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Ingest ARS (Analysis Results Standard) metadata, produce ARD (Analysis Results Dataset) code for each output

Source: R/readARS.R
readARS.Rd

Ingest ARS (Analysis Results Standard) metadata, and meta-programme R scripts that could be run as-is to produce Analysis Results Datasets when ingesting ADaM datasets

Usage

readARS(
  ARS_path,
  output_path = tempdir(),
  adam_path = tempdir(),
  spec_output = "",
  output_format = "none"
)

Arguments

ARS_path

A file containing ARS metadata for a reporting event

output_path

Path to store .R ARD scripts

adam_path

Path to folder containing ADaM datasets, to be run in ARD program. Datasets may be supplied as CSV (`.csv`) or SAS transport (`.xpt`) files. siera chooses the reader for each dataset from the file extension found in this folder — `.csv` files are read with readr::read_csv() and `.xpt` files with haven::read_xpt() — so no extra argument is required (mirroring how the ARS input format is inferred from `.json` vs `.xlsx`). Reading `.xpt` datasets in the generated script requires the haven package. When both a `.csv` and a `.xpt` exist for the same dataset, the `.csv` is used.

spec_output

The output ID for a specific output to be run from the metadata

output_format

Format for emitting the generated ARD. Must be exactly one of `"none"` or `"datasetjson"` (no partial matching). `"none"` (default) generates the ARD scripts only. `"datasetjson"` additionally appends code that writes each ARD as a CDISC Dataset-JSON file (`ARD_<OutputId>.json`) when the generated script is run. The Dataset-JSON export requires the optional datasetjson package to be installed in the environment that runs the generated script.

Value

R programmes generating ARDs - one for each output (or analysis from an output) specified in the ARS metadata

Examples

# path to file containing ARS metadata

ARS_path <- ARS_example("Common_Safety_Displays_cards.xlsx")

# output path for R programs
output_dir <- tempdir()

# folder containing ADaM datasets
adam_folder <- tempdir()

# run function, write to temp directory
readARS(ARS_path, output_dir, adam_folder)
#> New names:
#> • `` -> `...11`
#> • `` -> `...12`
#> • `` -> `...13`