├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── pkgdown.yaml ├── .gitignore ├── CRAN-RELEASE ├── CRAN-SUBMISSION ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── bayesdfa-package.R ├── converge_rhat.R ├── dfa_cv.R ├── dfa_fitted.R ├── dfa_loadings.R ├── dfa_trends.R ├── find_dfa_trends.R ├── find_regimes.R ├── find_swans.R ├── fit_dfa.R ├── fit_regimes.R ├── hmm_init.R ├── invert_chains.R ├── loo.R ├── plot_fitted.R ├── plot_loadings.R ├── plot_regime_model.R ├── plot_trends.R ├── predicted.R ├── print.R ├── rotate_trends.R ├── sim.R ├── stanmodels.R └── trend_cor.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── bayesdfa.Rproj ├── configure ├── configure.win ├── cran-comments.md ├── docs ├── 404.html ├── articles │ ├── a1_bayesdfa.html │ ├── a1_bayesdfa_files │ │ └── figure-html │ │ │ ├── fit-extreme-dfa-1.png │ │ │ ├── plot-1-fitted-example-1.png │ │ │ ├── plot-1-trend-1.png │ │ │ ├── plot-2-fitted-example-1.png │ │ │ ├── plot-extreme-loadings-1.png │ │ │ ├── plot-loadings-1.png │ │ │ ├── simulate-data-plot-1.png │ │ │ ├── simulate-data-plot2-1.png │ │ │ └── simulate-data-plot3-1.png │ ├── a2_combining_data.html │ ├── a2_combining_data_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── a3_covariates.html │ ├── a3_covariates_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ └── unnamed-chunk-5-1.png │ ├── a4_smooth.html │ ├── a4_smooth_files │ │ └── figure-html │ │ │ └── unnamed-chunk-3-1.png │ ├── a5_estimate_process_sigma.html │ ├── a5_estimate_process_sigma_files │ │ └── figure-html │ │ │ └── simulate-data-plot-1.png │ ├── a6_compositional.html │ ├── a6_compositional_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-12-1.png │ │ │ └── unnamed-chunk-7-1.png │ ├── a7_bigdata.html │ ├── a7_bigdata_files │ │ └── figure-html │ │ │ └── unnamed-chunk-3-1.png │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── extra.css ├── extra.ss ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Rplot004.png │ ├── Rplot005.png │ ├── Rplot006.png │ ├── bayesdfa-package.html │ ├── dfa_cv.html │ ├── dfa_fitted.html │ ├── dfa_loadings.html │ ├── dfa_trends.html │ ├── find_dfa_trends.html │ ├── find_inverted_chains-1.png │ ├── find_inverted_chains.html │ ├── find_regimes.html │ ├── find_swans-1.png │ ├── find_swans-2.png │ ├── find_swans-3.png │ ├── find_swans.html │ ├── fit_dfa.html │ ├── fit_regimes.html │ ├── hmm_init.html │ ├── index.html │ ├── invert_chains.html │ ├── is_converged.html │ ├── loo.html │ ├── plot_fitted-1.png │ ├── plot_fitted-2.png │ ├── plot_fitted.html │ ├── plot_loadings-1.png │ ├── plot_loadings-2.png │ ├── plot_loadings-3.png │ ├── plot_loadings-4.png │ ├── plot_loadings.html │ ├── plot_regime_model-1.png │ ├── plot_regime_model-2.png │ ├── plot_regime_model-3.png │ ├── plot_regime_model.html │ ├── plot_trends-1.png │ ├── plot_trends.html │ ├── predicted.html │ ├── rotate_trends-1.png │ ├── rotate_trends.html │ ├── sim_dfa-1.png │ ├── sim_dfa-2.png │ ├── sim_dfa-3.png │ ├── sim_dfa-4.png │ ├── sim_dfa-5.png │ ├── sim_dfa-6.png │ ├── sim_dfa.html │ ├── trend_cor-1.png │ ├── trend_cor-2.png │ └── trend_cor.html └── sitemap.xml ├── inst ├── include │ └── stan_meta_header.hpp └── stan │ ├── corr.stan │ ├── dfa.stan │ ├── hmm_gaussian.stan │ ├── include │ └── license.stan │ └── regime_1.stan ├── man ├── bayesdfa-package.Rd ├── dfa_cv.Rd ├── dfa_fitted.Rd ├── dfa_loadings.Rd ├── dfa_trends.Rd ├── find_dfa_trends.Rd ├── find_inverted_chains.Rd ├── find_regimes.Rd ├── find_swans.Rd ├── fit_dfa.Rd ├── fit_regimes.Rd ├── hmm_init.Rd ├── invert_chains.Rd ├── is_converged.Rd ├── loo.Rd ├── plot_fitted.Rd ├── plot_loadings.Rd ├── plot_regime_model.Rd 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