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Source Dissemination Scripts

Source: R/execute.R
sourceDisseminationScripts.Rd

Dissemination scripts are sourced from dissemination/pretty/R/ in alphabetical order. Each script is sourced in the global environment, so any variables, functions, or file outputs are available at the console level. A disseminationEnv object is automatically created (via createDisseminationEnv) and injected into the global environment for use by dissemination scripts. Call createDisseminationEnv directly to build the same object at the console while authoring a dissemination script.

Usage

sourceDisseminationScripts(
  projectPath = here::here(),
  pipelineVersion = NULL,
  databaseIds = NULL,
  outputPath = here::here("dissemination/pretty"),
  verbose = TRUE,
  warnMissing = TRUE
)

Arguments

projectPath

Character. Path to the project root directory. Defaults to here::here().

pipelineVersion

Character. The pipeline/study version being disseminated (e.g., "1.0.0"). Available to scripts via disseminationEnv$pipelineVersion. If NULL (default), attempts to auto-detect from config.yml.

databaseIds

Character vector. Database IDs that were included in postprocessing (e.g., c("database_1", "database_2")). Available to scripts via disseminationEnv$databaseIds. If NULL (default), can be set manually by user.

outputPath

Character. Base output directory for dissemination scripts. Available to scripts via disseminationEnv$outputPath. Defaults to here::here("dissemination/pretty").

verbose

Logical. If TRUE (default), displays which scripts are being sourced.

warnMissing

Logical. If TRUE (default), warns when the dissemination scripts directory doesn't exist.

Value

Invisibly returns a list with:

  • sourced_files: Character vector of sourced files (absolute paths)

  • directories_checked: Character vector of directories checked

  • error_summary: List of any errors encountered

  • disseminationEnv: List containing pipelineVersion, databaseIds, outputPath

Details

A convenience function that sources all R scripts from the dissemination scripts directory in alphabetical order. After the pipeline runs and runPostProcessing merges results, this function allows users to source custom dissemination/formatting scripts to prepare results for Excel export, StudyHub submission, or other dissemination targets.

Typical workflow:

  1. Run sourceInputBuilderScripts to load input definitions

  2. Run execStudyPipeline to execute the analysis

  3. Run runPostProcessing to merge results across databases

  4. Use makeDisseminationScript to create a template for formatting

  5. Edit the template script with your custom formatting/export logic

  6. Run sourceDisseminationScripts(pipelineVersion = "1.0.0", databaseIds = c("db1", "db2")) to execute your dissemination scripts with metadata

The disseminationEnv object is made available to all sourced scripts and contains:

  • pipelineVersion: The version string

  • databaseIds: Vector of database IDs

  • outputPath: Base output directory for results

  • resultsPath: Inferred merged results path based on version