The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

Type: Package
Title: Generate Analysis Results Programmes Using ARS Metadata
Version: 0.5.0
Maintainer: Malan Bosman <malanbos@gmail.com>
Description: Analysis Results Standard (ARS), a foundational standard by CDISC (Clinical Data Interchange Standards Consortium), provides a logical data model for metadata describing all components to calculate Analysis Results. https://www.cdisc.org/standards/foundational/analysis-results-standard Using 'siera' package, ARS metadata is ingested (JSON or Excel format), producing programmes to generate Analysis Results Datasets (ARDs).
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports: magrittr, dplyr, tibble, tidyr, jsonlite, stringr, readxl, cli
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://clymbclinical.github.io/siera/, https://github.com/clymbclinical/siera
BugReports: https://github.com/clymbclinical/siera/issues
NeedsCompilation: no
Packaged: 2025-07-29 15:04:44 UTC; mbosm
Author: Malan Bosman [aut, cre], Clymb Clinical [cph, fnd]
Repository: CRAN
Date/Publication: 2025-07-29 15:30:02 UTC

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

lhs

A value or the magrittr placeholder.

rhs

A function call using the magrittr semantics.

Value

The result of calling 'rhs(lhs)'.


Get path to example ARD scripts, auto-generated by siera

Description

siera comes bundled with some example ARD-producing scripts in its 'inst/script' directory. This function make them easy to access.

Usage

ARD_script_example(path = NULL)

Arguments

path

Name of R file. If 'NULL', the example files will be listed.

Value

A list of example R files (if path is NULL), or a file itself if path is used.

Examples

ARD_script_example()
ARD_script_example("ARD_Out14-1-1.R")

Get path to ARS example files

Description

siera comes bundled with some example files in its 'inst/extdata' directory. This function make them easy to access.

Usage

ARS_example(path = NULL)

Arguments

path

Name of file. If 'NULL', the example files will be listed.

Value

A list of example files (if path is NULL), or a file itself if path is used.

Examples

ARS_example()
ARS_example("ARS_V1_Common_Safety_Displays.json")

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

Description

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 = "",
  spec_analysis = "",
  example = FALSE
)

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

spec_output

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

spec_analysis

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

example

Default is FALSE. If TRUE, example-based operations will be applied to CDISC example ARS. If FALSE, AnalysisMethodCodeTemplateCode will be expected as source of the Method (and Operations) code

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_xl(ARS_path, output_dir, adam_folder)


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

Description

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_xl(
  ARS_path,
  output_path = tempdir(),
  adam_path = tempdir(),
  spec_output = "",
  spec_analysis = "",
  example = FALSE
)

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

spec_output

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

spec_analysis

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

example

Default is FALSE. If TRUE, example-based operations will be applied to CDISC example ARS. If FALSE, AnalysisMethodCodeTemplateCode will be expected as source of the Method (and Operations) code

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_xl(ARS_path, output_dir, adam_folder)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.