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Improve code efficiency - #2
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- Removed obsolete 'cap' file. - Updated framework design documentation to reflect changes in the pipeline structure and method organization. - Added a comprehensive 'getting started' guide for running the v2 baseline, reading outputs, and testing changes. - Enhanced clarity on the roles of specs, stages, engines, and selection rules in the modeling process. - Improved organization of methods and modules for better maintainability and usability.
- Modified the parity_summary.csv to reflect updated metrics and draw limits for various taxa across climate and habitat stages. - Adjusted the documentation in getting_started.md to point to the correct section for output definitions.
- Updated README.md to include new engine `gbm` and details on `replace_stage_method()` and `extend_models()`. - Revised flowchart and steps in README.md to clarify experiment comparisons and outputs. - Added section in framework_design.md on handling new covariates not present in the dataset, detailing extraction and integration processes. - Expanded getting_started.md with instructions for adding covariates from experiments and automatic comparison with exp_000.
- Replaced `gbm` with `xgboost` in the engines section of README.md and framework_design.md. - Updated selection rules to include `hurdle` in README.md and framework_design.md. - Modified experiment configuration in framework_design.md to use `xgboost`. - Clarified hurdle structure in taxon_quirks.md to reflect the new generic `hurdle` rule. - Adjusted experiment names and descriptions to align with the new engine and its capabilities.
- Updated comments and documentation across multiple scripts to clarify that the test dataset and v2 results are read from the published copies on ABMI-DATA2. - Introduced a new `data_source.R` file to centralize the logic for resolving dataset paths and checking their integrity. - Modified functions to utilize `test_dataset_dir()` for retrieving the dataset folder, ensuring consistency and clarity in data access. - Enhanced README and documentation to reflect changes in dataset handling and clarify the workflow for accessing datasets.
- Deleted the script `05_harmonize_v2_results.R` which was responsible for harmonizing the v2 results into a single parity reference. - This script included functions for reading and processing plant, mammal, and bird coefficient data, as well as assembling the final results into a CSV format. - The removal is part of a refactor to streamline the data processing pipeline and eliminate legacy code that is no longer needed.
… and update references to ABMIexploreR results. Add run script for rebuilding test dataset and v2 reference with logging.
- Changed references from `comparison_*.csv` to `comparison_metrics.csv` in README.md to clarify the output files generated during experiments. - Enhanced descriptions of the comparison metrics in README.md, including details about the data contained in `comparison_metrics.csv`. - Updated the getting_started.md to reflect the changes in output files and provide clearer instructions on how to interpret the comparison results.
… across multiple scripts
…ty and consistency - Updated comments in `single.R` to clarify the purpose of the `single` rule. - Revised notes in `staged_bic.R` to enhance understanding of model selection process. cleaned up wrong or stale comments, condensed narrative explanations, dropped changelog notes, and removed duplicate comments repeated for the same shared logic across files, keeping the one at the definition.
…les, and tests - Introduced README.md files in the following directories: - `1_code/_setup/`: Details the process for building the frozen test dataset and v2 reference, including script descriptions and environment variables. - `1_code/experiments/`: Outlines the structure for experiments, including how to add new experiments and the required folder organization. - `1_code/harness/`: Describes the shared pipeline, its functions, and the experiment configuration process. - `1_code/modules/`: Provides guidelines for taxon modules, including the module interface and how to add new modules. - `1_code/tests/`: Lists available tests and their purposes, along with instructions for running them. These changes enhance the clarity and usability of the codebase for current and future contributors.
- Created .github/workflows/docs.yaml to automate building and deploying the Quarto documentation site to GitHub Pages on pushes to the main branch. - Added docs/.gitignore to exclude Quarto build artifacts from version control. - Introduced docs/_quarto.yml to configure the Quarto project, specifying the website structure and rendering settings. - Created index.md as the homepage for the documentation site, providing an overview and links to getting started. - Added mermaid.lua filter to render Mermaid diagrams in Markdown, enabling compatibility with both GitHub and Quarto rendering.
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