| 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)