inst/README.md

In niloyb/CoupledHalfT: What the package does (short line)

Figures and examples from the article

• Folder one_scale_coupling contains scripts which reproduce the one-scale coupling algorithm meeting time plot:
  • one_scale_coupling_meeting_times.R generates meeting times.
  • one_scale_coupling_plots.R generates the meeting times plot.
• Folder two_scale_coupling contains scripts which reproduce figures related to the two-scale coupling algorithm:
  • two_scale_coupling_meeting_times.R generates two-scale coupling meeting time for synthetic datasets, and one_scale_two_scale_coupling_comparison_plots.R reproduces the meeting times comparison plot under the one-scale and the two-scale coupling algorithms.
  • metric_comparison_plot.R reproduces metric trajectories plot.
  • d_threshold_trajectory_plots.R reproduces the metric trajectories under different values of the metric threshold plot (Appendices).
  • d_threshold_crn_distance_by_p.R reproduces the metric histrogram with common random numbers under different dimensions plot (Appendices).
  • d_threshold_meeting_times_p500.R reproduces the meeting times under different values of the metric threshold plot (Appendices).
• Folder switch_to_crn_coupling contains scripts which reproduce figures related to the two-scale coupling algorithm:
  • switch_to_crn_coupling_comparison_plots.R generates meeting times and the plot comparing the two scale and switch to CRN coupling algorithms.
• Folder half_t_degree_of_freedom contains scripts which reproduce figures related to different degrees of freedom for the the Half-t prior:
  • degree_of_freedom_meet_times.R reproduces plots related to meeting times of the two-scale algorithm under different degrees of freedom.
  • degree_of_freedom_stat_performance.R reproduces plots related to statistical performance under different degrees of freedom.
  • degree_of_freedom_crn_distance_by_p.R reproduces metric trajectories plot under different degrees of freedom (Appendices).
  • degree_of_freedom_Llag.R reproduces plots related to L-Lag total variation bounds and mixing times based on the two-scale algorithm under different degrees of freedom (Appendices).
• Folder gwas contains scripts related to the GWAS dataset example in Section 4.
  • gwas_riboflavin_tv_bounds.R simulates meeting times and reproduces plots related to L-Lag total variation bounds for the riboflavin example. The riboflavin GWAS dataset from Bühlmann et al. [2014] is included.
  • gwas_riboflavin_unbiased_estimates.R generates unbiased estimates of the posterior for the riboflavin example. The riboflavin GWAS dataset from Bühlmann et al. [2014] is included.
  • The maize GWAS dataset is not available publicly, but we have included the cluster computing scripts here for reference.
• Folder beta_marginal_density contains a script which reproduces bivariate density plots (Appendices).
• Folder truncated_prior_xi contains scripts which reproduce figures with a compactly supported prior for the global scale parameter (Appendices).

niloyb/CoupledHalfT documentation built on Aug. 31, 2022, 2:35 a.m.