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Wrapper function to prepare and apply the datacut of SDTMv datasets

Source: R/process_cut.R
process_cut.Rd

Applies the selected type of datacut on each SDTMv dataset based on the chosen SDTMv date variable, and outputs the resulting cut datasets, as well as the datacut dataset, as a list. It provides an option to perform a "special" cut on the demography (dm) domain in which any deaths occurring after the datacut date are removed. It also provides an option to produce a .html file that summarizes the changes applied to the data during the cut, where you can inspect the records that have been removed and/or modified.

Usage 

process_cut(
  source_sdtm_data,
  patient_cut_v = NULL,
  date_cut_m = NULL,
  no_cut_v = NULL,
  dataset_cut,
  cut_var,
  special_dm = TRUE,
  read_out = FALSE,
  out_path = "."
)

Arguments

source_sdtm_data

A list of uncut SDTMv dataframes

patient_cut_v

A vector of quoted SDTMv domain names in which a patient cut should be applied. To be left blank if a patient cut should not be performed on any domains.

date_cut_m

A 2 column matrix, where the first column is the quoted SDTMv domain names in which a date cut should be applied and the second column is the quoted SDTMv date variables used to carry out the date cut for each SDTMv domain. To be left blank if a date cut should not be performed on any domains.

no_cut_v

A vector of quoted SDTMv domain names in which no cut should be applied. To be left blank if no domains are to remain exactly as source.

dataset_cut

Input datacut dataset, e.g. dcut

cut_var

Datacut date variable within the dataset_cut dataset, e.g. DCUTDTM

special_dm

A logical input indicating whether the special dm cut should be performed. Note that, if TRUE, dm should not be included in patient_cut_v, date_cut_m or no_cut_v inputs.

read_out

A logical input indicating whether a summary file for the datacut should be produced. If TRUE, a .html file will be returned containing a summary of the cut and records removed. Default set to FALSE.

out_path

A character vector of file save path for the summary file if read_out = TRUE; the default corresponds to the working directory, getwd().

Value

Returns a list of all input SDTMv datasets, plus the datacut dataset, after performing the selected datacut on each SDTMv domain.

Examples 

dcut <- data.frame(
  USUBJID = c("a", "b"),
  DCUTDTC = c("2022-02-17", "2022-02-17")
)
dcut <- impute_dcutdtc(dcut, DCUTDTC, DCUTDTM)
sc <- data.frame(USUBJID = c("a", "a", "b", "c"))
ts <- data.frame(USUBJID = c("a", "a", "b", "c"))
ae <- data.frame(
  USUBJID = c("a", "a", "b", "c"),
  AESTDTC = c("2022-02-16", "2022-02-18", "2022-02-16", "2022-02-16")
)
source_data <- list(sc = sc, ae = ae, ts = ts)

cut_data <- process_cut(
  source_sdtm_data = source_data,
  patient_cut_v = c("sc"),
  date_cut_m = rbind(c("ae", "AESTDTC")),
  no_cut_v = c("ts"),
  dataset_cut = dcut,
  cut_var = DCUTDTM,
  special_dm = FALSE
)