Updates - #6
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Moved R package to the root directory and removed legacy app, Docker, and auxiliary files. Updated project configuration files (.Rbuildignore, .gitignore, pkgdown) to reflect the new structure.
Created data-raw/simulated_data.R for generating package datasets and data-raw/generate_figures.R for consolidating documentation figure production. Removed legacy simulation and test scripts.
Built the documentation site using the updated package structure, data, and parameter names. Includes new figures reflecting the dual legend system.
Updated README, homepage, and 'About' vignette to focus exclusively on the R package. Regenerated the documentation site to ensure all stale references (including the web-app article) are removed.
Merged origin/master into updates. Resolved conflicts in DESCRIPTION and man/circos_plot.Rd by preferring the new package structure and versioning (0.1). Accepted new 'analysis' data and scripts from the master branch.
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