by user-defined grouping, which groups dose_var as specified in grp_brks, and returns grp_lbls as the values for new_var.

Input dataset with additional column new_var.

Ben Straub

derive_vars_last_dose(), cut()

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

ae %>%
   head(100) %>%
   derive_var_last_dose_grp(
   head(ex_single, 100),
   filter_ex = (EXDOSE > 0 | (EXDOSE == 0 & grepl("PLACEBO", EXTRT))) &
   nchar(EXENDTC) >= 10,
   by_vars = vars(STUDYID, USUBJID),
   dose_date = EXSTDTC,
   new_var = LDGRP,
   grp_brks = c(0, 20, 40, 60),
   grp_lbls = c("Low", "Medium", "High"),
   include_lowest = TRUE,
   right = TRUE,
   dose_var = EXDOSE,
   analysis_date = AESTDTC,
   single_dose_condition = (EXSTDTC == EXENDTC),
   traceability_vars = dplyr::vars(LDOSEDOM = "EX", LDOSESEQ = EXSEQ, LDOSEVAR = "EXENDTC")
   ) %>%
   select(USUBJID, LDGRP, LDOSEDOM, LDOSESEQ, LDOSEVAR)