FSK2R 0.2.0

Major New Features

• Dynamic Script Detection: import_fsk() now dynamically detects model and visualization script filenames from metadata.rdf instead of hardcoding “model.r” and “visualization.r”. This enables support for FSKX files with non-standard script names.

• Complete Temporary Folder Execution: run_simulation() now executes models in their unpacked temporary directory, solving file loading issues for models that depend on CSV, Excel, and other data files (e.g., QMRA models).

• Workspace Copying Functionality: Added optional workspace copying with intelligent directory naming:

  • New parameters: copy_workspace and workspace_mode in run_simulation() and run_all_simulations()
  • Creates directories named: fsk_workspace_[model_name]_[simulation_name]/
  • Three copy modes: “all” (complete workspace), “generated” (new files only), “modified” (changed files only)

• Model Chaining Support: Added inject_to_global parameter enabling seamless model chaining workflows:

  • New parameter: inject_to_global in run_simulation() and run_all_simulations()
  • When TRUE, simulation variables are injected directly into the user’s global environment
  • Enables users to access simulation results directly without complex variable extraction
  • Facilitates model chaining: use results from Model A as inputs to Model B
  • Maintains backward compatibility (FALSE by default)

Bug Fixes and Improvements

• Cross-platform line endings: All textual files exported into FSKX archives now use LF line endings on every OS (including Windows). This applies to:

  • README.txt, metaData.json, packages.json, manifest.xml, metadata.rdf
  • model and visualization scripts
  • workspace.r
  • sim.sedml and model.sbml

• Other files: R scripts included via other_files are normalized to LF on export; other file types are copied unchanged.

• Encoding: All textual exports are written as UTF-8 (no BOM).

• Internal: Introduced write_text_lf() helper to normalize line endings and write via binary connections; XML writers now use binary connections; zipping uses utils::zip to preserve directory structure.

• File Loading Fix: Models that load external files (CSV, Excel, etc.) now work correctly by executing in the proper temporary directory with automatic working directory restoration.

• Enhanced Return Values: run_simulation() now returns all user-created variables with preserved data types (scalars, vectors, data frames, lists, matrices) .

• Improved Visualization Handling: Enhanced automatic display of ggplot objects created by visualization scripts.

• Package Build Optimization: Added comprehensive .Rbuildignore file to exclude development files (test projects, debug scripts, session artifacts) from package builds.

• Robust Error Handling: Added proper error handling and cleanup for working directory management and workspace copying operations.

• Updated Documentation: Enhanced function documentation to reflect new parameters and capabilities.

Breaking Changes

• None - all changes are backward compatible with existing workflows.

FSK2R 0.1.3

• Removed the googlesheets dependencies due to archiving of that package.
• Small updates in the documentation, especially to adapt to new terminologies.

FSK2R 0.1.2

• Added a NEWS.md file to track changes to the package.
• Improved the function documentation.

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