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Function to generate datacut summary file

Source: R/read_out.R
read_out.Rd

Produces a .html file summarizing the changes applied to data during a data cut. The file will contain an overview for the change in number of records for each dataset, the types of cut applied and the opportunity to inspect the removed records.

Usage

read_out(
  dcut = NULL,
  patient_cut_data = NULL,
  date_cut_data = NULL,
  dm_cut = NULL,
  no_cut_list = NULL,
  out_path = "."
)

Arguments

dcut

The output datacut dataset (DCUT), created via the create_dcut() function, containing the variable DCUTDTC.

patient_cut_data

A list of quoted SDTMv domain names in which a patient cut has been. applied (via the pt_cut() function). To be left blank if a patient cut has not been performed on any domains.

date_cut_data

A list of quoted SDTMv domain names in which a date cut has been applied. (via the date_cut() function). To be left blank if a date cut has not been performed on any domains.

dm_cut

The output dataset, created via the special_dm_cut() function, containing the variables DCUT_TEMP_REMOVE and DCUT_TEMP_DTHCHANGE.

no_cut_list

List of 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.

out_path

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

Value

Returns a .html file summarizing the changes made to data during a datacut.

Examples

if (FALSE) { # \dontrun{
dcut <- tibble::tribble(
  ~USUBJID, ~DCUTDTM, ~DCUTDTC,
  "subject1", lubridate::ymd_hms("2020-10-11T23:59:59"), "2020-10-11T23:59:59",
  "subject2", lubridate::ymd_hms("2020-10-11T23:59:59"), "2020-10-11T23:59:59",
  "subject4", lubridate::ymd_hms("2020-10-11T23:59:59"), "2020-10-11T23:59:59"
)

ae <- tibble::tribble(
  ~USUBJID, ~AESEQ, ~AESTDTC,
  "subject1", 1, "2020-01-02T00:00:00",
  "subject1", 2, "2020-08-31T00:00:00",
  "subject1", 3, "2020-10-10T00:00:00",
  "subject2", 2, "2020-02-20T00:00:00",
  "subject3", 1, "2020-03-02T00:00:00",
  "subject4", 1, "2020-11-02T00:00:00",
  "subject4", 2, ""
)

dm <- tibble::tribble(
  ~USUBJID, ~DTHDTC, ~DTHFL,
  "subject1", "2020-10-11", "Y",
  "subject2", "2020-10-12", "Y",
)

dt_ae <- date_cut(
  dataset_sdtm = ae,
  sdtm_date_var = AESTDTC,
  dataset_cut = dcut,
  cut_var = DCUTDTM
)

pt_ae <- pt_cut(
  dataset_sdtm = ae,
  dataset_cut = dcut
)

dm_cut <- special_dm_cut(
  dataset_dm = dm,
  dataset_cut = dcut,
  cut_var = DCUTDTM
)

read_out(dcut, patient_cut_data = list(ae = pt_ae), date_cut_data = list(ae = dt_ae), dm_cut)
} # }