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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.

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.