├── .gitignore ├── GAMs-biomedical-research.Rproj ├── LICENSE.md ├── Main_manuscript.Rmd ├── README.md ├── appendices ├── Appendix_A.Rmd ├── Appendix_A.pdf ├── Appendix_A.tex ├── Appendix_A_files │ └── figure-latex │ │ ├── final-GAM-diag-1.pdf │ │ ├── first-GAM-diag-1.pdf │ │ ├── pairwise-comp-workflow-fig-1.pdf │ │ └── second-GAM-diag-1.pdf ├── Appendix_B.Rmd ├── Appendix_B.pdf ├── Appendix_B.tex ├── Appendix_B_files │ └── figure-latex │ │ ├── linear-cases-Appendix-1.pdf │ │ └── quadratic-cases-Appendix-1.pdf └── latex_docs │ ├── orcid.png │ ├── preamble_Appendix_A.sty │ └── preamble_Appendix_B.sty ├── bibliography ├── american-medical-association.csl └── refs.bib ├── html_docs └── style.css ├── latex_docs ├── orcid.png └── preamble.sty ├── scripts ├── basis_functions.R ├── difference_smooths.R ├── example.R ├── gam_diagnostics.R ├── pairwise_limits.R ├── plot_example.R ├── pointwise_comparisons.R └── simulate_data.R └── sections ├── 01-Background.Rmd ├── 02-Challenges.Rmd ├── 03-GAM 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