Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

Value

The result of calling 'rhs(lhs)'.

Generate ADaM loading code

Description

Internal helper that inspects the analyses referenced by an output and builds the code required to read the relevant ADaM datasets. Only datasets referenced in the analyses, analysis sets, or data subsets are included in the returned code block.

Usage

.generate_adam_loading_code(
  Anas,
  Analyses,
  AnalysisSets,
  DataSubsets,
  adam_path
)

Arguments

Value

Character string containing the code used to load ADaM datasets.

Format numeric values consistently

Description

Internal helper to apply consistent number formatting across analyses.

Usage

.generate_analysis_method_section(
  analysis_methods,
  analysis_method_code_template,
  analysis_method_code_parameters,
  method_id,
  analysis_id,
  output_id,
  envir = parent.frame()
)

Arguments

Value

Character vector with formatted numbers.

Generate analysis set code and context

Description

Internal helper that builds the code needed to apply an analysis set to the current analysis. The function inspects the ARS metadata to determine filter conditions and returns the templated code together with the name of the resulting population dataset.

Usage

.generate_analysis_set_code(
  j,
  analysis_sets,
  analyses,
  anas,
  analysis_set_id,
  analysis_id
)

Arguments

Value

A list containing the generated code and the name of the dataset that holds the filtered analysis population.

Generate data subset code

Description

Internal helper that assembles the code required to apply a data subset for a given analysis. The function prepares default code, augments it with conditional filters when required, and returns metadata describing the subset that was applied.

Usage

.generate_data_subset_code(
  data_subsets,
  subset_id,
  analysis_id,
  analysis_set_dataset,
  file_ext
)

Arguments

Value

A list containing the generated code, subset name, and filter expression.

Build a data subset condition

Description

Internal helper that translates ARS data-subset metadata into a filter expression suitable for inclusion in generated R code. Handles comparator translation, type coercion, and workbook-specific formatting differences.

Usage

.generate_data_subset_condition(variable, comparator, value, file_ext)

Arguments

Value

Character string representing the filter expression to apply.

Generate library loading code

Description

Internal helper that returns the boilerplate code used to load the packages required by generated ARD scripts.

Usage

.generate_library_code()

Value

Character string containing the library load block.

Generate the programme header banner

Description

Internal helper that produces the standardised programme banner inserted at the top of each generated ARD script.

Usage

.generate_program_header(OutputId, Output_Name, date)

Arguments

Value

Character string containing the formatted programme header.

Read ARS metadata from JSON

Description

Internal helper that ingests ARS metadata stored as JSON and converts it into the harmonised list of tibbles used elsewhere in the package.

Usage

.read_ars_json_metadata(ARS_path)

Arguments

Value

A list of metadata tables extracted from the JSON file, or 'NULL' when required sections are missing.

Read ARS metadata from disk

Description

Internal helper that validates the ARS file extension and dispatches to the JSON or XLSX reader before returning the harmonised metadata list.

Usage

.read_ars_metadata(ARS_path)

Arguments

Value

A list containing harmonised metadata tables, or 'NULL' if the file cannot be parsed.

Read ARS metadata from XLSX

Description

Internal helper that ingests ARS metadata stored in Excel workbooks and converts each worksheet into the harmonised metadata list.

Usage

.read_ars_xlsx_metadata(ARS_path)

Arguments

Value

A list of metadata tables extracted from the workbook, or 'NULL' when required sheets are missing.

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

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

Value

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

Examples

ARS_example()
ARS_example("Common_Safety_Displays_cards.xlsx")

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 = ""
)

Arguments

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)