├── .gitignore ├── LICENSE.md ├── README.md ├── algorithms ├── examples.R └── mcmc.R ├── citation analysis ├── Citation analysis.xlsx ├── CountsByYear.csv ├── FindDupsGetCounts.r └── READEME.txt ├── load_data.R ├── make_plots.R ├── models ├── growth │ ├── fits │ │ └── temp.txt │ ├── generate_data.R │ ├── growth.jags │ ├── growth.stan │ ├── jags.samplers.csv │ ├── plots │ │ ├── growth_adapt_empirical.png │ │ ├── growth_adapt_simulated.png │ │ ├── growth_perf_empirical.png │ │ ├── growth_perf_simulated.png │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplots01.png │ │ ├── model_comparison_qqplots02.png │ │ ├── model_comparison_qqplots03.png │ │ └── simulated_growth.png │ ├── run_model.R │ └── sims.ind.RDS ├── growth_nc │ ├── fits │ │ └── temp.txt │ ├── generate_data.R │ ├── growth_nc.jags │ ├── growth_nc.stan │ ├── jags.samplers.csv │ ├── plots │ │ ├── growth_nc_adapt_empirical.png │ │ ├── growth_nc_adapt_simulated.png │ │ ├── growth_nc_perf_empirical.png │ │ ├── growth_nc_perf_simulated.png │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplots01.png │ │ ├── model_comparison_qqplots02.png │ │ ├── model_comparison_qqplots03.png │ │ └── simulated_growth.png │ ├── run_model.R │ └── sims.ind.RDS ├── mvnc │ ├── fits │ │ └── temp.txt │ ├── generate_data.R │ ├── jags.samplers.csv │ ├── mvnc.jags │ ├── mvnc.stan │ ├── plots │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplot.png │ │ ├── model_comparison_qqplots.pdf │ │ ├── model_comparison_qqplots01.png │ │ ├── mvnc_adapt_empirical.png │ │ ├── mvnc_adapt_simulated.png │ │ ├── mvnc_perf_empirical.png │ │ └── mvnc_perf_simulated.png │ ├── run_model.R │ └── sims.ind.RDS ├── mvnd │ ├── fits │ │ └── temp.txt │ ├── generate_data.R │ ├── jags.samplers.csv │ ├── mvnd.jags │ ├── mvnd.stan │ ├── plots │ │ ├── model_comparison.png │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplot.png │ │ ├── model_comparison_qqplots.pdf │ │ ├── model_comparison_qqplots01.png │ │ ├── mvnd_adapt_empirical.png │ │ ├── mvnd_adapt_simulated.png │ │ ├── mvnd_perf_empirical.png │ │ └── mvnd_perf_simulated.png │ ├── run_model.R │ └── sims.ind.RDS ├── redkite │ ├── data.RDS │ ├── fits │ │ └── temp.txt │ ├── jags.samplers.csv │ ├── original.R │ ├── plots │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplots.pdf │ │ ├── model_comparison_qqplots01.png │ │ ├── redkite_adapt_empirical.png │ │ └── redkite_perf_empirical.png │ ├── redkite.jags │ ├── redkite.stan │ ├── run_model.R │ └── sims.ind.RDS ├── ss_logistic │ ├── fits │ │ └── temp.txt │ ├── model.xlsx │ ├── plots │ │ ├── initial_fits.png │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplots.pdf │ │ ├── ss_logistic_adapt_empirical.png │ │ └── ss_logistic_perf_empirical.png │ ├── run_model.R │ ├── sims.ind.RDS │ ├── ss_logistic.jags │ ├── ss_logistic.stan │ ├── tuna_data.csv │ └── tuna_tests.R ├── ss_logistic_nc │ ├── fits │ │ └── temp.txt │ ├── jags.samplers.csv │ ├── model.xlsx │ ├── plots │ │ ├── initial_fits.png │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplots.pdf │ │ ├── model_comparison_qqplots01.png │ │ ├── model_comparison_qqplots02.png │ │ ├── ss_logistic_nc_adapt_empirical.png │ │ └── ss_logistic_nc_perf_empirical.png │ ├── run_model.R │ ├── sims.ind.RDS │ ├── ss_logistic_nc.jags │ ├── ss_logistic_nc.stan │ ├── tuna_data.csv │ └── tuna_tests.R ├── swallows │ ├── data.RDS │ ├── fits │ │ └── temp.txt │ ├── plots │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplots01.png │ │ ├── model_comparison_qqplots02.png │ │ ├── model_comparison_qqplots03.png │ │ ├── model_comparison_qqplots04.png │ │ ├── model_comparison_qqplots05.png │ │ ├── model_comparison_qqplots06.png │ │ ├── model_comparison_qqplots07.png │ │ ├── model_comparison_qqplots08.png │ │ ├── swallows_adapt_empirical.png │ │ └── swallows_perf_empirical.png │ ├── run_model.R │ ├── sims.ind.RDS │ ├── swallows.jags │ ├── swallows.rda │ └── swallows.stan ├── swallows_nc │ ├── data.RDS │ ├── fits │ │ └── temp.txt │ ├── jags.samplers.csv │ ├── plots │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplots01.png │ │ ├── model_comparison_qqplots02.png │ │ ├── model_comparison_qqplots03.png │ │ ├── model_comparison_qqplots04.png │ │ ├── model_comparison_qqplots05.png │ │ ├── model_comparison_qqplots06.png │ │ ├── model_comparison_qqplots07.png │ │ ├── model_comparison_qqplots08.png │ │ ├── swallows_nc_adapt_empirical.png │ │ └── swallows_nc_perf_empirical.png │ ├── run_model.R │ ├── sims.ind.RDS │ ├── swallows_nc.jags │ ├── swallows_nc.rda │ └── swallows_nc.stan ├── wildflower │ ├── data.RDS │ ├── fits │ │ └── temp.txt │ ├── jags.samplers.csv │ ├── plots │ │ ├── model_comparison_convergence.png │ │ ├── model_comparison_qqplots01.png │ │ ├── model_comparison_qqplots02.png │ │ ├── model_comparison_qqplots03.png │ │ ├── model_comparison_qqplots04.png │ │ ├── model_comparison_qqplots05.png │ │ ├── model_comparison_qqplots06.png │ │ ├── model_comparison_qqplots07.png │ │ ├── model_comparison_qqplots08.png │ │ ├── model_comparison_qqplots09.png │ │ ├── model_comparison_qqplots10.png │ │ ├── model_comparison_qqplots11.png │ │ ├── model_comparison_qqplots12.png │ │ ├── model_comparison_qqplots13.png │ │ ├── model_comparison_qqplots14.png │ │ ├── model_comparison_qqplots15.png │ │ ├── model_comparison_qqplots16.png │ │ ├── model_comparison_qqplots17.png │ │ ├── model_comparison_qqplots18.png │ │ ├── model_comparison_qqplots19.png │ │ ├── model_comparison_qqplots20.png │ │ ├── model_comparison_qqplots21.png │ │ ├── model_comparison_qqplots22.png │ │ ├── model_comparison_qqplots23.png │ │ ├── model_comparison_qqplots24.png │ │ ├── model_comparison_qqplots25.png │ │ ├── model_comparison_qqplots26.png │ │ ├── model_comparison_qqplots27.png │ │ ├── model_comparison_qqplots28.png │ │ ├── model_comparison_qqplots29.png │ │ ├── model_comparison_qqplots30.png │ │ ├── model_comparison_qqplots31.png │ │ ├── model_comparison_qqplots32.png │ │ ├── model_comparison_qqplots33.png │ │ ├── model_comparison_qqplots34.png │ │ ├── model_comparison_qqplots35.png │ │ ├── model_comparison_qqplots36.png │ │ ├── model_comparison_qqplots37.png │ │ ├── model_comparison_qqplots38.png │ │ ├── model_comparison_qqplots39.png │ │ ├── model_comparison_qqplots40.png │ │ ├── model_comparison_qqplots41.png │ │ ├── model_comparison_qqplots42.png │ │ ├── model_comparison_qqplots43.png │ │ ├── model_comparison_qqplots44.png │ │ ├── model_comparison_qqplots45.png │ │ ├── wildflower_adapt_empirical.png │ │ └── wildflower_perf_empirical.png │ ├── run_model.R │ ├── sims.ind.RDS │ ├── wildflower.jags │ └── wildflower.stan └── wildflower_nc │ ├── data.RDS │ ├── fits │ └── temp.txt │ ├── jags.samplers.csv │ ├── plots │ ├── model_comparison_convergence.png │ ├── model_comparison_qqplots01.png │ ├── model_comparison_qqplots02.png │ ├── model_comparison_qqplots03.png │ ├── model_comparison_qqplots04.png │ ├── model_comparison_qqplots05.png │ ├── model_comparison_qqplots06.png │ ├── model_comparison_qqplots07.png │ ├── model_comparison_qqplots08.png │ ├── model_comparison_qqplots09.png │ ├── model_comparison_qqplots10.png │ ├── model_comparison_qqplots11.png │ ├── model_comparison_qqplots12.png │ ├── model_comparison_qqplots13.png │ ├── model_comparison_qqplots14.png │ ├── model_comparison_qqplots15.png │ ├── model_comparison_qqplots16.png │ ├── model_comparison_qqplots17.png │ ├── model_comparison_qqplots18.png │ ├── model_comparison_qqplots19.png │ ├── model_comparison_qqplots20.png │ ├── model_comparison_qqplots21.png │ ├── model_comparison_qqplots22.png │ ├── model_comparison_qqplots23.png │ ├── model_comparison_qqplots24.png │ ├── model_comparison_qqplots25.png │ ├── model_comparison_qqplots26.png │ ├── model_comparison_qqplots27.png │ ├── model_comparison_qqplots28.png │ ├── model_comparison_qqplots29.png │ ├── model_comparison_qqplots30.png │ ├── model_comparison_qqplots31.png │ ├── model_comparison_qqplots32.png │ ├── model_comparison_qqplots33.png │ ├── model_comparison_qqplots34.png │ ├── model_comparison_qqplots35.png │ ├── model_comparison_qqplots36.png │ ├── model_comparison_qqplots37.png │ ├── model_comparison_qqplots38.png │ ├── model_comparison_qqplots39.png │ ├── model_comparison_qqplots40.png │ ├── model_comparison_qqplots41.png │ ├── model_comparison_qqplots42.png │ ├── model_comparison_qqplots43.png │ ├── model_comparison_qqplots44.png │ ├── model_comparison_qqplots45.png │ ├── wildflower_nc_adapt_empirical.png │ └── wildflower_nc_perf_empirical.png │ ├── run_model.R │ ├── sims.ind.RDS │ ├── wildflower_nc.jags │ └── wildflower_nc.stan ├── plots ├── ESS_comparison.png ├── ESS_percentages.png ├── adapt_delta.png ├── adapt_eps.png ├── adapt_eps_vs_nsteps.png ├── adapt_max_treedepths.png ├── adapt_ndivergent.png ├── adapt_nsteps.png ├── perf_by_N_cor.png ├── perf_growth_simulated.png ├── perf_mvnd_simulated.png └── runtime.png ├── results ├── empirical.csv ├── growth_adapt_empirical.csv ├── growth_adapt_simulated.csv ├── growth_divergences.RDS ├── growth_nc_adapt_empirical.csv ├── growth_nc_adapt_simulated.csv ├── growth_nc_divergences.RDS ├── growth_nc_perf_empirical.csv ├── growth_nc_perf_simulated.csv ├── growth_perf_empirical.csv ├── growth_perf_simulated.csv ├── mvnc_adapt_empirical.csv ├── mvnc_adapt_simulated.csv ├── mvnc_perf_empirical.csv ├── mvnc_perf_simulated.csv ├── mvnd_adapt_empirical.csv ├── mvnd_adapt_simulated.csv ├── mvnd_perf_empirical.csv ├── mvnd_perf_simulated.csv ├── redkite_adapt_empirical.csv ├── redkite_perf_empirical.csv ├── simulated.csv ├── ss_logistic_adapt_empirical.csv ├── ss_logistic_nc_adapt_empirical.csv ├── ss_logistic_nc_perf_empirical.csv ├── ss_logistic_perf_empirical.csv ├── swallows_adapt_empirical.csv ├── swallows_nc_adapt_empirical.csv ├── swallows_nc_perf_empirical.csv ├── swallows_perf_empirical.csv ├── table_cor.csv ├── table_growth.csv ├── table_perf.csv ├── wildflower_adapt_empirical.csv ├── wildflower_nc_adapt_empirical.csv ├── wildflower_nc_perf_empirical.csv └── wildflower_perf_empirical.csv ├── run_simulation.R └── startup.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/colemonnahan/gradmcmc/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/colemonnahan/gradmcmc/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/colemonnahan/gradmcmc/HEAD/README.md -------------------------------------------------------------------------------- /algorithms/examples.R: 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