siera
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Overview
With siera, users ingest Analysis Results Standard (ARS) metadata and auto-generate R scripts that, when run with corresponding ADaM datasets, provide Analysis Results Datasets (ARDs).
The CDISC Analysis Results Standard is a foundational standard that facilitates automation, reproducibility, reusability and traceability of analysis results data.
ARS metadata is officially represented using JSON format (though there is also an Excel representation for easier readability, but the JSON format is recommended for official ARS usage). Such a JSON file contains all relevant metadata to be able to calculate the Analysis Results for a specific Reporting Event. This metadata includes (but is not limited to):
- Analysis Sets (e.g. SAFFL = “Y”)
- AnalysisGroupings (e.g. group by Treatment)
- DataSubsets (e.g. filter by Treatment-Emergent Adverse Events)
- AnalysisMethods (e.g. calculate ‘n’, ‘Mean’, ‘Min’, ‘Max’, ‘Q1’, ‘Q3’)
Applying all these concepts to ADaM input data, yields Analysis Results in Dataset format (ARDs).
Installation
siera can be installed from
CRAN with:
install.packages("siera")The development version can be installed from Github using
devtools::install_github("clymbclinical/siera")Usage
The siera package has one main function, called readARS. This
function takes ARS metadata as input (either JSON or xlsx format), and
makes use of the various metadata pieces to populate R scripts, which an
be run as-is to produce ARDs. One R script is created for each output
(table) as defined in the ARS metadata for the reportingg event.
In order to make use of this function, the following are required as arguments:
- A functional ARS file, representing ARS Metadata for a Reporting Event (JSON or xlsx)
- An output directory where the R scripts will be placed
- A folder containing the related ADaM datasets for the ARDs to be generated
See the Getting Started vignette for examples and more detail on the process.