Repository Cleanup & bayesTPC Updates (June 2025)

June 12–14, 2025: bayesTPC Function Updates • Updated to the development version of bayesTPC from GitHub (johnwilliamsmithjr/bayesTPC). • Renamed data loading function: • get_datasets() → get_VB_datasets() • Removed deprecated function bayesTPC_summary(); replaced with standard S3 method: summary(). • Posterior prediction functions (plot_prediction, posterior_predictive) now return custom objects (e.g., "btpc_prediction"), requiring manual extraction (e.g., $summary). • plot_prediction() returns NULL unless temp_range is explicitly provided.

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June 29, 2025: Model Fitting Error & NIMBLE Compatibility • Encountered error with b_TPC() due to missing internal getNimbleOption() function in newer versions of nimble. • Fixed by downgrading nimble to version 0.13.2:

remotes::install_version("nimble", version = "0.13.2")

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June 30, 2025: GitHub Push Failed Due to Large Files • Updated .gitignore to exclude cache, site output, and large intermediate files:

*_cache/ _site/ *.rdb *.rdx *.RData *.tar.gz

•	Removed large files from Git history using git filter-repo:

git filter-repo --force --path-glob '*.rdb' --invert-paths

•	Reconnected origin remote and force-pushed cleaned history:

git remote add origin https://github.com/VectorByteOrg/bayesTPC-tutorials.git git push --set-upstream origin yusi --force